CN1790021A - Screening of precancerous, carcinoma in situ, and carcinomatous lesions using circulating Ibovirus DNA - Google Patents
Screening of precancerous, carcinoma in situ, and carcinomatous lesions using circulating Ibovirus DNA Download PDFInfo
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技术领域technical field
本发明涉及以下发现:可在患者血液的不含细胞的液体中发现伊波(Epstein-barr)病毒(EBV),且当发现该病毒时,该患者可能已患有前癌、原位癌或其它任意形式的、不限于与伊波病毒相关的癌症。本发明依据的理论是,我们发现血浆中存在阳性EBV DNA的正常个体和癌症患者的循环CD25+CD4+调节T(Treg)淋巴细胞上升。我们还发现在某些与伊波病毒关系未知的癌症中,其患者的血清或血浆中的循环EBV DNA的滴定度呈阳性。将上述观测结果结合得出的发现证明EBV再活化可导致对细胞毒T细胞的抑制,进而导致癌症免疫监视的丧失。本发明提出一种新的通用的筛查方法,其使用血清或血浆中的循环EBV DNA对前癌、原位癌和癌病灶进行筛查。The present invention relates to the discovery that Epstein-barr virus (EBV) can be found in the cell-free fluid of a patient's blood, and when the virus is found, the patient may already have precancer, carcinoma in situ, or other Any form of, but not limited to, Ebovirus-associated cancer. The present invention is based on the theory that we found that circulating CD25+CD4+regulatory T (T reg ) lymphocytes were elevated in normal individuals and cancer patients with positive EBV DNA in their plasma. We also found positive titers of circulating EBV DNA in the serum or plasma of patients with certain cancers of unknown relationship to Ibovirus. Combining the above observations, the findings demonstrate that EBV reactivation can lead to suppression of cytotoxic T cells, leading to a loss of cancer immune surveillance. The present invention proposes a new universal screening method, which uses circulating EBV DNA in serum or plasma to screen precancer, carcinoma in situ and cancer lesions.
技术背景technical background
公知地,多种肿瘤的癌细胞都可释放出肿瘤衍生(tumor-derived)DNA(Anker et al.,Cancer Metastasis Rev.18:65-73(1999))。其例子包括由胰腺癌产生的致癌基因突变(Anker et al.,Gastroenterology.112:4-1120(1997)),由肺癌产生的微卫星改变(Chen etal.,Cancer Res.59:3(1999))和由肝癌产生的渐成(epigenetic)变化(Wong et al.,Cancer Res.59:3(1999)).此外,在许多公知与病毒感染有关的癌症中,可在循环中发现病毒DNA。例子包括由鼻咽癌(Mutirangura et al.,Clin Cancer Res.4:665-9(1998));Lo et al.,Cancer Res.59:1188-91(1999))和某些淋巴瘤(Lei et al.,Br JHaematol.111:239-46(2000);Gallagher et al.,Int J Cancer.84:442-8(1999);Drouet et al.,J Med Virol.57:383-9(1999))产生的伊波病毒(EBV)DNA和由头部和颈部癌症产生的人体乳头癌病毒DNA(Capone et al.,ClinCancer Res.6:4171-5(2000))。Cancer cells of various tumors are known to release tumor-derived DNA (Anker et al., Cancer Metastasis Rev. 18:65-73 (1999)). Examples include oncogene mutations arising from pancreatic cancer (Anker et al., Gastroenterology. 112:4-1120 (1997)), microsatellite alterations arising from lung cancer (Chen et al., Cancer Res. 59:3 (1999) ) and epigenetic changes produced by liver cancer (Wong et al., Cancer Res. 59:3 (1999)). In addition, in many cancers known to be associated with viral infection, viral DNA can be found in circulation. Examples include nasopharyngeal carcinoma (Mutirangura et al., Clin Cancer Res. 4:665-9 (1998)); Lo et al., Cancer Res. 59:1188-91 (1999)) and certain lymphomas (Lei et al., Br JHaematol.111:239-46(2000); Gallagher et al., Int J Cancer.84:442-8(1999); Drouet et al., J Med Virol.57:383-9(1999 )) and human papillary carcinoma virus DNA from head and neck cancers (Capone et al., Clin Cancer Res. 6:4171-5 (2000)).
目前,研究者非常关注癌症患者血浆和血清中肿瘤衍生DNA的存在(Chen,X.Q.et al.,Nat.Med.,2:1033-1035(1996);Nawroz,H.et al.,Nat.Med.,2:1035-1037(1996))。在与病毒相关的癌症中,其患者血浆和血清中检测到无细胞的肿瘤相关病毒DNA(Mutirangura,A.et al.,Cancer Res.,4:665-669(1998);Lo,Y.M.D.et al.,Clin.Cancer Res.59:1188-1191(1999);Capone,R.B.Clin.Cancer Res.,6:4171-4175(2000))。一种重要的与多种类型的恶性肿瘤相关的病毒是EBV(Cohen,J.I.N.Engl.J.Med.,343:481-492(2000))。EBV是能够感染大多数人群的人体疱疹病毒。EBV通常是通过唾液传播的,并且在B淋巴细胞中形成潜伏感染,该感染可伴随宿主终生。基于这种原因,在鼻咽癌(NPC)(Mutirangura,A.et al.,Cancer Res.,4:665-669(1998);Lo,Y.M.D.et al.,Clin.Cancer Res.,59:1188-1191(1999))患者和某些恶性淋巴肿瘤(Lei,K.I.et al.,Br.J.Haematol.,111:239-246(2000);Drouet,E.et al.,J.Med.Virol.,57:383-389(1999);Gallagher,A.et al.,Int.J.Cancer,84:442-228(1999))患者的血浆和血清中已经检测到循环EBV DNA。Currently, investigators are very concerned about the presence of tumor-derived DNA in the plasma and serum of cancer patients (Chen, X.Q. et al., Nat. Med., 2: 1033-1035 (1996); Nawroz, H. et al., Nat. Med ., 2:1035-1037 (1996)). In virus-associated cancers, cell-free tumor-associated viral DNA has been detected in the plasma and serum of patients (Mutirangura, A. et al., Cancer Res., 4:665-669 (1998); Lo, Y.M.D. et al ., Clin. Cancer Res. 59: 1188-1191 (1999); Capone, R.B. Clin. Cancer Res., 6: 4171-4175 (2000)). An important virus associated with various types of malignancies is EBV (Cohen, J.I.N. Engl. J. Med., 343:481-492 (2000)). EBV is a human herpes virus that infects most people. EBV is usually transmitted through saliva and forms a latent infection in B lymphocytes that can accompany the host for life. For this reason, in nasopharyngeal carcinoma (NPC) (Mutirangura, A. et al., Cancer Res., 4: 665-669 (1998); Lo, Y.M.D. et al., Clin. Cancer Res., 59: 1188 -1191(1999)) patients and certain malignant lymphoid tumors (Lei, K.I.et al., Br.J.Haematol., 111:239-246(2000); Drouet, E.et al., J.Med.Virol , 57: 383-389 (1999); Gallagher, A. et al., Int. J. Cancer, 84: 442-228 (1999)) circulating EBV DNA has been detected in the plasma and serum of patients.
