JP2019024455A - A method to determine the risk of developing tuberculosis in a specific strain - Google Patents

Abstract

Provided is a method for determining the risk of developing tuberculosis in a subject infected with M. tuberculosis based on genetic information of the subject specifically for each M. tuberculosis genetic strain. In a subject, a base of a single nucleotide polymorphism site of a subject genome associated with the onset of tuberculosis is identified, and a tuberculosis genetic strain latently infected with the subject is typed, and tuberculosis is identified. A method for determining the risk of developing tuberculosis due to Mycobacterium tuberculosis latently infected in a subject, specifically in a fungal genetic lineage. [Selection figure] None

Description

  The present invention relates to a method for determining the risk of developing tuberculosis.

  Identification of human gene polymorphisms associated with the onset of tuberculosis has been performed in various ways throughout the genome by candidate gene research and the like (see Non-Patent Document 1). On the other hand, research on gene mutations related to the onset of the tubercle bacillus genome has been conducted (see Non-Patent Document 2). However, there has never been an example in which these human genomes and Mycobacterium tuberculosis genomes were analyzed at the same time, and genes involved in pathogenesis specific to Mycobacterium tuberculosis were comprehensively analyzed from the entire genome. This is because it is rare to obtain both human genome information and M. tuberculosis genome information from a patient who has developed a disease.

Fol M et al. Acta Biochim Pol. 2015; 62 (4): 633-40. Coscolla M et al. Semin Immunol. 2014 Dec; 26 (6): 431-44.

  The present invention identifies human genes related to the onset of tuberculosis from the elucidation of the interaction between the human genome and pathogen genome related to the onset of tuberculosis, and in a subject infected with tuberculosis. An object of the present invention is to provide a method for determining the risk of developing tuberculosis specifically for each Mycobacterium tuberculosis strain based on the genetic information of the subject.

  In addition to acquiring information on single nucleotide polymorphism (SNP) in the entire human genome, the present inventors also acquired information on the genome of Mycobacterium tuberculosis, which is related to the onset of tuberculosis. Analysis was performed. This analysis identified SNPs in the human genome related to the onset of tuberculosis and its nearby genes that could not be identified when the human genome and M. tuberculosis genome were independently analyzed.

  SNP information of the human genome was obtained by DNA extracted from the blood of patients who developed tuberculosis and healthy individuals and a microarray for SNP typing.

  Simultaneously, the genome of Mycobacterium tuberculosis was extracted from the patient and the genetic strain of Mycobacterium tuberculosis was identified. In the analysis, principal component analysis was performed using SNPs information of the whole genome in order to align the genetic background of the tuberculosis patient group and the healthy group. The patient groups were also classified using the age information of patients.

  Then, the group of tuberculosis patients is classified according to the genetic strain of the infected M. tuberculosis, and a related analysis is performed to compare the allele frequency of each SNPs in the group of patients infected with M. tuberculosis of the common genetic strain and the healthy group. As a result, SNPs showing a statistical relationship specific to the genetic lineage of Mycobacterium tuberculosis were searched, and the present invention was completed.

That is, the present invention is as follows.
[1] In a subject, the base of a single nucleotide polymorphism site in the subject's human genome associated with the onset of tuberculosis is identified, and the M. tuberculosis genetic strain latently infected with the subject is typed, and the subject A method for determining the risk of developing tuberculosis, specifically in the M. tuberculosis genetic lineage, by the latently infected M. tuberculosis.
[2] The method according to [1], wherein the M. tuberculosis genetic line to be typed is selected from the group consisting of Beijing strains, non-Beijing strains, EAI strains and non-EAI strains.
[3] When the M. tuberculosis infecting the subject is a Beijing strain, the base of at least one single nucleotide polymorphism site of the following (b1) to (b14) is identified, and the subject is infected When the Mycobacterium tuberculosis is a non-Beijing strain, the base of at least one single nucleotide polymorphism site of the following (nb1) to (nb12) is identified, and the tubercle bacillus that the subject is infected is the EAI strain Sometimes, the base of at least one single nucleotide polymorphism site of the following (e1) to (e8) is identified, and when the tuberculosis infecting the subject is a non-EAI strain, the following (ne1) The method of [1] or [2], comprising identifying the base of at least one single nucleotide polymorphism site of (ne5):
(b1) rs9348878
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 1, which is G or A;
(b2) rs2070600
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 2, which is A or G;
(b3) rs401864
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 3, which is C or T;
(b4) rs673119
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 4 is C or T;
(b5) rs1321267
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 5, which is C or A;
(b6) rs2076625
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 6, G or T;
(b7) rs7142055
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 7, which is T or C;
(b8) rs1157619
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 8, which is T or C;
(b9) rs4924568
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 9, which is A or G;
(b10) rs1899820
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 10, which is A or C;
(b11) rs2695163
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 11, which is G or A;
(b12) rs1197772
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 12, which is G or A;
(b13) rs1081022
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 13, which is T or G;
(b14) rs1648835
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 14, which is T or G;
(nb1) rs12144738
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 15, C or T;
(nb2) rs1494320
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 16 and C or T;
(nb3) rs1712674
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 17 and G or T;
(nb4) rs1418425
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 18, which is T or C;
(nb5) rs4688637
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 19, C or A;
(nb6) rs12374531
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 20, G or A;
(nb7) rs11784415
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 21, which is C or A;
(nb8) rs2182093
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 22, which is T or C;
(nb9) rs10798
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 23, which is A or G;
(nb10) rs4267316
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 24, which is C or T;
(nb11) rs6071980
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 25, which is C or T;
(nb12) rs743057
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 26, which is A or G;
(e1) rs1178938
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 27, which is C or A;
(e2) rs800065
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 28, which is C or T;
(e3) rs1372667
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 29, which is G or T;
(e4) rs13174549
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 30, which is T or C;
(e5) rs7087410
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 31, which is C or T;
(e6) rs10898382
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 32, which is A or C;
(e7) rs951729
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 33, which is A or C;
(e8) rs1658693
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 34, which is C or T;
(ne1) rs1820920
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 35, which is C or T;
(ne2) rs11737270
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 36, which is G or A;
(ne3) rs10832678
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 37, which is G or A;
(ne4) rs10507084
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 38, which is T or C; or
(ne5) rs1440548
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 39, which is C or T.
[4] (1) When the base of the 26th single nucleotide polymorphism site ((b1) rs9348878) of the base sequence shown in SEQ ID NO: 1 is G, in younger age (under 45 years) than in the case of A Determined that the risk of developing tuberculosis is high,
(2) When the base of the 26th single nucleotide polymorphism site ((b2) rs2070600) of the base sequence shown in SEQ ID NO: 2 is A, tuberculosis is younger (under 45 years) than in the case of G Determined that the risk of developing is high,
(3) When the base of the 26th single nucleotide polymorphism site ((b3) rs401864) of the nucleotide sequence shown in SEQ ID NO: 3 is C, there is a higher risk of developing tuberculosis at any age than T And
(4) When the base of the 26th single nucleotide polymorphism site ((b4) rs673119) of the base sequence shown in SEQ ID NO: 4 is C, tuberculosis is observed in the elderly (45 years or older) compared to T. Determined that the risk of developing is high,
(5) When the base of the 26th single nucleotide polymorphism site ((b5) rs1321267) of the base sequence shown in SEQ ID NO: 5 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(6) When the base of the 26th single nucleotide polymorphism site ((b6) rs2076625) of the base sequence shown in SEQ ID NO: 6 is G, the risk of developing tuberculosis is lower than in any age compared to T And
(7) When the base of the 26th single nucleotide polymorphism site ((b7) rs7142055) of the nucleotide sequence shown in SEQ ID NO: 7 is T, tuberculosis is observed in younger age (under 45 years) than in C Determined that the risk of developing is high,
(8) When the base of the 26th single nucleotide polymorphism site ((b8) rs1157619) of the base sequence shown in SEQ ID NO: 8 is T, there is a higher risk of developing tuberculosis at any age than in C And
(9) When the base of the 26th single nucleotide polymorphism site ((b9) rs4924568) of the nucleotide sequence shown in SEQ ID NO: 9 is A, tuberculosis is observed in the elderly (45 years or older) compared to G. Determined that the risk of developing is high,
(10) When the base of the 26th single nucleotide polymorphism site ((b10) rs1899820) of the nucleotide sequence shown in SEQ ID NO: 10 is A, tuberculosis is observed in older age (45 years or older) than in C Determined that the risk of developing is high,
(11) When the base of the 26th single nucleotide polymorphism site ((b11) rs2695163) of the nucleotide sequence represented by SEQ ID NO: 11 is G, tuberculosis is observed in the elderly (45 years old or older) compared to A. Determined that the risk of developing is high,
(12) When the base of the 26th single nucleotide polymorphism site ((b12) rs1197772) of the nucleotide sequence shown in SEQ ID NO: 12 is G, tuberculosis is observed in older age (45 years or older) than in the case of A. Determined that the risk of developing is high,
(13) When the base of the 26th single nucleotide polymorphism site ((b13) rs1081022) of the nucleotide sequence shown in SEQ ID NO: 13 is T, tuberculosis is observed in the elderly (45 years or older) compared to G. Determined that the risk of developing is high,
(14) When the base of the 26th single nucleotide polymorphism site ((b14) rs1648835) of the nucleotide sequence shown in SEQ ID NO: 14 is T, tuberculosis is observed in older age (45 years or older) than in the case of G Determined that the risk of developing is high,
(15) When the base of the 26th single nucleotide polymorphism site ((nb1) rs12144738) of the base sequence shown in SEQ ID NO: 15 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(16) When the base of the 26th single nucleotide polymorphism site ((nb2) rs1494320) of the nucleotide sequence shown in SEQ ID NO: 16 is C, tuberculosis is observed in older age (45 years or older) compared to T Determined that the risk of developing is high,
(17) When the base of the 26th single nucleotide polymorphism site ((nb3) rs1712674) of the base sequence shown in SEQ ID NO: 17 is G, tuberculosis is observed in older age (45 years or older) compared to T Determined that the risk of developing is high,
(18) When the base of the 26th single nucleotide polymorphism site ((nb4) rs1418425) of the nucleotide sequence shown in SEQ ID NO: 18 is T, tuberculosis is observed in older age (45 years or older) compared to C Determined that the risk of developing is high,
(19) When the base of the 26th single nucleotide polymorphism site ((nb5) rs4688637) of the base sequence shown in SEQ ID NO: 19 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A Determined that the risk of developing is high,
(20) When the base of the 26th single nucleotide polymorphism site ((nb6) rs12374531) of the nucleotide sequence shown in SEQ ID NO: 20 is G, tuberculosis is observed in older age (45 years or older) than in the case of A Determined that the risk of developing is low,
(21) When the base of the 26th single nucleotide polymorphism site ((nb7) rs11784415) of the base sequence shown in SEQ ID NO: 21 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A Determined that the risk of developing is high,
(22) When the base of the 26th single nucleotide polymorphism site ((nb8) rs2182093) of the nucleotide sequence shown in SEQ ID NO: 22 is T, tuberculosis is observed in younger age (under 45 years) than in the case of C Determined that the risk of developing is high,
(23) When the base of the 26th single nucleotide polymorphic site ((nb9) rs10798) of the nucleotide sequence shown in SEQ ID NO: 23 is A, there is a higher risk of developing tuberculosis at any age than in G And
(24) When the base of the 26th single nucleotide polymorphic site ((nb10) rs4267316) of the base sequence shown in SEQ ID NO: 24 is C, there is a higher risk of developing tuberculosis at any age than T And
(25) When the base of the 26th single nucleotide polymorphism site ((nb11) rs6071980) of the nucleotide sequence shown in SEQ ID NO: 25 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(26) When the base of the 26th single nucleotide polymorphism site ((nb12) rs743057) of the base sequence shown in SEQ ID NO: 26 is A, the risk of developing tuberculosis is lower than that of G in any age And
(27) When the base of the 26th single nucleotide polymorphism site ((e1) rs1178938) of the nucleotide sequence shown in SEQ ID NO: 27 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(28) When the base of the 26th single nucleotide polymorphism site ((e2) rs800065) of the base sequence represented by SEQ ID NO: 28 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(29) When the base of the 26th single nucleotide polymorphism site ((e3) rs1372667) of the nucleotide sequence shown in SEQ ID NO: 29 is G, tuberculosis is observed in younger (under 45 years) than in the case of T. Determined that the risk of developing is high,
(30) When the base of the 26th single nucleotide polymorphism site ((e4) rs13174549) of the base sequence shown in SEQ ID NO: 30 is T, the risk of developing tuberculosis is lower than in C at all ages And
(31) When the base of the 26th single nucleotide polymorphism site ((e5) rs7087410) of the base sequence shown in SEQ ID NO: 31 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(32) When the base of the 26th single nucleotide polymorphism site ((e6) rs10898382) of the nucleotide sequence shown in SEQ ID NO: 32 is A, tuberculosis is observed in the elderly (45 years or older) compared to C Determined that the risk of developing is high,
(33) When the base of the 26th single nucleotide polymorphic site ((e7) rs951729) of the nucleotide sequence shown in SEQ ID NO: 33 is A, tuberculosis is observed in the elderly (45 years or older) compared to C Determined that the risk of developing is high,
(34) When the base of the 26th single nucleotide polymorphism site ((e8) rs1658693) of the base sequence shown in SEQ ID NO: 34 is C, tuberculosis is observed in the elderly (45 years old or older) compared to T. Determined that the risk of developing is low,
(35) When the base of the 26th single nucleotide polymorphism site ((ne1) rs1820920) of the base sequence shown in SEQ ID NO: 35 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(36) When the base of the 26th single nucleotide polymorphism site ((ne2) rs11737270) of the nucleotide sequence shown in SEQ ID NO: 36 is G, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(37) When the base of the 26th single nucleotide polymorphism site ((ne3) rs10832678) of the nucleotide sequence shown in SEQ ID NO: 37 is G, tuberculosis is observed in the elderly (45 years old or older) compared to A. Determined that the risk of developing is high,
(38) When the base of the 26th single nucleotide polymorphism site ((ne4) rs10507084) of the nucleotide sequence shown in SEQ ID NO: 38 is T, tuberculosis is observed in the elderly (45 years old or older) compared to C. Determine that the risk of developing is low, or
(39) When the base of the 26th single nucleotide polymorphism site ((ne5) rs1440548) of the nucleotide sequence shown in SEQ ID NO: 39 is C, there is a higher risk of developing tuberculosis at any age than T To determine,
The method of [3].
[5] A primer for the human genome for determining the risk of developing tuberculosis in a tuberculosis-infected subject, and the risk of developing tuberculosis in any of the following Beijing strain-infected subjects: (p1) to (p14) Primers for determining the risk, any of the following (p15) to (p26): a primer for determining the risk of developing tuberculosis in a non-Beijing strain-infected subject, any of the following (p27) to (p34) In order to determine the risk of developing tuberculosis in a non-EAI strain-infected subject of any of the following (p35) to (p39): Primer:
(p1) a primer that can amplify a region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1;
(p2) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 2 (the base of the polymorphic site of rs2070600);
(p3) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs401864) in the base sequence of SEQ ID NO: 3;
(p4) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 4 (the base of the polymorphic site of rs673119);
(p5) a primer that can amplify a region containing the 26th base (base of rs1321267 polymorphic site) in the base sequence of SEQ ID NO: 5;
(p6) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 6 (the base of the polymorphic site of rs2076625);
(p7) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 7 (the base of the polymorphic site of rs7142055);
(p8) a primer capable of amplifying a region containing the 26th base (base of rs1157619 polymorphic site) in the base sequence of SEQ ID NO: 8;
(p9) a primer capable of amplifying a region containing the 26th base (base of rs4924568 polymorphic site) in the base sequence of SEQ ID NO: 9;
(p10) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 10 (the base of the polymorphic site of rs1899820);
(p11) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 11 (the base of the polymorphic site of rs2695163);
(p12) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs1197772) in the base sequence of SEQ ID NO: 12;
(p13) a primer capable of amplifying a region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13;
(p14) a primer capable of amplifying a region containing the 26th base (base of rs1648835 polymorphic site) in the base sequence of SEQ ID NO: 14;
(p15) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 15 (the base of the polymorphic site of rs12144738);
(p16) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 16 (the base of the polymorphic site of rs1494320);
(p17) Primer capable of amplifying a region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17
(p18) a primer capable of amplifying a region containing the 26th base (base of rs1418425 polymorphic site) in the base sequence of SEQ ID NO: 18;
(p19) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 19 (the base of the polymorphic site of rs4688637);
(p20) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 20 (the base of the polymorphic site of rs12374531);
(p21) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 21 (the base of the polymorphic site of rs11784415);
(p22) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs2182093) in the base sequence of SEQ ID NO: 22;
(p23) a primer capable of amplifying a region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23;
(p24) a primer capable of amplifying a region containing the 26th base (base of rs4267316 polymorphic site) in the base sequence of SEQ ID NO: 24;
(p25) a primer that can amplify a region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25;
(p26) a primer capable of amplifying a region containing the 26th base (base of rs743057 polymorphic site) in the base sequence of SEQ ID NO: 26;
(p27) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 27 (the base of the polymorphic site of rs1178938);
(p28) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 28 (the base of the polymorphic site of rs800065);
(p29) a primer capable of amplifying a region containing the 26th base (base of rs1372667 polymorphic site) in the base sequence of SEQ ID NO: 29;
(p30) a primer that can amplify a region containing the 26th base (base of rs13174549 polymorphic site) in the base sequence of SEQ ID NO: 30;
(p31) a primer capable of amplifying a region containing the 26th base (base of rs7087410 polymorphic site) in the base sequence of SEQ ID NO: 31;
(p32) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 32 (the base of the polymorphic site of rs10898382);
(p33) a primer capable of amplifying a region containing the 26th base (base of rs951729 polymorphic site) in the base sequence of SEQ ID NO: 33;
(p34) a primer capable of amplifying a region containing the 26th base (base of rs1658693 polymorphic site) in the base sequence of SEQ ID NO: 34;
(p35) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 35 (the base of the polymorphic site of rs1820920);
(p36) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 36 (the base of the polymorphic site of rs11737270);
(p37) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 37 (the base of the polymorphic site of rs10832678);
(p38) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs10507084) in the base sequence of SEQ ID NO: 38; or
(p39) A primer capable of amplifying a region containing the 26th base (base of rs1440548 polymorphic site) in the base sequence of SEQ ID NO: 39.
[6] A probe for determining the risk of developing tuberculosis in a tuberculosis-infected subject,
Probes for determining the risk of developing tuberculosis in any of the following (q1) to (q14) Beijing strain-infected subjects, and any of the following (q15) to (q26) non-Beijing strain-infected subjects A probe for determining the risk of developing tuberculosis in the following, a probe for determining the risk of developing tuberculosis in an EAI strain-infected subject of any of the following (q27) to (q34), or the following (q35) A probe for determining the risk of developing tuberculosis in a non-EAI strain-infected subject of any of-(q39):
(q1) a probe capable of hybridizing to a region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1;
(q2) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs2070600) in the base sequence of SEQ ID NO: 2;
(q3) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs401864) in the base sequence of SEQ ID NO: 3;
(q4) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs673119) in the base sequence of SEQ ID NO: 4;
(q5) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs1321267) in the base sequence of SEQ ID NO: 5;
(q6) a probe capable of hybridizing to a region containing the 26th base (base of rs2076625 polymorphic site) in the base sequence of SEQ ID NO: 6;
(q7) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs7142055) in the base sequence of SEQ ID NO: 7;
(q8) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs1157619) in the base sequence of SEQ ID NO: 8;
(q9) a probe capable of hybridizing to a region containing the 26th base (base of rs4924568 polymorphic site) in the base sequence of SEQ ID NO: 9;
(q10) a probe capable of hybridizing to a region containing the 26th base (base of rs1899820 polymorphic site) in the base sequence of SEQ ID NO: 10;
(q11) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs2695163) in the base sequence of SEQ ID NO: 11;
(q12) a probe capable of hybridizing to a region containing the 26th base (base of rs1197772 polymorphic site) in the base sequence of SEQ ID NO: 12;
(q13) a probe capable of hybridizing to a region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13;
(q14) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs1648835) in the base sequence of SEQ ID NO: 14;
(q15) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs12144738) in the base sequence of SEQ ID NO: 15;
(q16) a probe capable of hybridizing to a region containing the 26th base (base of rs1494320 polymorphic site) in the base sequence of SEQ ID NO: 16;
(q17) a probe capable of hybridizing to a region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17;
(q18) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs1418425) in the base sequence of SEQ ID NO: 18;
(q19) a probe capable of hybridizing to a region containing the 26th base (base of rs4688637 polymorphic site) in the base sequence of SEQ ID NO: 19;
(q20) a probe capable of hybridizing to a region containing the 26th base (base of rs12374531 polymorphic site) in the base sequence of SEQ ID NO: 20;
(q21) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 21 (the base of the polymorphic site of rs11784415);
(q22) a probe capable of hybridizing to a region containing the 26th base (base of rs2182093 polymorphic site) in the base sequence of SEQ ID NO: 22;
(q23) a probe capable of hybridizing to a region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23;
(q24) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs4267316) in the base sequence of SEQ ID NO: 24;
(q25) a probe capable of hybridizing to a region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25;
(q26) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 26 (the base of the polymorphic site of rs743057);
(q27) a probe capable of hybridizing to a region containing the 26th base (base of rs1178938 polymorphic site) in the base sequence of SEQ ID NO: 27;
(q28) a probe capable of hybridizing to a region containing the 26th base (base of rs800065 polymorphic site) in the base sequence of SEQ ID NO: 28;
(q29) a probe capable of hybridizing to a region containing the 26th base (base of rs1372667 polymorphic site) in the base sequence of SEQ ID NO: 29;
(q30) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 30 (the base of the polymorphic site of rs13174549);
(q31) a probe capable of hybridizing to a region containing the 26th base (base of rs7087410 polymorphic site) in the base sequence of SEQ ID NO: 31;
(q32) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 32 (the base of the polymorphic site of rs10898382);
(q33) a probe capable of hybridizing to a region containing the 26th base (base of rs951729 polymorphic site) in the base sequence of SEQ ID NO: 33;
(q34) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs1658693) in the base sequence of SEQ ID NO: 34;
(q35) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs1820920) in the base sequence of SEQ ID NO: 35;
(q36) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs11737270) in the base sequence of SEQ ID NO: 36;
(q37) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 37 (the base of the polymorphic site of rs10832678);
(q38) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs10507084) in the base sequence of SEQ ID NO: 38; or
(q39) A probe capable of hybridizing to a region containing the 26th base (base of rs1440548 polymorphic site) in the base sequence of SEQ ID NO: 39.
[7] A kit for determining the risk of developing tuberculosis, comprising the primer of [5] or the probe of [6].
[8] In a subject, the expression level of a gene located in the vicinity of a single nucleotide polymorphism site in the subject genome associated with the onset of tuberculosis is measured, and the inheritance of Mycobacterium tuberculosis that is latently infected in the subject A method of typing a strain and determining the risk of developing tuberculosis due to a latently infected tuberculosis bacterium in a subject.
[9] Located in the vicinity of a single nucleotide polymorphism ((nb2) rs1494320) at the 26th base of the nucleotide sequence shown in SEQ ID NO: 16 when the subject is a non-Beijing strain of Mycobacterium tuberculosis [8] The method according to [8], wherein the expression of CD53 gene, which is a gene, is measured, and when the expression of the gene is increased, it is determined that the risk of developing tuberculosis is high.
[10] Located in the vicinity of a single nucleotide polymorphism ((nb11) rs6071980) at the 26th base of the nucleotide sequence shown in SEQ ID NO: 25 when the subject is a non-Beijing strain of Mycobacterium tuberculosis The method according to [8], wherein the expression of MAFB gene, which is a gene, is measured, and when the expression of the gene is increased, it is determined that the risk of developing tuberculosis is high.

  According to the method of the present invention, by identifying a single nucleotide polymorphism or measuring the expression of a gene in the vicinity of the single nucleotide polymorphism site, for each genetic strain of Mycobacterium tuberculosis, It is possible to determine the risk of onset, efficiently select those infected with M. tuberculosis who have a high risk of developing tuberculosis from unaffected persons, treat them before onset, and prevent the onset.

It is a figure which shows the list | wrist of the single nucleotide polymorphism related with the onset of tuberculosis specific on M. tuberculosis genetic strain, and the gene of the vicinity (Beijing strain). It is a figure which shows the list | wrist of the single nucleotide polymorphism related with the onset of tuberculosis specific on M. tuberculosis genetic strain, and the gene of the vicinity (continuation of FIG. 1-1). It is a figure which shows the list | wrist of the single nucleotide polymorphism relevant to the onset of tuberculosis, and the gene of the vicinity in the Mycobacterium tuberculosis genetic strain specific (non-Beijing strain). It is a figure which shows the list | wrist of the single nucleotide polymorphism relevant to the onset of tuberculosis, and the nearby gene (non-Beijing strain) (continuation of FIG. 2-1). It is a figure which shows the list | wrist of the single nucleotide polymorphism related with the onset of tuberculosis specific on M. tuberculosis genetic strain, and the gene of the vicinity (EAI strain). It is a figure which shows the list | wrist of the single nucleotide polymorphism related with the onset of tuberculosis specific on M. tuberculosis genetic strain, and the gene of the vicinity (non-EAI strain). It is a figure which shows the result of the expression analysis in the tuberculosis patient of the CD53 gene which is a tuberculosis onset risk candidate gene. It is a figure which shows the result of the expression analysis in the tuberculosis patient of the MAFB gene which is a tuberculosis onset risk candidate gene.