还有报道称部分胃癌也与EBV的感染有关(Shibata,D.et al.,Am.J.Pathol.,140:769-774(1992))。在香港,有大约10%的胃癌病例发现与EBV感染有关(Yuen,S.T.et al.,Am.J.Surg.Pathol.,18:1158-1163(1994))。It has also been reported that some gastric cancers are also related to EBV infection (Shibata, D. et al., Am. J. Pathol., 140:769-774 (1992)). In Hong Kong, about 10% of gastric cancer cases were found to be associated with EBV infection (Yuen, S.T. et al., Am. J. Surg. Pathol., 18: 1158-1163 (1994)).
目前,已发现具有CD3+CD4+CD25+表型的抑制T细胞在癌症的发展中起作用。虽然,最初发现这些T细胞可保护宿主对抗自体免疫的发生,但它们也可同时防碍对宿主进行有效的肿瘤抗原的免疫监视。因此,具有这种表型的细胞上升可导致癌症的形成及从前癌、原位癌发展成发育成熟的癌症。Currently, suppressor T cells with a CD3+CD4+CD25+ phenotype have been found to play a role in the development of cancer. Although these T cells were originally found to protect the host against the occurrence of autoimmunity, they also simultaneously prevent effective immune surveillance of the host against tumor antigens. Thus, the rise of cells with this phenotype can lead to cancer formation and progression from precancerous, carcinoma in situ to full-fledged cancer.
此外,我们也能发现某些与EBV无关的癌症的患者其血浆中也含有EBV DNA,这进一步证明EBV确实在癌症(除了由不同病原体引起的鼻咽癌、胃癌和淋巴瘤之外)中起作用。In addition, we can also find EBV DNA in the plasma of patients with some cancers not related to EBV, which further proves that EBV does play a role in cancer (except nasopharyngeal carcinoma, gastric cancer and lymphoma caused by different pathogens). effect.
发明内容Contents of the invention
本发明的第一方面提供了通过测定患者血清或血浆中存在的伊波病毒DNA(EBV DNA)的含量来对癌症进行常规筛查的方法。因此,本发明在临床医学中,尤其在潜伏EBV感染(某些人群中超过90%的人都存在)中具有广泛的应用。A first aspect of the present invention provides a method for routine screening for cancer by determining the amount of Ebovirus DNA (EBV DNA) present in a patient's serum or plasma. Therefore, the present invention has wide applications in clinical medicine, especially in latent EBV infection (existing in more than 90% of certain populations).
本发明的方法通常包括如下步骤:Method of the present invention generally comprises the steps:
从患者获取血液样本;obtaining a blood sample from a patient;
从该血液样本中提取DNA;Extract DNA from the blood sample;
分析提取的DNA中存在的循环EBV DNA的含量;analyzing the amount of circulating EBV DNA present in the extracted DNA;
重复上述步骤;以及Repeat the above steps; and
将所述血液样本中存在的循环EBV DNA的含量与对照进行对比,comparing the amount of circulating EBV DNA present in said blood sample with a control,
其中所述EBV DNA的含量恒定或上升的趋势表明所述患者患有癌症或前癌。Wherein the constant or rising trend of the content of the EBV DNA indicates that the patient suffers from cancer or precancer.
本发明所述的癌症优选选自鼻咽癌、胃癌和淋巴瘤;或者选自肺癌、结肠癌、腮腺癌、乳腺癌和肝癌。除上述癌症以外的其它癌症亦可用于本发明。The cancer described in the present invention is preferably selected from nasopharyngeal cancer, gastric cancer and lymphoma; or from lung cancer, colon cancer, parotid gland cancer, breast cancer and liver cancer. Cancers other than those described above may also be used in the present invention.
优选地,本发明血液样本是非细胞液体样本。所述非细胞液体部分指该样本是提取细胞后的血清或血浆,其中血清的提取是通过凝聚并将细胞与剩余液体分离而获得的,或者通过抑制凝聚并进行离心来实现液体部分(血浆)的提取。在该液体部分中分析EBV DNA。Preferably, the blood sample of the present invention is an acellular fluid sample. The cell-free liquid fraction means that the sample is serum or plasma after extraction of cells, wherein the extraction of serum is obtained by coagulation and separation of cells from the remaining liquid, or the liquid fraction (plasma) is achieved by inhibiting coagulation and centrifuging extraction. EBV DNA was analyzed in this liquid fraction.
优选地,本发明方法中的重复步骤在第一次测定后的4-12周内进行。也可在4-12周以外的时间进行。Preferably, repeated steps in the methods of the invention are performed within 4-12 weeks of the first assay. It can also be done at a time other than 4-12 weeks.
在本发明的某实施方案中,分析EBV DNA的含量的方法是通过杂交、扩增、定量的方法进行,并选择EBV基因组的任意序列或序列片段作为任意引物和探针或其组合的结合位点。In a certain embodiment of the present invention, the method for analyzing the content of EBV DNA is carried out by hybridization, amplification, and quantitative methods, and any sequence or sequence fragment of the EBV genome is selected as the binding site of any primer and probe or a combination thereof point.