  Hereinafter, the present invention will be described in detail.

  The present invention is a method for determining the risk of developing tuberculosis (TB) in a subject based on genetic information of humans and tuberculosis bacteria. Here, determining the risk of developing tuberculosis in a subject means determining the ease of developing or difficulty in developing tuberculosis in the subject. In the present invention, a subject who is infected with Mycobacterium tuberculosis but has not developed a disease, that is, a subject that is latently infected with Mycobacterium tuberculosis is used. The present invention is also a method for obtaining auxiliary data for determining the risk of developing tuberculosis in a subject. In the present invention, evaluation and determination are also referred to as prediction.

  Tuberculosis refers to an infection caused by Mycobacterium tuberculosis. The most common site is the lung, but it infects organs and organs throughout the body and develops pulmonary tuberculosis or extrapulmonary tuberculosis such as tuberculous meningitis and tuberculous lymphadenitis.

  One in three people worldwide is infected with Mycobacterium tuberculosis. Among humans infected with M. tuberculosis, about 1 in 10 people develop TB disease. In addition, humans who develop symptoms often develop symptoms after 10 to several decades after infection. When the risk of developing tuberculosis is determined by the method of the present invention and it is determined that the risk is high, the onset can be avoided by administering antibiotics against tuberculosis bacteria in advance.

  Specifically, we analyzed SNPs (single nucleotide polymorphisms) on the human genome, which are related to the likelihood of developing tuberculosis in latently infected subjects, and based on the type of base at the single nucleotide polymorphism site To assess and determine the risk of developing tuberculosis. Here, single nucleotide polymorphism analysis refers to identifying the base of a single nucleotide polymorphism site.

  In addition, the expression of a gene located in the vicinity of a single nucleotide polymorphism site associated with the ease of onset of tuberculosis is measured, and the risk of developing tuberculosis is evaluated and determined based on the expression level. A gene located in the vicinity of a single nucleotide polymorphism site refers to a gene that is close in distance to the single nucleotide polymorphism site, preferably the gene that is closest in distance. Expression of a gene located in the vicinity of a single nucleotide polymorphism site is decreased or increased due to the allele of the single nucleotide polymorphism site. Therefore, by measuring the expression of a gene located in the vicinity of a single nucleotide polymorphism site, the risk of developing tuberculosis can be determined using the base of the single nucleotide polymorphism site as an index, and the onset of tuberculosis is developed. The risk of developing tuberculosis can be determined using the expression of a gene located in the vicinity of a single nucleotide polymorphism site associated with ease as an index.

  The genetic lineage (Lineage) of Mycobacterium tuberculosis genome shows diversity, including Beijing strain, EAI (East-African Indian) strain, CAS (Central Asian Strain) strain, and Euro-American strain. In addition, since Beijing shares are often infected, non-Beijing shares are collectively referred to as non-Beijing shares. Non-Beijing shares include EAI shares, CAS shares, and Euro-American shares. Similarly, since EAI strains are often infected, strains other than EAI strains are collectively referred to as non-EAI strains, and non-EAI strains include Beijing, CAS and Euro-American strains.

  The single nucleotide polymorphisms associated with the risk of developing tuberculosis in a subject vary depending on the strain of Mycobacterium tuberculosis that is latently infected. Furthermore, the risk of developing tuberculosis varies depending on the age of the subject, and is referred to as senile onset or juvenile onset depending on age. When the age of the onset subject is 45 years or older, it is called senile onset, and when it is less than 45 years old, it is called juvenile onset (Mahasirimongkol S et al. J Hum Genet. 2012 Jun; 57 (6): 363-7 ).

  M. tuberculosis is isolated from patients who actually develop tuberculosis, and the genetic strain of M. tuberculosis is determined by typing, and single nucleotide polymorphisms of the entire genome of the patient are analyzed. At this time, by performing principal component analysis using single nucleotide polymorphism information for the entire human genome, a group of patients with the same genetic background as the healthy group is collected from patients collected before the association analysis is performed. It becomes possible to extract. Moreover, it becomes possible to extract a patient group considered to have a common onset mechanism by considering the onset age information of patients.

  Using the patient group extracted by such a method, based on the genome information of the infected M. tuberculosis, Beijing strain infected patient group, non-Beijing strain infected patient group, EAI strain infected patient group, non EAI strain infection By classifying the entire group of patients with tuberculosis into each patient group and conducting a related analysis comparing the allele frequency of each single nucleotide polymorphism in the group of patients infected with M. tuberculosis with a common genetic strain and the group of healthy subjects, It is possible to identify single nucleotide polymorphisms that have a specific association with the onset of fungal genetic strains.

  The present inventors have found that a plurality of single nucleotide polymorphisms on the human genome are related to the onset of tuberculosis by the method of human whole genome analysis (GWAS), and have completed the present invention. The term “related to the onset of” means that the single nucleotide polymorphism allele and the risk of developing tuberculosis are statistically related.

  Single nucleotide polymorphism analysis is the determination of the type of base at a single nucleotide polymorphism site, that is, allele, which may be detected for one chromosome on a pair of chromosomes or for both chromosomes. Including and detecting for both chromosomes also includes detection of homozygous or heterozygous at single nucleotide polymorphism sites. Each allele that opposes a particular allele in a sample isolated from a subject can be detected and genotyped. When only a certain allele is detected, it is homozygous with the allele homozygous, and when two alleles are detected, it is heterozygous with the two alleles heterozygous.

  The risk of developing tuberculosis in a subject with a latent infection with M. tuberculosis is determined by the following method.

  M. tuberculosis is isolated from the site of M. tuberculosis infection in the subject. Usually, it may be isolated from the subject's cage. For isolation of Mycobacterium tuberculosis, sputum of tuberculosis patients are applied to Lowenstein-Jensen medium and cultured at 37 ° C. for 4-6 weeks. Genomic DNA is extracted from the cultured cells. Specifically, the cells were suspended in TE (10 mM Tris HCl pH 8.0, 1 mM EDTA), sterilized by heat treatment at 80 ° C for 20 minutes, added with 10 mg / ml lysozyme solution, and reacted overnight. Let it lyse. Furthermore, after adding 10% SDS / proteinase K solution and reacting at 65 ° C. for 10 minutes, 5M NaCl and CTAB / NaCl solution are added, and further reacted at 65 ° C. for 10 minutes. Thereafter, the mixture is mixed with a chloroform / isoamyl alcohol solution, and DNA precipitation is performed on the aqueous layer using 2-propanol. After washing with 70% ethanol, the remaining pellet is suspended in TE buffer and the DNA concentration is measured.

  The isolated M. tuberculosis genomic DNA is typed to determine the genetic lineage. Markers and methods for typing Mycobacterium tuberculosis are known. For example, Gagneux S et al. Proc Natl Acad Sci US A. 2006 Feb 21; 103 (8): The LSP (Large Sequence Polymorphism) determination method described in 2869-73. And the determination method applied to the SNP typing of Mycobacterium tuberculosis genome using the DigiTag2 method developed by the present inventors (Srilohasin P et al. J. Clin. Microbiol. 2014, 52 (6): 1962-8). Specifically, the LSP determination method can be classified into EAI strain, Beijing strain, CAS strain, and Euro-American strain as genomic regions serving as markers: RD239, TbD1, RD105, RD750, 7bp deletion at pks 15 / 5 of 1 are used in combination. By amplifying the target region with a specific primer set, the presence or absence of the target region is determined based on the size of the amplified product, and the genetic strain can be determined. EAI strain is RD239 (-) and TbD1 (+), Beijing strain is RD105 (-) and TbD1 (-), CAS strain is RD750 (-) and TbD1 (-), Euro-American strain is TbD1 (-) and 7bp deletion at pks 15/1.

  These typing methods are examples. M. tuberculosis genetic lines can be classified not only into the above-mentioned genetic lines but also into sub-lines. Further, it is possible to determine a single nucleotide polymorphism related to the onset of tuberculosis for each strain by further subclassification.

  Simultaneously with the typing of M. tuberculosis, the genome may be extracted from the peripheral blood cells of the subject and analyzed for single nucleotide polymorphism, or the expression level of a gene located near the single nucleotide polymorphism site may be measured. For example, the expression level in blood may be measured. That is, in the present invention, tuberculosis bacteria that are latently infected in the subject are collected, typed to determine the genetic lineage of the tubercle bacillus, and at the same time, related to the likelihood of developing tuberculosis in the human genome of the subject. The single nucleotide polymorphism present is analyzed, or the expression level of a gene located in the vicinity of the single nucleotide polymorphism is measured. For each type of M. tuberculosis finally infected, the risk of developing tuberculosis is determined from the single nucleotide polymorphism analysis of the subject or the expression level of the gene.

  Specifically, in the method of the present invention, the following single nucleotide polymorphisms are analyzed for a Beijing strain-infected subject, a non-Beijing strain-infected subject, an EAI strain-infected subject, and a non-EAI strain-infected subject, respectively. . “RsXXXXXX (X is an arbitrary number)” indicating a single nucleotide polymorphism indicates an rs number which is a reference number of the SNP database (dbSNP BUILD137) of NCBI (National Center for Biotechnology Information).

The following single nucleotide polymorphism is a single nucleotide polymorphism of 1 × 10 ⁻⁵ or less when the relation with the onset of tuberculosis at the time of infection to M. tuberculosis of a specific genetic strain is expressed by P value. Here, the P value is a value indicating whether there is a difference in the frequency of single nucleotide polymorphisms in the group of patients who develop tuberculosis and the group of healthy individuals who do not develop, and the smaller the value, the more likely the correlation is Determined.

  Moreover, the base of the single nucleotide polymorphism site is represented by the base in either the normal chain or the reverse chain registered in the SNP database. The other strand sequence is a complementary base.

Beijing strain infected subjects
rs9348878, rs2070600, rs401864, rs673119, rs1321267, rs2076625, rs7142055, rs1157619, rs4924568, rs1899820, rs2695163, rs1197772, rs1081022, rs1648835

Non-Beijing strain infected subjects
rs12144738, rs1494320, rs1712674, rs1418425, rs4688637, rs12374531, rs11784415, rs2182093, rs10798, rs4267316, rs6071980, rs743057

EAI strain infected subjects
rs1178938, rs800065, rs1372667, rs13174549, rs7087410, rs10898382, rs951729, rs1658693

Non-EAI strain infected subjects
rs1820920, rs11737270, rs10832678, rs10507084, rs1440548

  The single nucleotide polymorphism represented by the rs number is a single nucleotide polymorphism described below. In the following description, for each single nucleotide polymorphism, an odds ratio (OR) (95% confidence interval) indicating the magnitude of the risk of developing a specific M. tuberculosis genetic line and a P value are shown. When the odds ratio of a single nucleotide polymorphism is 1 or more, a subject having a minor allele in the single nucleotide polymorphism has a higher possibility of developing tuberculosis. For example, in the case of 1.94, the chance of developing tuberculosis increases 1.94 times. On the other hand, when the odds ratio of a single nucleotide polymorphism is less than 1, a subject having a minor allele in the single nucleotide polymorphism is less likely to develop tuberculosis. For example, in the case of 0.61, the possibility of developing tuberculosis decreases 0.61 times.

Beijing strain infected subjects
(b1) rs9348878
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 1, and is G or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allyl. The odds ratio is 1.98 (1.48-2.64), and the P value is 2.69 × 10 ⁻⁶ .

(b2) rs2070600
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 2, and is A or G. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than that of G. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis in younger age (under 45 years) than a subject having G allyl. The odds ratio is 2.00 (1.50-2.67), and the P value is 2.07 × 10 ⁻⁶ .

(b3) rs401864
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 3, and is C or T. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at any age is significantly higher than that of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at any age than a subject having T allyl. The odds ratio is 1.63 (1.32-2.02), and the P value is 5.36 × 10 ⁻⁶ .

(b4) rs673119
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 4, and is C or T. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having T allyl. The odds ratio is 1.80 (1.39-2.33), and the P value is 6.97 × 10 ⁻⁶ .

(b5) rs1321267
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 5, and is C or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allele. The odds ratio is 1.95 (1.46-2.60), and the P value is 5.35 × 10 ⁻⁶ .

(b6) rs2076625
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 6, and is G or T. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis at any age is significantly smaller than that of T. That is, it can be determined that the risk of developing tuberculosis at any age is lower in subjects who possess G allyl (minor allele) than subjects who possess T allyl. The odds ratio is 0.61 (0.49-0.75), and the P value is 4.31 × 10 ⁻⁶ .