本发明的第二方面提供了包含适当的检测患者血清或血浆中EBVDNA的试剂的诊断试剂盒。本发明的试剂盒还可包含一种或多种从患者获取血液样本的装置、从该血液样本中分离EBV DNA的装置以及定量该血液样本中存在的EBV DNA的含量的装置。该试剂盒可用于癌症的常规筛查,所述筛查是通过测定患者血清或血液中存在的伊波病毒DNA(EBVDNA)的含量来实现的。A second aspect of the present invention provides a diagnostic kit comprising suitable reagents for detecting EBV DNA in a patient's serum or plasma. Kits of the invention may also comprise one or more devices for obtaining a blood sample from a patient, for isolating EBV DNA from the blood sample, and for quantifying the amount of EBV DNA present in the blood sample. The kit can be used for routine screening of cancer, and the screening is realized by measuring the content of Epstein-Barr virus DNA (EBV DNA) existing in serum or blood of patients.
附图的简要说明Brief description of the drawings
图1显示了以下结果:对一组血浆EBV DNA滴定度呈阳性的癌症患者,对其滴定度进行的一系列分析的结果显示所有未接受治疗的患者在第二次及后续的分析中表现出水平升高。Figure 1 shows the results of a series of analyzes of titers in a cohort of cancer patients with positive plasma EBV DNA titers, all untreated patients exhibiting level up.
图2显示了以下结果:对一组血浆EBV DNA滴定度呈阳性的正常个体,分别在第一次和第二次测定之后间隔4-12周进行一系列的第二次或第三次分析,结果显示除一例个体外所有个体的EBV DNA滴定度读数都为零。Figure 2 shows the results of a series of second or third analyzes performed at intervals of 4-12 weeks after the first and second determinations, respectively, of a group of normal individuals with positive plasma EBV DNA titers, Results showed zero EBV DNA titer readings for all but one individual.
图3显示了以下结果:在一批怀疑患有不同类型癌症的不同患者中,与EBV非直接相关的癌症患者的EBV DNA滴定度也呈阳性。对一例有完全反应的结肠癌患者的治疗也同时伴随着其EBV DNA滴定度的消失。Figure 3 shows the results of EBV DNA titers also positive in patients with cancers not directly related to EBV in a cohort of different patients suspected of having different types of cancer. Treatment of a patient with colon cancer who had a complete response was also accompanied by disappearance of her EBV DNA titer.
发明的详细描述Detailed description of the invention
本发明涉及通过测定患者血清或血浆中存在的伊波病毒DNA(EBVDNA)的含量来对癌症进行常规筛查的方法。该方法涉及检测和测定这些患者血浆液中存在的EBV DNA的含量。本发明的方法在临床医学中有广泛的应用。The present invention relates to a method for routine screening for cancer by determining the amount of Ebovirus DNA (EBV DNA) present in a patient's serum or plasma. The method involves detecting and measuring the amount of EBV DNA present in the plasma fluid of these patients. The method of the present invention has wide application in clinical medicine.
临床上,循环EBV DNA早已应用在诊断和控制鼻咽癌上(Lo,Y.M.D.et al.,Cancer Res.,60:6878-6881)。Clinically, circulating EBV DNA has long been used in the diagnosis and control of nasopharyngeal carcinoma (Lo, Y.M.D. et al., Cancer Res., 60:6878-6881).
类似地,循环EBV DNA也可应用在一部分有资料支持的且已确定与伊波病毒有关的胃癌和淋巴瘤的诊断中。然而,上述检测还从未应用于在普通人群中筛查与EBV相关的癌症。Similarly, circulating EBV DNA can also be used in the diagnosis of some documented gastric cancers and lymphomas that have been associated with Ibovirus. However, these assays have never been applied to screen for EBV-associated cancers in the general population.
任何常规的DNA扩增或信号放大方法都可应用于检测EBV DNA。在大多数情况下,需要使用任意本领域公知的核酸扩增步骤使目标序列扩增。特别地,核酸扩增是指核酸扩增子(拷贝)的酶合成,其中该核酸扩增子包含被扩增的核酸序列的互补序列。本领域采用的核酸扩增步骤的例子包括聚合酶链反应(PCR)、链替代扩增(SDA)、连接酶链反应(LCR)和转录相关扩增(TAA)。当样本中存在的目标序列的含量非常少时,核酸扩增的效果尤其显著。为了更好地检测样本中目标生物体或病毒的核酸,在分析开始时需要的目标序列较少,因此通过将目标序列扩增并检测合成的扩增子,可大幅度提高分析的灵敏度。Any conventional DNA amplification or signal amplification method can be applied to detect EBV DNA. In most cases, the target sequence will need to be amplified using any of the nucleic acid amplification procedures known in the art. In particular, nucleic acid amplification refers to the enzymatic synthesis of nucleic acid amplicons (copies) comprising the complement of the nucleic acid sequence being amplified. Examples of nucleic acid amplification procedures employed in the art include polymerase chain reaction (PCR), strand displacement amplification (SDA), ligase chain reaction (LCR) and transcription associated amplification (TAA). Nucleic acid amplification is especially effective when the target sequence is present in very small amounts in the sample. In order to better detect the nucleic acid of the target organism or virus in the sample, fewer target sequences are required at the beginning of the analysis, so by amplifying the target sequence and detecting the synthesized amplicon, the sensitivity of the analysis can be greatly improved.
在文献中对核酸扩增的方法进行了详尽的描述。例如,Mullis等人在美国专利第4,683,195、4,683,202和4,800,159号中,以及在Methods inEnzymology,155:335-350(1987)中描述了PCR扩增方法。SDA的例子可以在Walker的PCR Methods and Applications,3:25-30(1993)、Walker等人的Nucleic Acids Res.,20:1691-1996(1992)和Proc.Natl.Acad.Sci.,89:392-396(1991)中找到。在美国专利第5,427,930和5,686,272中描述了LCR方法。而且,在各种出版物中提供了TAA的不同形式,如Burg等人在美国专利第5,437,990号;Kacian等人在美国专利第5,339,491和5,554,516号中;以及Gingeras等人在公开号为WO 88/01302、国际申请号为PCT/US87/01966和公开号为WO88/01315、国际申请号为PCT/US88/02108的国际申请。Methods of nucleic acid amplification are well described in the literature. For example, Mullis et al. describe PCR amplification methods in US Pat. Examples of SDA can be found in Walker, PCR Methods and Applications, 3: 25-30 (1993), Walker et al., Nucleic Acids Res., 20: 1691-1996 (1992) and Proc. Natl. Acad. Sci., 89: 392-396 (1991). The LCR method is described in US Patent Nos. 5,427,930 and 5,686,272. Moreover, different forms of TAA are provided in various publications, such as Burg et al. in U.S. Patent No. 5,437,990; Kacian et al. in U.S. Patent Nos. 5,339,491 and 5,554,516; 01302, international application number PCT/US87/01966 and publication number WO88/01315, international application number PCT/US88/02108.
实时定量PCR是监测EBV DNA的优选方式,其基于对荧光PCR反应进程的连续光监测(Heide et al.Genome Res.6:986-694,1996 and Lo etal.Am J.Hum.Genet.62:768-775,1998)。在该体系中,除了常规PCR中使用的两种扩增引物外,还包括双标记的荧光杂交探针(Livak,et al.PCRMethods Appl.,4357-362,1995)。一种荧光染料被用作报告分子(FAM),且其发射光谱被第二荧光染料(TAMRA)抑制。在PCR的扩展阶段,Taq DNA聚合酶(9)的5’到3’核酸外切酶活性将报告分子从探针上剥离,从而将其从抑制物中释放出来,进而导致518nm处的荧光放射增强。Real-time quantitative PCR is the preferred way to monitor EBV DNA, which is based on continuous light monitoring of the progress of the fluorescent PCR reaction (Heide et al. Genome Res. 6: 986-694, 1996 and Lo et al. Am J. Hum. Genet. 62: 768-775, 1998). In this system, in addition to the two amplification primers used in conventional PCR, a double-labeled fluorescent hybridization probe (Livak, et al. PCRMethods Appl., 4357-362, 1995) is also included. One fluorochrome is used as a reporter molecule (FAM) and its emission spectrum is suppressed by a second fluorochrome (TAMRA). During the extension phase of PCR, the 5' to 3' exonuclease activity of Taq DNA polymerase (9) strips the reporter molecule from the probe, thereby releasing it from the inhibitor, resulting in fluorescent emission at 518nm enhanced.
本发明的方法通常包含如下步骤:Method of the present invention generally comprises the steps:
从患者获取血液样本;obtaining a blood sample from a patient;
从所述血液样本中提取DNA;extracting DNA from said blood sample;
分析提取的DNA中存在的循环EBV DNA的含量;analyzing the amount of circulating EBV DNA present in the extracted DNA;
重复上述步骤;以及Repeat the above steps; and
将所述血液样本中存在的循环EBV DNA的含量与对照进行对比,其中所述EBV DNA的含量恒定或上升的趋势表明所述患者患有癌症或前癌。The amount of circulating EBV DNA present in the blood sample is compared to a control, wherein a constant or increasing trend in the amount of EBV DNA indicates that the patient has cancer or precancer.
通常,本发明中可经过将血液样本离心而获得液体部分,且EBVDNA是在该液体部分中分析的。Generally, in the present invention, the liquid fraction can be obtained by centrifuging the blood sample, and EBV DNA is analyzed in the liquid fraction.
本领域所属技术人员应当理解,从患者获取血液样本的步骤以及将该血液样本中存在的循环EBV DNA的含量与对照进行对比对本发明来说并非必要的技术特征。所以,在本发明的实施方案中,可以不含或含其一。Those skilled in the art should understand that the step of obtaining a blood sample from a patient and comparing the circulating EBV DNA content in the blood sample with the control is not an essential technical feature of the present invention. Therefore, in the embodiment of the present invention, none or one of them may be included.
本领域所属技术人员可通过许多本领域公知的方法从血液样本中提取DNA。一种优选的方法是使用QIAamp Blood Kit。同时,循环EBV DNA也可通过使用一种本领域公知的或新的方法进行分析。尤其优选包含实时PCR扩增体系的方法。可以很容易设计出将通过上述方法检测到的EBV DNA水平与对照进行对比的标准步骤,从而通过统计学方法评估所得数值的显著性。Those skilled in the art can extract DNA from blood samples by many methods known in the art. A preferred method is to use the QIAamp Blood Kit. Meanwhile, circulating EBV DNA can also be analyzed by using a method known or new in the art. Especially preferred are methods involving real-time PCR amplification systems. Standard procedures for comparing the levels of EBV DNA detected by the methods described above to controls can be readily devised to assess the significance of the resulting values statistically.
可在一段时间后分析到EBV DNA拷贝的数量,且如我们的临床发现所证明的,这一系列的分析可将筛查出前癌、癌或恶性肿瘤阳性的患者与没有癌症但因为EBV病毒再活化而导致他们的EBV DNA滴定度出现偶然的尖峰的个体区分开。因此,本发明(单独使用或用于连续分析)提供了通过确定此种患者血清或血浆中存在的EBV DNA的含量来进行癌症的常规筛查的非侵入性的方法。The number of copies of EBV DNA can be analyzed over a period of time, and as demonstrated in our clinical findings, this series of analyzes can separate patients who screen positive for precancer, cancer, or malignancy from those who do not have cancer but because of EBV viral relapse. Individuals whose activation caused sporadic spikes in their EBV DNA titers were distinguished. Thus, the present invention (used alone or for serial analysis) provides a non-invasive method for the routine screening of cancer by determining the amount of EBV DNA present in the serum or plasma of such patients.
本发明的第二方面涉及包含适当的用于检测患者血清或血浆中的EBV DNA的试剂的诊断试剂盒。本发明的试剂盒还可包含一种或多种从患者获得血液样本的装置、从该血液样本中分离EBV DNA的装置以及定量该血液样本中存在的EBV DNA的含量的装置。该试剂盒可用于癌症的常规筛查,该筛查是通过测定患者血清或血液中存在的EBV DNA的含量来实现的。A second aspect of the invention relates to a diagnostic kit comprising appropriate reagents for the detection of EBV DNA in a patient's serum or plasma. Kits of the invention may also comprise one or more devices for obtaining a blood sample from a patient, for isolating EBV DNA from the blood sample, and for quantifying the amount of EBV DNA present in the blood sample. The kit can be used for routine screening of cancer, which is achieved by measuring the content of EBV DNA present in the patient's serum or blood.