(b7) rs7142055
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 7, and is T or C. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of C. That is, it can be determined that a subject having T allyl (minor allyl) has a higher risk of developing tuberculosis in younger age (under 45 years) than a subject having C allyl. The odds ratio is 2.08 (1.50-2.89), and the P value is 7.78 × 10 ⁻⁶ .

(b8) rs1157619
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 8, and is T or C. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis at any age is significantly higher than in C. That is, it can be determined that a subject having T allyl (minor allyl) has a higher risk of developing tuberculosis at any age than a subject having C allyl. The odds ratio is 2.49 (1.70-3.64), and the P value is 1.27 × 10 ⁻⁶ .

(b9) rs4924568
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 9, and is A or G. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of G. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having G allele. The odds ratio is 2.31 (1.60-3.35), and the P value is 5.15 × 10 ⁻⁶ .

(b10) rs1899820
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 10, which is A or C. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in C. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having C allyl. The odds ratio is 2.31 (1.60-3.35), and the P value is 5.15 × 10 ⁻⁶ .

(b11) rs2695163
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 11, and is G or A. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of A. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having A allele. The odds ratio is 2.35 (1.63-3.38), and the P value is 2.97 × 10 ⁻⁶ .

(b12) rs1197772
This is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 12, and is G or A. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of A. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having A allele. The odds ratio is 2.36 (1.64-3.40), and the P value is 2.02 × 10 ⁻⁶ .

(b13) rs1081022
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 13, and is T or G. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of G. That is, it can be determined that a subject having T allyl (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having G allyl. The odds ratio is 2.27 (1.62-3.18), and the P value is 9.83 × 10 ⁻⁷ .

(b14) rs1648835
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 14, and is T or G. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of G. That is, it can be determined that a subject having T allyl (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having G allyl. The odds ratio is 2.33 (1.65-3.29), and the P value is 8.60 × 10 ⁻⁷ .

Non-Beijing strain infected subjects
(nb1) rs12144738
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 15, and is C or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in younger age (under 45 years) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.22 (1.59-3.10) and the P value is 2.08 × 10 ⁻⁶ .

(nb2) rs1494320
It is a polymorphism at the 26th base in the base sequence represented by SEQ ID NO: 16, and is C or T. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having T allyl. The odds ratio is 1.71 (1.40-2.08), and the P value is 7.84 × 10 ⁻⁸ .

(nb3) rs1712674
This is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 17, and is G or T. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly larger than in the case of T. That is, it can be determined that a subject having G allele (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having T allyl. The odds ratio is 1.77 (1.40-2.25), and the P value is 1.63 × 10 ⁻⁶ .

(nb4) rs1418425
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 18, and is T or C. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of C. That is, it can be determined that a subject having T allyl (minor allyl) has a higher risk of developing tuberculosis in younger age (under 45 years) than a subject having C allyl. The odds ratio is 1.74 (1.43-2.12), and the P value is 2.54 × 10 ⁻⁸ .

(nb5) rs4688637
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 19, and is C or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allele. The odds ratio is 2.08 (1.50-2.88), and the P value is 7.15 × 10 ⁻⁶ .

(nb6) rs12374531
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 20, which is G or A. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis in the old age of tuberculosis (over 45 years) is significantly smaller than in the case of A. That is, it can be determined that the risk of developing tuberculosis in the elderly (45 years or older) is lower in subjects who have G allyl (minor allele) than in subjects who have A allyl. The odds ratio is 0.58 (0.45-0.74) and the P value is 8.54 × 10 ⁻⁶ .

(nb7) rs11784415
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 21 is C or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allele. The odds ratio is 2.03 (1.50-2.74), and the P value is 2.54 × 10 ⁻⁶ .

(nb8) rs2182093
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 22, and is T or C. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of C. That is, it can be determined that a subject having T allyl (minor allyl) has a higher risk of developing tuberculosis in younger age (under 45 years) than a subject having C allyl. The odds ratio is 2.38 (1.65-3.43), and the P value is 1.80 × 10 ⁻⁶ .

(nb9) rs10798
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 23 is A or G. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis at any age is significantly higher than that of G. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis at any age than a subject having G allele. The odds ratio is 1.60 (1.32-1.95), and the P value is 2.31 × 10 ⁻⁶ .

(nb10) rs4267316
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 24 is C or T. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at any age is significantly higher than that of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at any age than a subject having T allyl. The odds ratio is 2.26 (1.58-3.23), and the P value is 5.29 × 10 ⁻⁶ .

(nb11) rs6071980
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 25, and is C or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in younger age (under 45 years) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.09 (1.51-2.90), and the P value is 6.77 × 10 ⁻⁶ .

(nb12) rs743057
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 26, which is A or G. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis at any age is significantly smaller than that of G. That is, it can be determined that a subject having A allyl (minor allyl) has a lower risk of developing tuberculosis at any age than a subject having G allele. The odds ratio is 0.59 (0.47-0.74), and the P value is 5.70 × 10 ⁻⁶ .

EAI strain infected subjects
(e1) rs1178938
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 27 is C or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allele. The odds ratio is 2.37 (1.67-3.35), and the P value is 5.97 × 10 ⁻⁷ .

(e2) rs800065
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 28, which is C or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in younger age (under 45 years) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.33 (1.65-3.30), and the P value is 9.72 × 10 ⁻⁷ .

(e3) rs1372667
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 29, and is G or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than that of T. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.29 (1.59-3.32), and the P value is 6.43 × 10 ⁻⁶ .

(e4) rs13174549
It is a polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 30, and is T or C. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis at any age is significantly smaller than in C. That is, it can be determined that a subject having T allyl (minor allyl) has a lower risk of developing tuberculosis at any age than a subject having C allyl. The odds ratio is 0.44 (0.31-0.62), and the P value is 2.02 × 10 ⁻⁶ .

(e5) rs7087410
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 31 is C or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in younger age (under 45 years) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.27 (1.58-3.25), and the P value is 5.94 × 10 ⁻⁶ .

(e6) rs10898382
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 32, which is A or C. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in C. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having C allyl. The odds ratio is 1.62 (1.32-2.00), and the P value is 3.66 × 10 ⁻⁶ .

(e7) rs951729
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 33, which is A or C. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is A, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in C. That is, it can be determined that a subject having A allyl (minor allyl) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having C allyl. The odds ratio is 1.61 (1.31-1.97), and the P value is 5.93 × 10 ⁻⁶ .

(e8) rs1658693
The polymorphism at the 26th base of the base sequence shown in SEQ ID NO: 34 is C or T. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly smaller than in the case of T. That is, it can be determined that the risk of developing tuberculosis in the elderly (45 years or older) is lower in subjects who possess C allyl (minor allele) than in subjects who possess T allyl. The odds ratio is 0.63 (0.51-0.77), and the P value is 8.57 × 10 ⁻⁶ .

Non-EAI strain infected subjects
(ne1) rs1820920
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 35, which is C or T. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis in younger age (under 45 years) is significantly higher than in the case of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having T allyl. The odds ratio is 2.04 (1.48-2.82), and the P value is 9.18 × 10 ⁻⁶ .

(ne2) rs11737270
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 36, which is G or A. This single nucleotide polymorphism is highly related to juvenile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis at a young age (under 45 years) is significantly higher than in the case of A. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis at a young age (under 45 years) than a subject having A allyl. The odds ratio is 1.81 (1.40-2.34), and the P value is 4.14 × 10 ⁻⁶ .

(ne3) rs10832678
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 37, which is G or A. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is G, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly higher than in the case of A. That is, it can be determined that a subject having G allyl (minor allele) has a higher risk of developing tuberculosis in the elderly (45 years or older) than a subject having A allele. The odds ratio is 1.66 (1.33-2.07), and the P value is 5.66 × 10 ⁻⁶ .

(ne4) rs10507084
It is a polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 38, and is T or C. This single nucleotide polymorphism is highly related to senile onset. When the base at the single nucleotide polymorphism site is T, the proportion of subjects who develop tuberculosis in the elderly (45 years or older) is significantly smaller than in C. That is, it can be determined that a subject having T allyl (minor allyl) has a lower risk of developing tuberculosis in the elderly (45 years or older) than a subject having C allyl. The odds ratio is 0.58 (0.46-0.73), and the P value is 4.21 × 10 ⁻⁶ .

(ne5) rs1440548
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 39, which is C or T. When the base at the single nucleotide polymorphism site is C, the proportion of subjects who develop tuberculosis at any age is significantly higher than that of T. That is, it can be determined that a subject having C allyl (minor allele) has a higher risk of developing tuberculosis at any age than a subject having T allyl. The odds ratio is 1.70 (1.35-2.13), and the P value is 4.12 × 10 ⁻⁶ .

  When the M. tuberculosis infecting the subject is a Beijing strain, at least one of the above (b1) to (b14), preferably 2, 3, 4, 5, 6, 7, 8, 9, 10 , 11, 12, 13 or 14 bases, and when the tubercle bacillus infecting the subject is a non-Beijing strain, at least one of the above (nb1) to (nb12), preferably 2 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 single nucleotide polymorphic site bases are identified, and when the tuberculosis infecting subject is an EAI strain, Tuberculosis in which at least one of the above (e1) to (e8), preferably 2, 3, 4, 5, 6, 7 or 8 single nucleotide polymorphism sites are identified and the subject is infected When the bacterium is a non-EAI strain, at least one of the above (ne1) to (ne5), preferably 2, 3, 4 or 5 single nucleotide polymorphic sites, is identified, and depending on the type of base To determine the risk of developing tuberculosis Can do.

  Moreover, instead of the single nucleotide polymorphism analysis described above, or together with the single nucleotide polymorphism analysis, the expression of a gene located in the vicinity of the single nucleotide polymorphism site in the subject may be measured. When the expression of the gene is increased or attenuated, it can be determined that the subject has a high risk of developing tuberculosis.

  Since the above single nucleotide polymorphism exists regardless of the human population, the method of the present invention can be applied to any human population worldwide. In the method of the present invention, analysis of single nucleotide polymorphism and typing of M. tuberculosis are performed at the same time. However, depending on the human population, there may be one type of M. tuberculosis that is infected. It may be omitted. For example, most Japanese are Beijing-type.

The genes located in the vicinity of each single nucleotide polymorphism site are as follows.
Beijing strain infected subjects
rs9348878 PRRT1 (Proline Rich Transmembrane Protein 1) (6.8kbp 3 ')
rs2070600 AGER (Advanced Glycosylation End-product specific Receptor) (Missense)
rs401864 ASCC3 (Activating Signal Cointegrator 1 Complex subunit 3) (Intron)
rs673119 ASCC3 (Activating Signal Cointegrator 1 Complex subunit 3) (43kbp 5 ')
rs1321267 LOC100507254 (Intron)
rs2076625 KIAA1549L (KIAA1549 Like) (Intron)
rs7142055 MIS18BP1 (MIS18 Binding Protein 1) (264kbp 3 ')
rs1157619 MEIS2 (Meis homeobox 2) (Intron)
rs4924568 MGA (MGA, MAX dimerization protein) (4.6kbp 5 ')
rs1899820 MGA (MGA, MAX dimerization protein) (1.0kbp 5 ')
rs2695163 MGA (MGA, MAX dimerization protein) (Synonymous)
rs1197772 MAPKBP1 (Mitogen-Activated Protein Kinase Binding Protein 1) (2.1kbp 5 ')
rs1081022 MAPKBP1 (Mitogen-Activated Protein Kinase Binding Protein 1) (Intron)
rs1648835 JMJD7-PLA2G4B (Jumonji Domain containing 7 and Phospholipase A2, Group IVB) (Intron)

Non-Beijing strain infected subjects
rs12144738 FHAD1 (Forkhead Associated phosphopeptide binding Domain 1) (Intron)
rs1494320 CD53 (Intron)
rs1712674 CD53 (23kbp 3 ')
rs1418425 LRIF1 (Ligand dependent nuclear Receptor Interacting Factor 1) (21kbp 3 ')
rs4688637 PTPRG (Protein Tyrosine Phosphatase, Receptor type G) (Intron)
rs12374531 PPP2R2B (Protein Phosphatase 2 Regulatory subunit Bbeta) (52kbp 5 ')
rs11784415 LRRC69 (Leucine Rich Repeat Containing 69) (Intron)
rs2182093 PLCE1 (Phospholipase C Epsilon 1) (Intron)
rs10798 KCNQ1 (Potassium voltage-gated channel subfamily Q member 1) (3'-UTR)
rs4267316 MAF (MAF bZIP transcription factor) (268kbp 5 ')
rs6071980 MAFB (MAF bZIP transcription factor B) (446kbp 3 ')
rs743057 FAM19A5 (Family with sequence similarity 19 member A5, CC motif chemokine like) (Intron)

EAI strain infected subjects
rs1178938 C3orf58 (Chromosome 3 open reading frame 58) (67kbp 3 ')
rs800065 C3orf58 (Chromosome 3 open reading frame 58) (68kbp 3 ')
rs1372667 CDH12 (Cadherin 12) (31kbp 5 ')
rs13174549 EBF1 (Early B-cell Factor 1) (Intron)
rs7087410 LOC220906 (106kbp 3 ')
rs10898382 DLG2 (Discs Large MAGUK scaffold protein 2) (Intron)
rs951729 DLG2 (Discs Large MAGUK scaffold protein 2) (Intron)
rs1658693 BTG1 (BTG anti-proliferation factor 1) (26kbp 5 ')

Non-EAI strain infected subjects
rs1820920 MIR4790 (MicroRNA 4790) (301kbp 5 ')
rs11737270 FBXW7 (F-box and WD repeat domain containing 7) (254kbp 3 ')
rs10832678 C11orf58 (Chromosome 11 open reading frame 58) (7.9kbp 3 ')
rs10507084 RMST (Rhabdomyosarcoma 2 associated transcript) (106kbp 5 ')
rs1440548 LOC284294 (450kbp 3 ')

  Among the above genes, when the expression of CD53 is increased in a non-Beijing strain-infected subject compared to a healthy subject, it can be determined that the subject has a high risk of developing tuberculosis. Moreover, when the expression of MAFB is increased in a non-Beijing strain-infected subject as compared with a healthy subject, it can be determined that the subject has a high risk of developing tuberculosis.