此处将本说明书引用的所有出版物和专利申请引入作为参考,其等同于对每一出版物或专利申请专门或单独说明将其引入作为参考。All publications and patent applications cited in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
虽然本发明以说明和举例的方式描述了一些细节,其目的是为了使理解更为清楚,本领域所属技术人员应该很清楚,在不脱离所附权利要求的精神和范围的条件下,根据本发明的教导可以对其作出各种改变和修改。While the present invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it should be apparent to those skilled in the art that, without departing from the spirit and scope of the appended claims, Various changes and modifications may be made to the teachings of the invention.
实施例Example
以下实施例只是以说明的方式提供的,而不是限制性的。本领域所属技术人员应该很容易确认各种非关键参数,通过改变或修改这些参数可以得到基本类似的结果。The following examples are offered by way of illustration only, not limitation. Those skilled in the art should readily identify various non-critical parameters by which substantially similar results can be obtained by changing or modifying them.
实施例IExample 1
材料和方法 Materials and methods
已经有132个癌症高危患者(A组)和3987大致正常的个体(B组)将其血液样本送到我们在香港的实验室用于循环EBV DNA的测定。Blood samples from 132 high-risk cancer patients (Group A) and 3987 approximately normal individuals (Group B) have been sent to our laboratory in Hong Kong for the determination of circulating EBV DNA.
从血浆样本中提取DNA从每个受验者收集外周血(5ml)注入EDTA试管中用于分离血浆。在1600×g对血液样本进行离心,并小心地将血浆从含EDTA的试管中分离并转移入空白的聚丙烯试管中。将该样本在-20℃下保存直到进一步操作。使用QIAamp Blood Kit(Qiagen,Hilden,Germany)根据生产商(2)的推荐使用血液和体液步骤从血浆样本中提取DNA。使用血浆样本(130-800μl/柱)进行DNA提取。记录精确的用量以便计算目标DNA的浓度。所用的从提取柱获得的最终洗脱液的体积为50μl。DNA Extraction from Plasma Samples Peripheral blood (5 ml) was collected from each subject and injected into EDTA tubes for separation of plasma. Blood samples were centrifuged at 1600 x g, and the plasma was carefully separated from the EDTA-containing tubes and transferred into blank polypropylene tubes. This sample was stored at -20°C until further manipulation. DNA was extracted from plasma samples using the QIAamp Blood Kit (Qiagen, Hilden, Germany) using the blood and body fluids procedure according to the manufacturer's recommendations (2). DNA extraction was performed using plasma samples (130-800 μl/column). Record the exact amount used to calculate the target DNA concentration. The volume of final eluate obtained from the extraction column used was 50 [mu]l.
使用针对EBV基因组的BamHI-W片段区域的实时定量PCR体系分析循环EBV DNA的浓度(Lo,Y.M.D et al.,Cancer Res.,59:1181-1191(1999))。实时定量PCR和反应准备过程的主要过程(principals)如前所述(Lo,Y.M.D et al.,Cancer Res.,59:1188-1191(1999))。使用ABI Prism 7700Sequence Detector收集数据,并用Applied Biosystems开发的SequenceDetection System软件(版本1.6.3)进行分析。结果用每毫升血清中所含的EBV基因组的拷贝数来表示。The concentration of circulating EBV DNA was analyzed using a real-time quantitative PCR system targeting the BamHI-W fragment region of the EBV genome (Lo, Y.M.D et al., Cancer Res., 59:1181-1191 (1999)). The principals of the real-time quantitative PCR and reaction preparation procedures were described previously (Lo, Y.M.D et al., Cancer Res., 59:1188-1191 (1999)). Data were collected using ABI Prism 7700 Sequence Detector and analyzed with Sequence Detection System software (version 1.6.3) developed by Applied Biosystems. Results are expressed as the number of copies of the EBV genome contained per milliliter of serum.
所有血清DNA样本也用实时PCR进行β球蛋白基因分析(Lo,Y.M.D.et al.,Cancer Res.,59:1188-1191(1999)),其在所有测试样本中都显示阳性信号,从而证明提取的DNA的质量。在每次分析中都包括多个阴性水空白液。All serum DNA samples were also analyzed for β-globin gene by real-time PCR (Lo, Y.M.D. et al., Cancer Res., 59:1188-1191 (1999)), which showed positive signals in all tested samples, thus demonstrating the extraction the quality of the DNA. Multiple negative water blanks were included in each analysis.
更具体地,开发出两种用于EBV DNA检测的实时定量PCR系统:(a)一种针对BamHI-W区域;且(b)另一种针对EBNA-I区域(Baer,et alNature,310:207-211,1984)。该BamHI-W体系由扩增引物(SEQ ID NO:1)W-44F(5’-CCCAACACTCCACCACACC-3’)和(SEQ ID NO:2)W-119R(5’-TCTTAGGAGCTGTCCGAGGG-3’)和双重标记的荧光探针(SEQ IDNO:3)W-67T[5’-(FAM)CACACACTACACACACCCAC-CCGTCTC(TAMRA)-3’]构成。该EBNA-1体系由扩增引物(SEQ ID NO:4)EBNA-1162F(5’-TCATCATCATCCGGGTCTCC-3’)和(SEQ ID NO:5)EBNA-1229R(5’-CCTACAGGGT-GGAAAAATGGC-3’)和双重标记的荧光探针(SEQ IDNO:6)EBNA-1186T[5’-(FAM)CGCAGGCCCCCTCCAGGTA-GAA(TAMRA)-3’]构成。这些荧光探针包含3’-封闭磷酸基从而防止探针在PCR过程中延伸。使用Primer Express软件设计引物/探针组合(Perkin-ElmerCorp.,Foster City,CA)。从GenBank Sequence Database获得EBV基因组的序列数据(登录号V01555)。如先前在Lo,et al.Am J.Hum Genet 62:768-775,1998中所述,使用β球蛋白基因的实时定量PCR的引物和探针进行PCR扩增作为血浆DNA扩增的对照。More specifically, two real-time quantitative PCR systems for EBV DNA detection were developed: (a) one targeting the BamHI-W region; and (b) the other targeting the EBNA-I region (Baer, et alNature, 310: 207-211, 1984). The BamHI-W system consists of amplification primers (SEQ ID NO: 1) W-44F (5'-CCCAACACTCCACCACACC-3') and (SEQ ID NO: 2) W-119R (5'-TCTTAGGAGCTGTCCGAGGG-3') and double The labeled fluorescent probe (SEQ ID NO: 3) W-67T[5'-(FAM)CACACACTACACACACCCAC-CCGTCTC(TAMRA)-3'] constituted. The EBNA-1 system consists of amplification primers (SEQ ID NO: 4) EBNA-1162F (5'-TCATCATCATCCGGGTCTCC-3') and (SEQ ID NO: 5) EBNA-1229R (5'-CCTACAGGGT-GGAAAAATGGC-3') and a double-labeled fluorescent probe (SEQ IDNO: 6) EBNA-1186T[5'-(FAM)CGCAGGCCCCCTCCAGGTA-GAA(TAMRA)-3']. These fluorescent probes contain a 3'-blocking phosphate group to prevent probe extension during PCR. Primer/probe combinations were designed using Primer Express software (Perkin-Elmer Corp., Foster City, CA). The sequence data of the EBV genome (accession number V01555) was obtained from the GenBank Sequence Database. As a control for plasma DNA amplification, PCR amplification was performed using primers and probes for real-time quantitative PCR of the beta globin gene as previously described in Lo, et al. Am J. Hum Genet 62:768-775, 1998.
使用TaqMan PCR Core Reagent Kit(Perkin-Elmer Corp.)提供的组分(除了荧光探针和扩增引物)进行反应体积为50μl的荧光PCR反应。荧光探针是在Perkin-Elmer Applied Biosystems定制的。PCR引物是由LifeTechnologies,Inc.(Gaithersburg,MD)合成的。每一反应包含5μl的10×缓冲液A;300nM的每种扩增引物;25nM(指EBV探针)或100nM(指β球蛋白探针)的对应荧光探针;4mM MgCl2;dATP、dCTP和dGTP各200μm;400μM dUTP;1.25单位AmpliTaq Gold;和0.5单位AmpErase尿嘧啶N-糖基化酶。A fluorescent PCR reaction with a reaction volume of 50 µl was performed using the components provided by TaqMan PCR Core Reagent Kit (Perkin-Elmer Corp.) except the fluorescent probe and amplification primers. Fluorescent probes were custom made at Perkin-Elmer Applied Biosystems. PCR primers were synthesized by Life Technologies, Inc. (Gaithersburg, MD). Each reaction contained 5 μl of 10× buffer A; 300 nM of each amplification primer; 25 nM (referring to EBV probe) or 100 nM (referring to beta globulin probe) of the corresponding fluorescent probe; 4 mM MgCl 2 ; dATP, dCTP 400 μM dUTP; 1.25 units of AmpliTaq Gold; and 0.5 units of AmpErase uracil N-glycosylase.
在Applied Biosystems 7900 Sequence Detector中以384-孔反应板进行DNA扩增。每一样本分析两次。在每次分析时均使用多个阴性空白水。DNA amplification was performed in an Applied Biosystems 7900 Sequence Detector in 384-well reaction plates. Each sample was analyzed twice. Multiple negative water blanks were used for each analysis.
使用从EBV-阳性细胞株Namalwa(American Type Culture CollectionCRL-1432;See Klein et al.,Int J.Cancer,10:44-57,1972)中提取的DNA作为标准,每次分析中平行并进行重复检测来绘制校准曲线。Namalwa是含有两组组合的病毒基因组/细胞的二倍体细胞株。使用DNA/二倍体细胞的6.6pg转化因子计算拷贝数量(Saiki et al.,Science,239:487-491,1988)。循环无细胞EBV DNA的浓度用EBV基因组拷贝数/ml血浆的形式表达。DNA extracted from the EBV-positive cell line Namalwa (American Type Culture Collection CRL-1432; See Klein et al., Int J. Cancer, 10:44-57, 1972) was used as a standard in parallel and repeated in each analysis detection to draw a calibration curve. Namalwa is a diploid cell strain containing two sets of combined viral genomes/cells. Copy number was calculated using a conversion factor of 6.6 pg for DNA/diploid cells (Saiki et al., Science, 239:487-491, 1988). Concentrations of circulating cell-free EBV DNA were expressed as EBV genome copies/ml plasma.
EBV BamHI-W PCR和EBNA-I PCR系统的温度特征是相同的。热循环包括:开始在50℃孵育2分钟使尿嘧啶N-糖基化酶作用,随后先在95℃进行10分钟的变性步骤,然后进行在95℃变性15秒以及56℃变性1分钟的循环40次。The temperature characteristics of the EBV BamHI-W PCR and EBNA-I PCR systems are the same. Thermal cycling consists of an initial incubation at 50°C for 2 minutes for uracil N-glycosylase, followed by a denaturation step at 95°C for 10 minutes, followed by cycles of denaturation at 95°C for 15 seconds and denaturation at 56°C for 1 minute 40 times.
使用Sequence Detector收集扩增数据,并储存在Dell电脑中,然后用Perkin-Elmer Applied Biosystems开发的Sequence Detection System软件进行分析。用每一重复检测的平均值进行进一步的浓度计算。用如下方程进行EBV DNA或β球蛋白基因的血浆浓度(以拷贝数/ml表示)计算。The amplification data was collected using Sequence Detector, stored in a Dell computer, and then analyzed with the Sequence Detection System software developed by Perkin-Elmer Applied Biosystems. Further concentration calculations were performed using the average of each replicate. The plasma concentration (expressed in copy number/ml) of EBV DNA or β-globin gene was calculated by the following equation.