  1-1 and 1-2, the rs number of the above single nucleotide polymorphism, the number of the human chromosome in which the single nucleotide polymorphism exists, the minor allele / major allele, the gene located near the single nucleotide polymorphism, the onset Shows the P value and odds ratio of each genetic line of M. tuberculosis.

  In the present invention, the single nucleotide polymorphism and the gene located in the vicinity of the single nucleotide polymorphism site can be referred to as genetic markers for determining the risk of developing tuberculosis.

  In the method of the present invention, a sample may be collected from a subject and a single nucleotide polymorphism may be analyzed for DNA or RNA of the sample. That is, genomic DNA containing a single nucleotide polymorphism is extracted from a subject, and the base of the single nucleotide polymorphism site of the allele contained in the extracted DNA may be identified. As a sample used for analysis, any sample containing chromosomal DNA can be used, and examples thereof include blood, skin, oral mucosa, hair, urine, nails, cells and the like. From these samples, nucleic acids such as chromosomes, DNA or RNA may be isolated and analyzed according to a conventional method.

  Single nucleotide polymorphism analysis can be performed by an ordinary gene polymorphism analysis method. For example, hybridization using a sequence analysis method for direct sequencing by a known method such as the dideoxy method or the Maxam-Gilbert method, a probe specific to a gene polymorphism, or a microarray (DNA chip) on which the probe is immobilized And various methods using primers specific to gene polymorphism, and more specifically, primer extension method (TaqMan (registered trademark) method), PCR-SSCP method, single-strand conformation polymorphism analysis (SSCP: single strand conformation polymorphism), Invader method, single nucleotide primer method, PCR method, NASBA method, LCR method, SDA method, LAMP method, method using restriction fragment length polymorphism (RFLP), denaturing gradient gel electrophoresis Method (DGGE), method using chemical cleavage of mismatch site (CCM), SNaPshot method, MassArray method, Pyrosequencing method, SNP-IT method, BeadArray method, Scorpion method, MADI-TOF / MS method etc. are mentioned. Alternatively, the DigiTag2 method can be used in which each single nucleotide polymorphism genotype is converted into an oligo DNA tag and analyzed by hybridization with a DNA chip. The DigiTag2 method is described in Srilohasin P et al. J. Clin. Microbiol. 2014, 52 (6): 1962-8, Nishida N et al., Analytical Biochemistry 346 (2): 281-288, Nishida et al., Analytical Biochemistry. 364 (1): 78-85 and the like.

  Analysis by sequence analysis can be performed by a normal method. Specifically, a sequence reaction is performed using a primer set at a position of several tens of bases on the 5 ′ side of the single nucleotide polymorphism site, and the base of the single nucleotide polymorphism site can be determined from the analysis result. it can.

  The method using a primer is performed by amplifying a nucleic acid sample isolated from a subject using a primer corresponding to a part of a gene sequence containing a single nucleotide polymorphism site. That is, for example, using a primer that is completely or almost completely complementary to one allele and a primer that is completely or almost completely complementary only to the other allele, and using each primer, a nucleic acid sample isolated from the subject. The single nucleotide polymorphism allele can be identified by whether or not is amplified. Moreover, you may use only the primer corresponding to one allyl.

  The method using a probe consists of an oligonucleotide corresponding to a part of a gene sequence containing a single nucleotide polymorphism site or a complementary sequence thereof, or an oligonucleotide consisting of a sequence that can hybridize to these sequences under stringent conditions. The probe can be used for analysis by hybridization with a nucleic acid sample isolated from a subject or a nucleic acid sample amplified by a known method such as PCR. That is, one allele is completely or almost completely (for example, the nucleotide sequence portion continuous to the target single nucleotide polymorphism site is 70% or more, preferably 80% or more, more preferably 90%. % Of sequence identity, particularly preferably 95% or more sequence identity) and a probe that is completely or almost completely complementary only to the other allele. The single nucleotide polymorphism allele can be identified based on whether it hybridizes with a nucleic acid sample isolated from a subject or an amplified nucleic acid sample. Moreover, you may use only the probe corresponding to one allyl. The hybridization conditions may be sufficient to distinguish single nucleotide polymorphisms. For example, hybridization occurs when a single nucleotide polymorphism site is a specific allele, but hybridization occurs when another allele is present. Conditions that do not soy, such as stringent conditions, can be set as appropriate by those skilled in the art. One end of the probe may be fixed to a substrate and used as a DNA chip (microarray). In this case, only a probe corresponding to one gene polymorphic site may be immobilized on the DNA chip, or probes corresponding to a plurality of single nucleotide polymorphic sites may be immobilized.

  Probes and primers for detecting a single nucleotide polymorphism can be appropriately designed based on the single nucleotide polymorphism sequence information.

  The probe consists of a nucleotide sequence (preferably a DNA fragment) comprising a nucleotide sequence containing a single nucleotide polymorphism site, a nucleotide sequence complementary to the nucleotide sequence, or a sequence that can hybridize to these sequences under stringent conditions. The number of bases is 5-50, preferably 10-30, more preferably 10-25.

  The primer is a primer capable of identifying an allele of a single nucleotide polymorphism site, for example, a sequence capable of amplifying a region having a sequence containing a single nucleotide polymorphism site. These primers may contain a sequence containing a single nucleotide polymorphic site, and also 3 'and 5' sides of a region containing a single nucleotide polymorphic site (preferably a region having a length of 40 to 1000 bases). It may be a primer pair of a forward primer and a reverse primer set at both ends. A primer consists of a nucleotide sequence (preferably a DNA fragment) comprising a nucleotide sequence containing a single nucleotide polymorphism site, a nucleotide sequence complementary to the nucleotide sequence, or a sequence that can hybridize to these sequences under stringent conditions. The number of bases is 5 to 50, preferably 10 to 30, and more preferably 15 to 25.

  The probe or primer may contain several mismatches, preferably 1 to 5, more preferably 1 or 2, and particularly preferably 1 mismatch in a continuous base sequence including a single nucleotide polymorphic site. Good.

  The present invention provides a probe used for analyzing the single nucleotide polymorphism and a primer used for amplification of a DNA fragment containing a single nucleotide polymorphism site for analyzing the single nucleotide polymorphism (preferably at least a pair of primer sets). ). It also includes a DNA chip on which a probe is immobilized. Furthermore, a kit for analyzing the above single nucleotide polymorphism site including a probe, a DNA chip, and a primer is also included.

  The kit may additionally contain a restriction enzyme, polymerase, nucleoside triphosphate, nucleic acid labeling molecule, buffer solution, instruction manual for the kit, etc. used for single nucleotide polymorphism analysis.

  Examples of probes or primers used for the analysis of single nucleotide polymorphism sites include the following.

Primers to determine the risk of developing tuberculosis in Beijing-infected subjects
(p1) A primer capable of amplifying a region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1.
(p2) Primer that can amplify the region containing the 26th base (base of polymorphic site of rs2070600) in the base sequence of SEQ ID NO: 2
(p3) Primer capable of amplifying a region containing the 26th base (base of rs401864 polymorphic site) in the base sequence of SEQ ID NO: 3
(p4) Primer capable of amplifying a region containing the 26th base (base of rs673119 polymorphic site) in the base sequence of SEQ ID NO: 4
(p5) A primer capable of amplifying a region containing the 26th base (base of rs1321267 polymorphic site) in the base sequence of SEQ ID NO: 5.
(p6) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs2076625) in the base sequence of SEQ ID NO: 6.
(p7) A primer capable of amplifying a region containing the 26th base (base of rs7142055 polymorphic site) in the base sequence of SEQ ID NO: 7.
(p8) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs1157619) in the base sequence of SEQ ID NO: 8
(p9) A primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 9 (the base of the polymorphic site of rs4924568)
(p10) A primer capable of amplifying a region containing the 26th base (base of rs1899820 polymorphic site) in the base sequence of SEQ ID NO: 10
(p11) A primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 11 (the base of the polymorphic site of rs2695163)
(p12) Primer capable of amplifying a region containing the 26th base (base of rs1197772 polymorphic site) in the base sequence of SEQ ID NO: 12
(p13) Primer capable of amplifying a region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13
(p14) Primer capable of amplifying a region containing the 26th base (base of rs1648835 polymorphic site) in the base sequence of SEQ ID NO: 14

Primers for determining the risk of developing tuberculosis in non-Beijing strain-infected subjects
(p15) Primer that can amplify a region containing the 26th base (base of rs12144738 polymorphic site) in the base sequence of SEQ ID NO: 15
(p16) Primer capable of amplifying a region containing the 26th base (base of rs1494320 polymorphic site) in the base sequence of SEQ ID NO: 16
(p17) Primer capable of amplifying a region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17
(p18) Primer capable of amplifying a region containing the 26th base (base of rs1418425 polymorphic site) in the base sequence of SEQ ID NO: 18
(p19) A primer capable of amplifying a region containing the 26th base (base of rs4688637 polymorphic site) in the base sequence of SEQ ID NO: 19.
(p20) A primer capable of amplifying a region containing the 26th base (base of rs12374531 polymorphic site) in the base sequence of SEQ ID NO: 20
(p21) Primer capable of amplifying a region containing the 26th base (base of rs11784415 polymorphic site) in the base sequence of SEQ ID NO: 21
(p22) Primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs2182093) in the base sequence of SEQ ID NO: 22
(p23) A primer capable of amplifying a region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23
(p24) Primer capable of amplifying a region containing the 26th base (base of rs4267316 polymorphic site) in the base sequence of SEQ ID NO: 24
(p25) Primer capable of amplifying a region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25
(p26) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs743057) in the base sequence of SEQ ID NO: 26

Primers to determine the risk of developing tuberculosis in EAI strain-infected subjects
(p27) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs1178938) in the base sequence of SEQ ID NO: 27
(p28) Primer capable of amplifying a region containing the 26th base (base of rs800065 polymorphic site) in the base sequence of SEQ ID NO: 28
(p29) A primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 29 (the base of the polymorphic site of rs1372667)
(p30) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs13174549) in the base sequence of SEQ ID NO: 30
(p31) Primer capable of amplifying a region containing the 26th base (base of rs7087410 polymorphic site) in the base sequence of SEQ ID NO: 31
(p32) A primer capable of amplifying a region containing the 26th base (base of rs10898382 polymorphic site) in the base sequence of SEQ ID NO: 32
(p33) Primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs951729) in the base sequence of SEQ ID NO: 33
(p34) Primer capable of amplifying a region containing the 26th base (base of rs1658693 polymorphic site) in the base sequence of SEQ ID NO: 34

Primers to determine the risk of developing tuberculosis in non-EAI strain-infected subjects
(p35) A primer capable of amplifying a region containing the 26th base (base of rs1820920 polymorphic site) in the base sequence of SEQ ID NO: 35
(p36) Primer capable of amplifying a region containing the 26th base (base of rs11737270 polymorphic site) in the base sequence of SEQ ID NO: 36
(p37) Primer capable of amplifying a region containing the 26th base (base of rs10832678 polymorphic site) in the base sequence of SEQ ID NO: 37
(p38) A primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs10507084) in the base sequence of SEQ ID NO: 38
(p39) A primer capable of amplifying a region containing the 26th base (base of rs1440548 polymorphic site) in the base sequence of SEQ ID NO: 39