其中:C代表血浆中的目标物的浓度(拷贝数/ml),Q代表在PCR中用序列检测器测定的目标物的数量(拷贝数),VDNA代表提取后获得的DNA的总体积(通常为50μl/Qiagen提取物),VPCR代表PCR使用的DNA溶液的体积(通常为5μl),而Vext代表被提取的血浆/血清的体积(通常为0.13-0.80ml)。Wherein: C represents the concentration (copy number/ml) of the target substance in blood plasma, Q represents the quantity (copy number) of the target substance determined with sequence detector in PCR, V DNA represents the total volume of the DNA that obtains after extracting ( Typically 50 μl/Qiagen extract), V PCR represents the volume of DNA solution used for PCR (typically 5 μl), and V ext represents the volume of extracted plasma/serum (typically 0.13-0.80 ml).
对且仅对那些EBV DNA滴定度为阳性的个体,才要求其在第一次测试的4-12周后返回进行第二次同样的测试以再次确证。在某些情况下,第二次系列测定可能需要在12周之后进行。更有些情况下,在第二次测定的12周后或更长时间进行第三次系列测定。For, and only those individuals with positive EBV DNA titers, they are asked to return for a second identical test 4-12 weeks after the first test for reconfirmation. In some cases, a second series of measurements may need to be performed after 12 weeks. More often than not, a third series of measurements was performed 12 weeks or more after the second measurement.
结果 result
在高危组A中测定出共有42例EBV DNA阳性。其中大部分是EBV相关癌症患者,例如鼻咽癌和头部及颈部区域的未分化淋巴上皮瘤。在该群体中,对3例患者在第一次测定后的4-12周进行了EBV DNA的系列分析。如图1所示,所有没有已知癌症治疗史的患者其EBV DNA滴定度都表现出上升的趋势。In the high-risk group A, a total of 42 cases were positive for EBV DNA. Most of these were patients with EBV-associated cancers, such as nasopharyngeal carcinoma and anaplastic lymphoepithelioma of the head and neck region. In this population, serial analysis of EBV DNA was performed in 3 patients 4-12 weeks after the first assay. As shown in Figure 1, all patients with no known history of cancer treatment showed an upward trend in EBV DNA titers.
在正常组B中测定出共有74例EBV DNA阳性。在该群体中,对27位患者在第一次分析后的4-12周之间进行了EBV DNA的系列测试。如图2所示,除一人外,所有这些个体的EBV DNA滴定度在第二次分析时降为零。第三次测定结果(如果作了)则都为阴性。A total of 74 cases of EBV DNA were positive in normal group B. In this cohort, 27 patients underwent serial testing for EBV DNA between 4-12 weeks after the first analysis. As shown in Figure 2, all but one of these individuals had EBV DNA titers that dropped to zero by the second analysis. The third test results (if done) were all negative.
很少具有未确认与伊波病毒有直接基因组关联的肿瘤类型的癌症患者在其血浆中从未表现出阳性EBV DNA滴定度(图3)。1例结肠癌患者一直带有上述阳性滴定度直到他的肿瘤产生完全的治疗反应,此时他的EBV DNA也变为阴性。Few cancer patients with tumor types for which no direct genomic association with Ibovirus were identified never exhibited positive EBV DNA titers in their plasma (Figure 3). A patient with colon cancer had the above positive titer until his tumor had a complete response to treatment, at which time he also became negative for EBV DNA.
实施例IIExample II
材料和方法 Materials and methods
对具有阳性EBV DNA滴定度的20例患者(C组),将其外周血中的CD4+CD25+T细胞的百分比与EBV DNA阴性的对照组进行对比。For 20 patients with positive EBV DNA titer (Group C), the percentage of CD4+CD25+ T cells in peripheral blood was compared with the EBV DNA-negative control group.
在血液采集时获取这20位患者的外周血,并注入含肝素的Vacutainer试管中,用不含钙和镁的1×Dulbecco’s磷酸盐缓冲液(Mediatech)进行2∶1稀释,然后室温下在聚糖体(ficoll)密度梯度上以1000×g离心20分钟进行分离。收集外周血单核细胞,清洗并在含20%胎牛血清和10%DMSO的RPMI1640中冷冻保存以备将来使用。Peripheral blood from these 20 patients was obtained at the time of blood collection, injected into a Vacutainer tube containing heparin, diluted 2:1 with 1×Dulbecco's phosphate buffer (Mediatech) without calcium and magnesium, and then incubated at room temperature on poly Glycosomes (ficoll) were separated by centrifugation at 1000×g for 20 minutes on a density gradient. Peripheral blood mononuclear cells were collected, washed and cryopreserved in RPMI1640 containing 20% fetal bovine serum and 10% DMSO for future use.
使用四色血细胞计数仪和使用抗-CD3-PerCP、抗-CD4-APC或抗-CD8-FIT、抗-CD25-PE的活性标记物进行流式细胞仪分析,从而测定细胞类型。简而言之,将细胞在室温及黑暗条件下孵育30分钟,用FACS缓冲液(PBS 0.05%,FCS 2mM,EDTA和0.01%叠氮化钠)洗涤一次,并用2%甲醛固定。然后进行流式细胞仪分析。Cell types were determined using a four-color hemocytometer and flow cytometric analysis using activity markers of anti-CD3-PerCP, anti-CD4-APC or anti-CD8-FIT, anti-CD25-PE. Briefly, cells were incubated for 30 min at room temperature in the dark, washed once with FACS buffer (PBS 0.05%, FCS 2 mM, EDTA and 0.01% sodium azide), and fixed with 2% formaldehyde. Flow cytometry analysis was then performed.
结果 result
与EBV DNA阴性的个体相比,EBV DNA阳性的个体的CD4+CD25+T细胞明显上升。Compared with EBV DNA-negative individuals, CD4+CD25+ T cells were significantly increased in EBV DNA-positive individuals.
讨论 discuss
这些数据表明,对从普通个体获得的血浆样本进行循环无细胞EBVDNA检测来筛查各种形式或类型的癌症的发病。These data demonstrate that circulating cell-free EBV DNA testing of plasma samples obtained from ordinary individuals can be used to screen for the development of various forms or types of cancer.