Probes to determine the risk of developing tuberculosis in Beijing strain-infected subjects
(q1) A probe capable of hybridizing to the region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1.
(q2) Probe capable of hybridizing to the region containing the 26th base (base of rs2070600 polymorphic site) in the base sequence of SEQ ID NO: 2
(q3) A probe capable of hybridizing to the region containing the 26th base (base of rs401864 polymorphic site) in the base sequence of SEQ ID NO: 3.
(q4) Probe that can hybridize to the region containing the 26th base (base of rs673119 polymorphic site) in the base sequence of SEQ ID NO: 4
(q5) A probe capable of hybridizing to a region containing the 26th base (base of rs1321267 polymorphic site) in the base sequence of SEQ ID NO: 5.
(q6) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 6 (the base of the polymorphic site of rs2076625)
(q7) A probe capable of hybridizing to the region containing the 26th base (base of rs7142055 polymorphic site) in the base sequence of SEQ ID NO: 7.
(q8) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 8 (the base of the polymorphic site of rs1157619)
(q9) Probe capable of hybridizing to the region containing the 26th base (base of rs4924568 polymorphic site) in the base sequence of SEQ ID NO: 9
(q10) A probe capable of hybridizing to the region containing the 26th base (base of rs1899820 polymorphic site) in the base sequence of SEQ ID NO: 10.
(q11) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 11 (the base of the polymorphic site of rs2695163)
(q12) A probe capable of hybridizing to a region containing the 26th base (base of rs1197772 polymorphic site) in the base sequence of SEQ ID NO: 12.
(q13) Probe that can hybridize to the region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13.
(q14) Probe capable of hybridizing to the region containing the 26th base (base of rs1648835 polymorphic site) in the base sequence of SEQ ID NO: 14

Probes to determine the risk of developing tuberculosis in non-Beijing strain-infected subjects
(q15) Probe capable of hybridizing to the region containing the 26th base (base of rs12144738 polymorphic site) in the base sequence of SEQ ID NO: 15
(q16) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 16 (the base of the polymorphic site of rs1494320)
(q17) Probe that can hybridize to the region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17
(q18) Probe that can hybridize to the region containing the 26th base (base of polymorphic site of rs1418425) in the base sequence of SEQ ID NO: 18.
(q19) Probe capable of hybridizing to the region containing the 26th base (base of rs4688637 polymorphic site) in the base sequence of SEQ ID NO: 19.
(q20) Probe that can hybridize to the region containing the 26th base (base of polymorphic site of rs12374531) in the base sequence of SEQ ID NO: 20
(q21) Probe that can hybridize to the region containing the 26th base (base of rs11784415 polymorphic site) in the base sequence of SEQ ID NO: 21
(q22) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 22 (the base of the polymorphic site of rs2182093)
(q23) Probe capable of hybridizing to the region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23
(q24) A probe capable of hybridizing to the region containing the 26th base (base of rs4267316 polymorphic site) in the base sequence of SEQ ID NO: 24
(q25) A probe capable of hybridizing to the region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25
(q26) A probe capable of hybridizing to a region containing the 26th base (base of rs743057 polymorphic site) in the base sequence of SEQ ID NO: 26

Probe to determine the risk of developing tuberculosis in EAI strain-infected subjects
(q27) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 27 (the base of the polymorphic site of rs1178938)
(q28) Probe that can hybridize to the region containing the 26th base (base of rs800065 polymorphic site) in the base sequence of SEQ ID NO: 28
(q29) Probe that can hybridize to the region containing the 26th base (base of rs1372667 polymorphic site) in the base sequence of SEQ ID NO: 29
(q30) Probe that can hybridize to the region containing the 26th base (base of polymorphic site of rs13174549) in the base sequence of SEQ ID NO: 30
(q31) Probe that can hybridize to the region containing the 26th base (base of polymorphic site of rs7087410) in the base sequence of SEQ ID NO: 31
(q32) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 32 (the base of the polymorphic site of rs10898382)
(q33) A probe capable of hybridizing to the region containing the 26th base (the base of the polymorphic site of rs951729) in the base sequence of SEQ ID NO: 33
(q34) A probe capable of hybridizing to a region containing the 26th base (base of rs1658693 polymorphic site) in the base sequence of SEQ ID NO: 34

Probe to determine the risk of developing tuberculosis in non-EAI strain-infected subjects
(q35) Probe that can hybridize to the region containing the 26th base (base of rs1820920 polymorphic site) in the base sequence of SEQ ID NO: 35
(q36) A probe capable of hybridizing to the region containing the 26th base (base of rs11737270 polymorphic site) in the base sequence of SEQ ID NO: 36
(q37) Probe that can hybridize to the region containing the 26th base (base of rs10832678 polymorphism) in the base sequence of SEQ ID NO: 37
(q38) A probe capable of hybridizing to a region containing the 26th base (base of rs10507084 polymorphic site) in the base sequence of SEQ ID NO: 38
(q39) A probe capable of hybridizing to the region containing the 26th base in the base sequence of SEQ ID NO: 39 (base of the polymorphic site of rs1440548)

  When the Mycobacterium tuberculosis infecting the subject is a Beijing strain, at least one of the above (p1) to (p14), preferably 2, 3, 4, 5, 6, 7, 8, 9, 10 , 11, 12, 13 or 14 and when the tuberculosis infecting the subject is a non-Beijing strain, at least one of the above (p15) to (p26), preferably 2, When 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 primers are used, and the tubercle bacillus infecting the subject is an EAI strain, the above (p27) to (p34) ), Preferably 2, 3, 4, 5, 6, 7 or 8 primers, and when the tuberculosis infecting the subject is a non-EAI strain (p35) above A single nucleotide polymorphism may be identified by using at least one, preferably 2, 3, 4 or 5 primers of (p39). The primer is preferably used as a primer pair of a forward primer and a reverse primer.

  In addition, when the tubercle bacillus infecting the subject is a Beijing strain, at least one of the above (q1) to (q14), preferably 2, 3, 4, 5, 6, 7, 8, 9 , 10, 11, 12, 13 or 14 and when the tuberculosis bacillus in which the subject is infected is a non-Beijing strain, preferably at least one of the above (q15) to (q26), preferably When 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 probes are used, and the tubercle bacillus in which the subject is infected is an EAI strain, the above (q27) to When at least one of (q34), preferably 2, 3, 4, 5, 6, 7 or 8 probes, is used, and the tuberculosis infecting the subject is a non-EAI strain, the above ( A single nucleotide polymorphism may be identified using at least one of q35) to (q39), preferably 2, 3, 4 or 5 probes.

  The present invention includes a reagent or kit for determining the risk of developing tuberculosis, comprising the above-described primer or probe.

  The expression of a gene located in the vicinity of the single nucleotide polymorphism site may be measured for the mRNA of each gene or the expressed protein. Preferably, mRNA is measured. What is necessary is just to measure the mRNA or protein extracted from a tissue or a cell.

  Measurement of mRNA in tissues or cells may be performed by, for example, extracting RNA from tissues or cells, reversely transcribing it to cDNA, and measuring the cDNA. The measurement of cDNA can be performed using a probe or primer that hybridizes complementarily to each gene using the sequence information of each gene. Measurement using a probe or primer can be performed according to the method for detecting a single nucleotide polymorphism.

  Protein measurement can be performed by immunoassay using an antigen-antibody reaction by extracting a protein from tissue or cells and using an antibody such as a monoclonal antibody against the protein. Moreover, it can also measure by dyeing | staining by the immunohistochemistry using the said antibody, and immunocytochemistry with respect to the extract | collected tissue or cell.

  If it is determined by the method of the present invention that the risk of developing tuberculosis is high, the subject may be (1) rifampicin, (2) isoniazid, (3) streptomycin, (4) ethambutol, (5) pyrazinamide, etc. What is necessary is just to administer antibiotics over several months combining suitably. For example, (1) and (2) and (4) or (3) and (5) may be administered for about 2 months, and then (1) and (2) may be administered for about 4 months.

  The present invention will be specifically described by the following examples, but the present invention is not limited to these examples.

  The present invention is based on the results of analysis of tuberculosis-onset and healthy subjects collected in the Kingdom of Thailand. The diagnosis of tuberculosis was based on the culture determination of Mycobacterium tuberculosis from the patient's sputum, and those that were positive were determined as those who developed tuberculosis. Patients who were co-infected with the HIV virus were excluded. A healthy person has no history of tuberculosis. DNA was extracted from the patient's blood and Mycobacterium tuberculosis.

  SNP information of the human genome was obtained with Illumina Human610-Quad v1.0 or Illumina HumanOmniExpressExome-8 v1.2, which are SNP typing microarrays manufactured by Illumina. Genotype information derived from 338,476 SNPs common to the two arrays is an object to be analyzed in the process of implementing the present invention. For quality control of specimen data, specimens with a genotype determination rate of 98% or more in SNPs throughout the genome were used. Quality control of SNP data (1) Genotypes are determined in 95% or more of all samples, (2) Minor allele frequency is 5% or more in all samples, and (3) In healthy subjects In the Hardy-Weinberg equilibrium test, SNP that satisfies all three conditions of P value of 0.001 or higher and not different from the theoretical value was adopted. Finally, 266,604 autosomal SNPs were used for association analysis.

  All specimens have been tested for identity by descent (IBD) using SNPs that have cleared the above data quality control, and confirmed that they do not contain duplicate specimens or first-degree relative samples. In addition, all Thai specimens used for association analysis are included in the Asian population by principal component analysis using the public data [GSE17205 (CEU), GSE17206 (CHB + JPT) and GSE17207 (YRI)] of the international Hapmap project. It is confirmed that Furthermore, since the Thai population has a variety of genetic backgrounds, we conducted a principal component analysis using SNPs information for the entire human genome, and before conducting a related analysis, collected Thai patients and healthy subjects. Patient groups with similar genetic background were extracted. As a result of the extraction, 1,457 samples with close genetic background were selected from all 1784 samples to be analyzed, including 686 tuberculosis patients and 771 healthy subjects. The genome of Mycobacterium tuberculosis has been extracted from all tuberculosis patient specimens.

  At the same time, the genetic strain of M. tuberculosis was identified using the extracted genome of M. tuberculosis. The determination was performed using the large sequence polymorphism (LSP) method based on the PCR method using the extracted genomic DNA as a template. Specifically, TbD1, RD105, RD239, 7bp deletion at pks15 / are used as the genomic region of Mycobacterium tuberculosis as a marker for classification into five genetic strains, EAI strain, Beijing strain, CAS strain, Euro-American strain and others. Five genomic regions, 1 and RD750, were combined. By amplifying the target region with a specific primer set for each genomic region, the presence or absence of the target region was determined based on the size of the amplified product, and the genetic strain was determined from the result. EAI strain is RD239 (-) and TbD1 (+), Beijing strain is RD105 (-) and TbD1 (-), CAS strain is RD750 (-) and TbD1 (-), Euro-American strain is TbD1 (-) and 7bp deletion at pks 15/1. The other strains were TbD1 (-) and all four other regions (+). Although classification by sporigotyping was also performed, it was consistent with the classification result by the LSP method. All specimens used this time were infected by a single genetic lineage. In the present invention, Beijing shares are often infected, so all other shares are called non-Beijing shares. Non-Beijing shares are EAI, CAS and Euro-American shares. Is included. Similarly, since EAI strains are often infected, strains other than EAI strains are collectively referred to as non-EAI strains, and non-EAI strains include Beijing, CAS and Euro-American strains.

  Based on the genome information of those infected tuberculosis bacteria, the group of all patients with tuberculosis is classified into the group of patients infected with Beijing strain, the group of patients infected with non-Beijing strain, the group of patients infected with EAI strain, and the group of patients infected with non-EAI strain. A related analysis comparing the allele frequencies of 266,604 SNPs in a group of patients infected with M. tuberculosis of a common genetic line and a healthy group of controls suggests a specific association with the M. tuberculosis line. Identified SNPs. At the same time, the patient group that is considered to have a common onset mechanism is extracted by an analysis that combines the classification of the patient group using the patient onset age information. We identified SNPs that suggest a general association. According to the previous report (Mahasirimongkol S et al. J Hum Genet. 2012 Jun; 57 (6): 363-7), patients were classified into an older age group of 45 years or older and a younger age group of less than 45 years. SNPs related to the onset of tuberculosis and its nearby genes, which are found by this search, are specific subjects of the invention (FIGS. 1 to 4).

  In the association analysis, chi-square test is performed on the count of alleles between the tuberculosis patient group and the healthy subject group, and the P value is calculated. The genomic inflation factor, which is an indicator of the deviation of the genetic background between the tuberculosis patient group and the healthy group, was 1.066, which was within the allowable range. Statistically, P values below 1E-05 are considered suggestively associated. For all SNPs with a P value below 1E-05, the genotyping raw data is confirmed to confirm that there is no problem in genotyping.

  As a concrete result, in the group of patients infected with Beijing strain in the collected population, although the number of specimens was small compared to the total patient group not considering the genetic strain information of M. tuberculosis (Total column in the table) Fourteen SNPs were identified that found a more statistically significant association (P value). These SNPs were not found to be significantly related in the non-Beijing strain-infected patient group. Ten genes were found as the closest genes of these 14SNPs (Gen item in the table). In other classifications, 12SNPs (11 genes) showing a significant association in the non-Beijing strain-infected patients group compared to all patients groups, and 8SNPs (6 genes) showing a significant association in the EAI strain-infected patients group than all patients groups In addition, 5SNPs (5 genes) were identified in the non-EAI strain-infected patient group, which were significantly more relevant than the entire patient group.

  In addition, the expression analysis of each tuberculosis risk candidate gene in tuberculosis patients, Gene Expression Omnibus registration data (GSE19435 and GSE19439) of the previous report (Berry MP et al. Nature. 2010 Aug 19; 466 (7309): 973-7.) It was performed using. In this data, RNA was collected from the blood of a tuberculosis patient living in the United Kingdom, and the expression level was measured using Illumina Human HT-12 V3 BeadChip arrays (Illumina). Data that has already been homogenized between arrays using Illumina BeadStudio version 1.5.1.3 software has been published. Sufficiently reliable data with a detection p-value of 0.05 or less, which is an indicator of the reliability of the expression level published accompanying the data, was used for the analysis. As a result, for each of the CD53 gene and MAFB gene, the gene expression level was significantly increased in the patient (before treatment start) (PTB_00) compared to the healthy subject (Control), and 2 months after treatment (PTB_02), 12 months ( The expression level decreased at the time of PTB_12). In addition, each of the CD53 gene and MAFB gene has a higher level of gene expression in patients with tuberculosis (Pulmonary TB, PTB) than in patients with latent infection (Latent TB, LTB) who are infected with M. tuberculosis but have not developed. It was. FIG. 5 shows the results for the CD53 gene, and FIG. 6 shows the results for the MAFB gene. In each figure, A shows the expression level at the time of healthy subjects (Control), patients (before treatment start, PTB_00), 2 months after treatment (PTB_02) and 12 months (PTB_12), and B shows healthy subjects (Control). ), Expression level in tubercle bacillus-infected unaffected persons (latent infection) (LTB) and (tuberculosis-onset patient) (PTB). In this analysis, the genetic lineage of Mycobacterium tuberculosis has not been taken into account, but when combined with the fact that there is a risk of developing Mycobacterium tuberculosis genetic lineage in nearby SNPs, it is It may be a useful marker for predicting the onset.

  According to the method of the present invention, in a subject infected with M. tuberculosis, the risk of developing M. tuberculosis can be determined for each genetic strain of M. tuberculosis, and used for diagnosis of the possibility of developing M. tuberculosis. Can do.

Claims (10)