同时,这也是第一次显示以下结果:具有CD3+CD4+CD25+表型且在癌症发展中起作用的调节T细胞在循环EBV DNA阳性的个体中百分比增加。虽然这些T细胞最初发现为防止宿主产生自体免疫的,但它们同时也妨碍了对宿主进行针对不同肿瘤抗原的免疫监视。因此,具有这种表型的细胞上升会导致癌症的形成,从前癌、原位癌发展为发育成熟的癌症。Also, for the first time, it was shown that the percentage of regulatory T cells with a CD3+CD4+CD25+ phenotype and a role in cancer development was increased in circulating EBV DNA-positive individuals. Although these T cells were originally discovered to prevent host autoimmunity, they also hinder the immune surveillance of the host against different tumor antigens. Thus, the rise of cells with this phenotype leads to the development of cancer, from precancerous, carcinoma in situ, to full-fledged cancer.
这种引起癌症发病的上升并不仅限于与EBV直接相关的诸如鼻咽癌、部分胃癌和不同的淋巴瘤的癌症,还在其它诸如乳癌、肺癌、肝癌和结肠癌等的普通癌症中得到证明。如下面进一步说明地,确实有一些原因可以解释为什么本发明可作为常规癌症筛查工具。This increase in cancer incidence is not limited to cancers directly related to EBV such as nasopharyngeal cancer, some gastric cancers, and various lymphomas, but has also been demonstrated in other common cancers such as breast, lung, liver, and colon cancers. As explained further below, there are indeed several reasons why the present invention may be useful as a routine cancer screening tool.
原因之一是EBV是最流行的其几乎终生都潜伏在人体内的病毒。此外,该病毒不仅在EBV有潜力致癌的、而且还在癌症基因组变化与该病毒直接关联的各种癌症中是大多数原癌病毒中的一种。当此高效原癌基因被束缚在调节性T细胞群上,会更容易导致癌症细胞的发展,因此理论假说是该EBV特性的有或无在没有基因组整合的条件下均可引起癌症发病。One reason is that EBV is the most prevalent virus that spends almost its entire life dormant in the human body. Furthermore, the virus is one of the most proto-oncoviruses not only in the oncogenic potential of EBV but also in a variety of cancers in which cancer genome changes are directly associated with the virus. When this highly efficient proto-oncogene is bound to the regulatory T cell population, it is more likely to lead to the development of cancer cells, so the theoretical hypothesis is that the presence or absence of this EBV characteristic can cause cancer in the absence of genomic integration.
除了使用EBV DNA滴定度的一次测定作为常规癌症筛查手段之外,我们还第一次显示,在第一次测定后的4-12周之内(或某些情况下超过该期限)进行系列测试,可将那些癌症患者与非癌症患者区分开(除一个例外)。In addition to using a single determination of EBV DNA titer as a routine cancer screening tool, we show for the first time that serial Tests that can distinguish those cancer patients from non-cancer patients (with one exception).
我们还显示与EBV无基因组关联的癌症患者通过本发明也筛查为阳性。在一个病例中,患者在完全康复后其EBV病毒滴定度变为阴性。We also show that cancer patients with no genomic association with EBV also screen positive by the present invention. In one case, the patient's EBV viral titer became negative after full recovery.
上述讨论的结论是:本发明是用于癌症常规筛查的非常有价值的工具,上述癌症包括前癌和原位癌病灶以及其它未显示出直接或在基因组上与EBV相关的癌症。当然,其可作为与EBV相关或伴随的癌症的筛查工具。The above discussion concludes that the present invention is a very valuable tool for routine screening of cancers including precancerous and carcinoma in situ lesions and other cancers that have not been shown to be directly or genomically associated with EBV. Of course, it can be used as a screening tool for EBV-related or concomitant cancers.
序列表Sequence Listing
SEQ ID NO:1:W-44F(5’-CCCAACACTCCACCACACC-3’)SEQ ID NO: 1: W-44F (5'-CCCAACACTCCACCACACC-3')
SEQ ID NO:2:W-119R(5’-TCTTAGGAGCTGTCCGAGGG-3’)SEQ ID NO: 2: W-119R (5'-TCTTAGGAGCTGTCCGAGGG-3')
SEQ ID NO:3:W-67T[5’-(FAM)CACACACTACACACACCCAC-CCGTCTC(TAMRA)-3’]SEQ ID NO: 3: W-67T[5'-(FAM)CACACACTACACACACCCAC-CCGTCTC(TAMRA)-3']
SEQ ID NO:4:EBNA-1162F(5’-TCATCATCATCCGGGTCTCC-3’)SEQ ID NO: 4: EBNA-1162F (5'-TCATCATCATCCGGGTCTCC-3')
SEQ ID NO:5:EBNA-1229R(5’-CCTACAGGGT-GGAAAAATGGC-3’)SEQ ID NO: 5: EBNA-1229R (5'-CCTACAGGGT-GGAAAAATGGC-3')
SEQ ID NO:6:EBNA-1186T[5’-(FAM)CGCAGGCCCCCTCCAGGTA-GAA(TAMRA)-3’]SEQ ID NO: 6: EBNA-1186T[5'-(FAM)CGCAGGCCCCCTCCAGGTA-GAA(TAMRA)-3']
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2018137685A1 (en) * | 2017-01-25 | 2018-08-02 | The Chinese University Of Hong Kong | Diagnostic applications using nucleic acid fragments |
| US11459616B2 (en) | 2016-10-24 | 2022-10-04 | The Chinese University Of Hong Kong | Methods and systems for tumor detection |
| US12234515B2 (en) | 2017-07-26 | 2025-02-25 | The Chinese University Of Hong Kong | Enhancement of cancer screening using cell-free viral nucleic acids |
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2004
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Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US11459616B2 (en) | 2016-10-24 | 2022-10-04 | The Chinese University Of Hong Kong | Methods and systems for tumor detection |
| WO2018137685A1 (en) * | 2017-01-25 | 2018-08-02 | The Chinese University Of Hong Kong | Diagnostic applications using nucleic acid fragments |
| US10633713B2 (en) | 2017-01-25 | 2020-04-28 | The Chinese University Of Hong Kong | Diagnostic applications using nucleic acid fragments |
| US11479825B2 (en) | 2017-01-25 | 2022-10-25 | The Chinese University Of Hong Kong | Diagnostic applications using nucleic acid fragments |
| US12234515B2 (en) | 2017-07-26 | 2025-02-25 | The Chinese University Of Hong Kong | Enhancement of cancer screening using cell-free viral nucleic acids |
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