  In the subject, the base of the single nucleotide polymorphism site of the subject genome associated with the onset of tuberculosis is identified, and the M. tuberculosis genetic strain that is latently infected with the subject is typed, and M. tuberculosis genetic strain specific In particular, a method for determining the risk of developing tuberculosis due to a latently infected tuberculosis bacterium in a subject.   The method according to claim 1, wherein the M. tuberculosis genetic line to be typed is selected from the group consisting of Beijing strain, non-Beijing strain, EAI strain and non-EAI strain. When the subject is infected with Mycobacterium tuberculosis, the base of at least one single nucleotide polymorphism site of (b1) to (b14) below is identified, and the subject is infected with Mycobacterium tuberculosis. Is a non-Beijing strain, the base of at least one single nucleotide polymorphism site of the following (nb1) to (nb12) is identified, and when the tubercle bacillus in which the subject is infected is an EAI strain, When the base of at least one single nucleotide polymorphism site of the following (e1) to (e8) is identified and the tuberculosis bacterium to which the subject is infected is a non-EAI strain, the following (ne1) to (ne5 3) identifying the base of at least one single nucleotide polymorphic site of
(b1) rs9348878
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 1, which is G or A;
(b2) rs2070600
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 2, which is A or G;
(b3) rs401864
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 3, which is C or T;
(b4) rs673119
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 4 is C or T;
(b5) rs1321267
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 5, which is C or A;
(b6) rs2076625
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 6, G or T;
(b7) rs7142055
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 7, which is T or C;
(b8) rs1157619
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 8, which is T or C;
(b9) rs4924568
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 9, which is A or G;
(b10) rs1899820
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 10, which is A or C;
(b11) rs2695163
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 11, which is G or A;
(b12) rs1197772
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 12, which is G or A;
(b13) rs1081022
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 13, which is T or G;
(b14) rs1648835
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 14, which is T or G;
(nb1) rs12144738
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 15, C or T;
(nb2) rs1494320
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 16 and C or T;
(nb3) rs1712674
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 17 and G or T;
(nb4) rs1418425
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 18, which is T or C;
(nb5) rs4688637
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 19, C or A;
(nb6) rs12374531
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 20, G or A;
(nb7) rs11784415
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 21, which is C or A;
(nb8) rs2182093
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 22, which is T or C;
(nb9) rs10798
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 23, which is A or G;
(nb10) rs4267316
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 24, which is C or T;
(nb11) rs6071980
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 25, which is C or T;
(nb12) rs743057
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 26, which is A or G;
(e1) rs1178938
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 27, which is C or A;
(e2) rs800065
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 28, which is C or T;
(e3) rs1372667
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 29, which is G or T;
(e4) rs13174549
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 30, which is T or C;
(e5) rs7087410
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 31, which is C or T;
(e6) rs10898382
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 32, which is A or C;
(e7) rs957129
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 33, which is A or C;
(e8) rs1658693
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 34, which is C or T;
(ne1) rs1820920
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 35, which is C or T;
(ne2) rs11737270
A polymorphism in the 26th base of the base sequence represented by SEQ ID NO: 36, which is G or A;
(ne3) rs10832678
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 37, which is G or A;
(ne4) rs10507084
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 38, which is T or C; or
(ne5) rs1440548
A polymorphism at the 26th base of the base sequence represented by SEQ ID NO: 39, which is C or T. (1) When the base of the 26th single nucleotide polymorphism site ((b1) rs9348878) of the base sequence shown in SEQ ID NO: 1 is G, tuberculosis is observed in younger age (under 45 years) than in the case of A Determined that the risk of developing is high,
(2) When the base of the 26th single nucleotide polymorphism site ((b2) rs2070600) of the base sequence shown in SEQ ID NO: 2 is A, tuberculosis is younger (under 45 years) than in the case of G Determined that the risk of developing is high,
(3) When the base of the 26th single nucleotide polymorphism site ((b3) rs401864) of the nucleotide sequence shown in SEQ ID NO: 3 is C, there is a higher risk of developing tuberculosis at any age than T And
(4) When the base of the 26th single nucleotide polymorphism site ((b4) rs673119) of the base sequence shown in SEQ ID NO: 4 is C, tuberculosis is observed in the elderly (45 years or older) compared to T. Determined that the risk of developing is high,
(5) When the base of the 26th single nucleotide polymorphism site ((b5) rs1321267) of the base sequence shown in SEQ ID NO: 5 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(6) When the base of the 26th single nucleotide polymorphism site ((b6) rs2076625) of the base sequence shown in SEQ ID NO: 6 is G, the risk of developing tuberculosis is lower than in any age compared to T And
(7) When the base of the 26th single nucleotide polymorphism site ((b7) rs7142055) of the nucleotide sequence shown in SEQ ID NO: 7 is T, tuberculosis is observed in younger age (under 45 years) than in C Determined that the risk of developing is high,
(8) When the base of the 26th single nucleotide polymorphism site ((b8) rs1157619) of the base sequence shown in SEQ ID NO: 8 is T, there is a higher risk of developing tuberculosis at any age than in C And
(9) When the base of the 26th single nucleotide polymorphism site ((b9) rs4924568) of the nucleotide sequence shown in SEQ ID NO: 9 is A, tuberculosis is observed in the elderly (45 years or older) compared to G. Determined that the risk of developing is high,
(10) When the base of the 26th single nucleotide polymorphism site ((b10) rs1899820) of the nucleotide sequence shown in SEQ ID NO: 10 is A, tuberculosis is observed in older age (45 years or older) than in C Determined that the risk of developing is high,
(11) When the base of the 26th single nucleotide polymorphism site ((b11) rs2695163) of the nucleotide sequence represented by SEQ ID NO: 11 is G, tuberculosis is observed in the elderly (45 years old or older) compared to A. Determined that the risk of developing is high,
(12) When the base of the 26th single nucleotide polymorphism site ((b12) rs1197772) of the nucleotide sequence shown in SEQ ID NO: 12 is G, tuberculosis is observed in older age (45 years or older) than in the case of A. Determined that the risk of developing is high,
(13) When the base of the 26th single nucleotide polymorphism site ((b13) rs1081022) of the nucleotide sequence shown in SEQ ID NO: 13 is T, tuberculosis is observed in the elderly (45 years or older) compared to G. Determined that the risk of developing is high,
(14) When the base of the 26th single nucleotide polymorphism site ((b14) rs1648835) of the nucleotide sequence shown in SEQ ID NO: 14 is T, tuberculosis is observed in older age (45 years or older) than in the case of G Determined that the risk of developing is high,
(15) When the base of the 26th single nucleotide polymorphism site ((nb1) rs12144738) of the base sequence shown in SEQ ID NO: 15 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(16) When the base of the 26th single nucleotide polymorphism site ((nb2) rs1494320) of the nucleotide sequence shown in SEQ ID NO: 16 is C, tuberculosis is observed in older age (45 years or older) compared to T Determined that the risk of developing is high,
(17) When the base of the 26th single nucleotide polymorphism site ((nb3) rs1712674) of the base sequence shown in SEQ ID NO: 17 is G, tuberculosis is observed in older age (45 years or older) compared to T Determined that the risk of developing is high,
(18) When the base of the 26th single nucleotide polymorphism site ((nb4) rs1418425) of the nucleotide sequence shown in SEQ ID NO: 18 is T, tuberculosis is observed in older age (45 years or older) compared to C Determined that the risk of developing is high,
(19) When the base of the 26th single nucleotide polymorphism site ((nb5) rs4688637) of the base sequence shown in SEQ ID NO: 19 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A Determined that the risk of developing is high,
(20) When the base of the 26th single nucleotide polymorphism site ((nb6) rs12374531) of the nucleotide sequence shown in SEQ ID NO: 20 is G, tuberculosis is observed in older age (45 years or older) than in the case of A Determined that the risk of developing is low,
(21) When the base of the 26th single nucleotide polymorphism site ((nb7) rs11784415) of the base sequence shown in SEQ ID NO: 21 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A Determined that the risk of developing is high,
(22) When the base of the 26th single nucleotide polymorphism site ((nb8) rs2182093) of the nucleotide sequence shown in SEQ ID NO: 22 is T, tuberculosis is observed in younger age (under 45 years) than in the case of C Determined that the risk of developing is high,
(23) When the base of the 26th single nucleotide polymorphic site ((nb9) rs10798) of the nucleotide sequence shown in SEQ ID NO: 23 is A, there is a higher risk of developing tuberculosis at any age than in G And
(24) When the base of the 26th single nucleotide polymorphic site ((nb10) rs4267316) of the base sequence shown in SEQ ID NO: 24 is C, there is a higher risk of developing tuberculosis at any age than T And
(25) When the base of the 26th single nucleotide polymorphism site ((nb11) rs6071980) of the nucleotide sequence shown in SEQ ID NO: 25 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(26) When the base of the 26th single nucleotide polymorphism site ((nb12) rs743057) of the base sequence shown in SEQ ID NO: 26 is A, the risk of developing tuberculosis is lower than that of G in any age And
(27) When the base of the 26th single nucleotide polymorphism site ((e1) rs1178938) of the nucleotide sequence shown in SEQ ID NO: 27 is C, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(28) When the base of the 26th single nucleotide polymorphism site ((e2) rs800065) of the base sequence represented by SEQ ID NO: 28 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(29) When the base of the 26th single nucleotide polymorphism site ((e3) rs1372667) of the nucleotide sequence shown in SEQ ID NO: 29 is G, tuberculosis is observed in younger (under 45 years) than in the case of T. Determined that the risk of developing is high,
(30) When the base of the 26th single nucleotide polymorphism site ((e4) rs13174549) of the base sequence shown in SEQ ID NO: 30 is T, the risk of developing tuberculosis is lower than in C at all ages And
(31) When the base of the 26th single nucleotide polymorphism site ((e5) rs7087410) of the base sequence shown in SEQ ID NO: 31 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(32) When the base of the 26th single nucleotide polymorphism site ((e6) rs10898382) of the nucleotide sequence shown in SEQ ID NO: 32 is A, tuberculosis is observed in the elderly (45 years or older) compared to C Determined that the risk of developing is high,
(33) When the base of the 26th single nucleotide polymorphic site ((e7) rs951729) of the nucleotide sequence shown in SEQ ID NO: 33 is A, tuberculosis is observed in the elderly (45 years or older) compared to C Determined that the risk of developing is high,
(34) When the base of the 26th single nucleotide polymorphism site ((e8) rs1658693) of the base sequence shown in SEQ ID NO: 34 is C, tuberculosis is observed in the elderly (45 years old or older) compared to T. Determined that the risk of developing is low,
(35) When the base of the 26th single nucleotide polymorphism site ((ne1) rs1820920) of the base sequence shown in SEQ ID NO: 35 is C, tuberculosis is observed in younger age (under 45 years) than in the case of T. Determined that the risk of developing is high,
(36) When the base of the 26th single nucleotide polymorphism site ((ne2) rs11737270) of the nucleotide sequence shown in SEQ ID NO: 36 is G, tuberculosis is observed in younger age (under 45 years) than in the case of A. Determined that the risk of developing is high,
(37) When the base of the 26th single nucleotide polymorphism site ((ne3) rs10832678) of the nucleotide sequence shown in SEQ ID NO: 37 is G, tuberculosis is observed in the elderly (45 years old or older) compared to A. Determined that the risk of developing is high,
(38) When the base of the 26th single nucleotide polymorphism site ((ne4) rs10507084) of the nucleotide sequence shown in SEQ ID NO: 38 is T, tuberculosis is observed in the elderly (45 years old or older) compared to C. Determined that the risk of developing is low,
(39) When the base of the 26th single nucleotide polymorphism site ((ne5) rs1440548) of the nucleotide sequence shown in SEQ ID NO: 39 is C, there is a higher risk of developing tuberculosis at any age than T To determine,
The method of claim 3. A primer for determining the risk of developing tuberculosis in a tuberculosis-infected subject,
Primers for determining the risk of developing tuberculosis in any of the following (p1) to (p14) Beijing strain-infected subjects, and any of the following (p15) to (p26) non-Beijing strain-infected subjects A primer for determining the risk of developing tuberculosis in the following, a primer for determining the risk of developing tuberculosis in the EAI strain-infected subject of any of the following (p27) to (p34), or the following (p35) Primers for determining the risk of developing tuberculosis in a non-EAI strain-infected subject of any of (p39):
(p1) a primer that can amplify a region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1;
(p2) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 2 (the base of the polymorphic site of rs2070600);
(p3) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs401864) in the base sequence of SEQ ID NO: 3;
(p4) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 4 (the base of the polymorphic site of rs673119);
(p5) a primer that can amplify a region containing the 26th base (base of rs1321267 polymorphic site) in the base sequence of SEQ ID NO: 5;
(p6) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 6 (the base of the polymorphic site of rs2076625);
(p7) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 7 (the base of the polymorphic site of rs7142055);
(p8) a primer capable of amplifying a region containing the 26th base (base of rs1157619 polymorphic site) in the base sequence of SEQ ID NO: 8;
(p9) a primer capable of amplifying a region containing the 26th base (base of rs4924568 polymorphic site) in the base sequence of SEQ ID NO: 9;
(p10) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 10 (the base of the polymorphic site of rs1899820);
(p11) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 11 (the base of the polymorphic site of rs2695163);
(p12) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs1197772) in the base sequence of SEQ ID NO: 12;
(p13) a primer capable of amplifying a region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13;
(p14) a primer capable of amplifying a region containing the 26th base (base of rs1648835 polymorphic site) in the base sequence of SEQ ID NO: 14;
(p15) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 15 (the base of the polymorphic site of rs12144738);
(p16) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 16 (the base of the polymorphic site of rs1494320);
(p17) Primer capable of amplifying a region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17
(p18) a primer capable of amplifying a region containing the 26th base (base of rs1418425 polymorphic site) in the base sequence of SEQ ID NO: 18;
(p19) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 19 (the base of the polymorphic site of rs4688637);
(p20) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 20 (the base of the polymorphic site of rs12374531);
(p21) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 21 (the base of the polymorphic site of rs11784415);
(p22) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs2182093) in the base sequence of SEQ ID NO: 22;
(p23) a primer capable of amplifying a region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23;
(p24) a primer capable of amplifying a region containing the 26th base (base of rs4267316 polymorphic site) in the base sequence of SEQ ID NO: 24;
(p25) a primer that can amplify a region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25;
(p26) a primer capable of amplifying a region containing the 26th base (base of rs743057 polymorphic site) in the base sequence of SEQ ID NO: 26;
(p27) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 27 (the base of the polymorphic site of rs1178938);
(p28) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 28 (the base of the polymorphic site of rs800065);
(p29) a primer capable of amplifying a region containing the 26th base (base of rs1372667 polymorphic site) in the base sequence of SEQ ID NO: 29;
(p30) a primer that can amplify a region containing the 26th base (base of rs13174549 polymorphic site) in the base sequence of SEQ ID NO: 30;
(p31) a primer capable of amplifying a region containing the 26th base (base of rs7087410 polymorphic site) in the base sequence of SEQ ID NO: 31;
(p32) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 32 (the base of the polymorphic site of rs10898382);
(p33) a primer capable of amplifying a region containing the 26th base (base of rs951729 polymorphic site) in the base sequence of SEQ ID NO: 33;
(p34) a primer capable of amplifying a region containing the 26th base (base of rs1658693 polymorphic site) in the base sequence of SEQ ID NO: 34;
(p35) a primer that can amplify a region containing the 26th base in the base sequence of SEQ ID NO: 35 (the base of the polymorphic site of rs1820920);
(p36) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 36 (the base of the polymorphic site of rs11737270);
(p37) a primer capable of amplifying a region containing the 26th base in the base sequence of SEQ ID NO: 37 (the base of the polymorphic site of rs10832678);
(p38) a primer capable of amplifying a region containing the 26th base (the base of the polymorphic site of rs10507084) in the base sequence of SEQ ID NO: 38; or
(p39) A primer capable of amplifying a region containing the 26th base (base of rs1440548 polymorphic site) in the base sequence of SEQ ID NO: 39. A probe for determining the risk of developing tuberculosis in a tuberculosis-infected subject,
Probes for determining the risk of developing tuberculosis in any of the following (q1) to (q14) Beijing strain-infected subjects, and any of the following (q15) to (q26) non-Beijing strain-infected subjects A probe for determining the risk of developing tuberculosis in the following, a probe for determining the risk of developing tuberculosis in an EAI strain-infected subject of any of the following (q27) to (q34), or the following (q35) A probe for determining the risk of developing tuberculosis in a non-EAI strain-infected subject of any of-(q39):
(q1) a probe capable of hybridizing to a region containing the 26th base (base of rs9348878 polymorphic site) in the base sequence of SEQ ID NO: 1;
(q2) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs2070600) in the base sequence of SEQ ID NO: 2;
(q3) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs401864) in the base sequence of SEQ ID NO: 3;
(q4) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs673119) in the base sequence of SEQ ID NO: 4;
(q5) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs1321267) in the base sequence of SEQ ID NO: 5;
(q6) a probe capable of hybridizing to a region containing the 26th base (base of rs2076625 polymorphic site) in the base sequence of SEQ ID NO: 6;
(q7) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs7142055) in the base sequence of SEQ ID NO: 7;
(q8) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs1157619) in the base sequence of SEQ ID NO: 8;
(q9) a probe capable of hybridizing to a region containing the 26th base (base of rs4924568 polymorphic site) in the base sequence of SEQ ID NO: 9;
(q10) a probe capable of hybridizing to a region containing the 26th base (base of rs1899820 polymorphic site) in the base sequence of SEQ ID NO: 10;
(q11) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs2695163) in the base sequence of SEQ ID NO: 11;
(q12) a probe capable of hybridizing to a region containing the 26th base (base of rs1197772 polymorphic site) in the base sequence of SEQ ID NO: 12;
(q13) a probe capable of hybridizing to a region containing the 26th base (base of rs1081022 polymorphic site) in the base sequence of SEQ ID NO: 13;
(q14) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs1648835) in the base sequence of SEQ ID NO: 14;
(q15) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs12144738) in the base sequence of SEQ ID NO: 15;
(q16) a probe capable of hybridizing to a region containing the 26th base (base of rs1494320 polymorphic site) in the base sequence of SEQ ID NO: 16;
(q17) a probe capable of hybridizing to a region containing the 26th base (base of rs1712674 polymorphic site) in the base sequence of SEQ ID NO: 17;
(q18) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs1418425) in the base sequence of SEQ ID NO: 18;
(q19) a probe capable of hybridizing to a region containing the 26th base (base of rs4688637 polymorphic site) in the base sequence of SEQ ID NO: 19;
(q20) a probe capable of hybridizing to a region containing the 26th base (base of rs12374531 polymorphic site) in the base sequence of SEQ ID NO: 20;
(q21) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 21 (the base of the polymorphic site of rs11784415);
(q22) a probe capable of hybridizing to a region containing the 26th base (base of rs2182093 polymorphic site) in the base sequence of SEQ ID NO: 22;
(q23) a probe capable of hybridizing to a region containing the 26th base (base of rs10798 polymorphic site) in the base sequence of SEQ ID NO: 23;
(q24) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs4267316) in the base sequence of SEQ ID NO: 24;
(q25) a probe capable of hybridizing to a region containing the 26th base (base of rs6071980 polymorphic site) in the base sequence of SEQ ID NO: 25;
(q26) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 26 (the base of the polymorphic site of rs743057);
(q27) a probe capable of hybridizing to a region containing the 26th base (base of rs1178938 polymorphic site) in the base sequence of SEQ ID NO: 27;
(q28) a probe capable of hybridizing to a region containing the 26th base (base of rs800065 polymorphic site) in the base sequence of SEQ ID NO: 28;
(q29) a probe capable of hybridizing to a region containing the 26th base (base of rs1372667 polymorphic site) in the base sequence of SEQ ID NO: 29;
(q30) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 30 (the base of the polymorphic site of rs13174549);
(q31) a probe capable of hybridizing to a region containing the 26th base (base of rs7087410 polymorphic site) in the base sequence of SEQ ID NO: 31;
(q32) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 32 (the base of the polymorphic site of rs10898382);
(q33) a probe capable of hybridizing to a region containing the 26th base (base of rs951729 polymorphic site) in the base sequence of SEQ ID NO: 33;
(q34) a probe capable of hybridizing to a region containing the 26th base (base of the polymorphic site of rs1658693) in the base sequence of SEQ ID NO: 34;
(q35) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs1820920) in the base sequence of SEQ ID NO: 35;
(q36) a probe capable of hybridizing to a region containing the 26th base (base of polymorphic site of rs11737270) in the base sequence of SEQ ID NO: 36;
(q37) a probe capable of hybridizing to a region containing the 26th base in the base sequence of SEQ ID NO: 37 (the base of the polymorphic site of rs10832678);
(q38) a probe capable of hybridizing to a region containing the 26th base (the base of the polymorphic site of rs10507084) in the base sequence of SEQ ID NO: 38; or
(q39) A probe capable of hybridizing to a region containing the 26th base (base of rs1440548 polymorphic site) in the base sequence of SEQ ID NO: 39.   A kit for determining a risk of developing tuberculosis, comprising the primer according to claim 5 or the probe according to claim 6.   In a subject, measure the expression level of a gene located in the vicinity of a single nucleotide polymorphic site in the subject's genome that is associated with the onset of tuberculosis, and type the M. tuberculosis genetic line that is latently infected in the subject And determining the risk of developing tuberculosis by tuberculosis bacteria that are latently infected in the subject.   This gene is located near the single nucleotide polymorphism ((nb2) rs1494320) at the 26th base of the nucleotide sequence shown in SEQ ID NO: 16 when the subject is a non-Beijing Mycobacterium tuberculosis strain. The method according to claim 8, wherein the expression of the CD53 gene is measured, and when the expression of the gene is increased, it is determined that the risk of developing tuberculosis is high.   This gene is located near the single nucleotide polymorphism ((nb11) rs6071980) at the 26th base of the nucleotide sequence shown in SEQ ID NO: 25 when the subject is infected with a non-Beijing strain. The method according to claim 8, wherein the expression of the MAFB gene is measured, and when the expression of the gene is increased, it is determined that the risk of developing tuberculosis is high.

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