从最初人们发现游离的肿瘤DNA, 到2010年后临床概念的建立和检测技术的成熟,液体活检的发展实际上经过了很漫长的过程。 液体活检的发展在很大程度上得益于无创产检领域的发展。 无创产检(NIPT)由于其在理论和实践上都和肿瘤的液体活检很相似,被认为是液体活检的一个分支。 从无创产检在90年代末建立的那一刻开始, 就成为了液体活检的发祥地和试验田。
我们在上一期的《液体活检通讯》中讨论了用来研究和鉴定游离DNA的身份的两个重要的模型系统, 即凝血系统和创伤系统。 这两个系统都是讯速变化的血液环境, 在这样的环境里的游离DNA的消长情况不仅提供了游离DNA的生物学指标, 更为诊断患者的生理病理情况,比如创伤患者的预后, 提供了有力的依据。 这两个系统都是同源系统,即增生的游离DNA和本底的游离DNA来自同一供体。
实际上,从科学发现的角度看,同源系统对于液体活检的科研来说是有很大难度的, 因为同源系统中增生和变化的DNA是很难追溯的。 相形之下, 异源系统中追溯DNA要容易得多。 最经典的异源系统就是母体和婴儿, 无创产检就是用母体血样来鉴定婴儿基因。 在这个系统中,异源的游离DNA在高分辨率的分子诊断方法学下,可以清晰地判断出来。
无创产检后来居上,引领液体活检
液体活检的主流市场和终极目标,是通过游离DNA和游离细胞来完成对肿瘤的检测。 在1996年发表在《自然医学》的两篇文章里, 美国和瑞士的两个项目组分别独立地构建了检测患者血液中的游离的肿瘤DNA的方法【1,2】。 其中的美国约翰霍普金斯大学的Sidransky项目组,他们研究了21位头颈癌患者的血清, 发现了其中6位患者有卫星DNA的突变, 这些突变和实体瘤的癌突变是一致的,而这6位患者都发生了癌症转移。
几乎在与此同时,瑞士的植物生化和生理实验室的Anker项目组,用肺癌患者的血浆为样本,发现了在大于70%的样本里可以检测到载有肿瘤突变的游离DNA。 这两篇文章为建立当代液体活检的方法学的提供了理论依据。从最初发现游离的肿瘤DNA【3】到这时建立了初步的方法学,20年已经过去了, 肿瘤的液体活检终于有了显著的进步,但是在展望的同时仍然有很多疑虑【4,5】。
在1996年《自然医学》的这两篇关于游离肿瘤DNA文章发表后,启发了香港中文大学的卢煜明教授。 卢教授当时刚刚建立了自己的独立课题组,他抓住了这个机会,从而开启了无创产检的系统【6-8】。卢教授的逻辑也很明确, 婴儿比肿瘤大多了,既然肿瘤的游离DNA可以检测到,婴儿的DNA就更能检测到。
无创产检领域的开创性文献,是卢煜明于1997年在《柳叶刀》上发表的论文,阐述了在母体的血清和血浆中发现了婴儿DNA【9】。 这篇文章里他研究了30位怀有男婴的孕妇, 用PCR扩增和检测DNA, 发现其中的21位(70%)在她们的血样里有Y染色体的DNA。 因为Y染色体是男性特征,只能来源于男婴, 而在非怀孕妇女以及怀有女婴的对照组样品里没有发现Y染色体DNA, 所以结论是母体血样中有游离的婴儿DNA, 这为无创产检提供了理论依据。 这篇论文充分发挥了异源DNA系统的优势,大繁至简, 用母体环境对照Y染色体这个直观明了的追踪系统, 迅速找到了目标DNA。
无创产检的系统和方法
无创产检的主要临床目标,是通过母体血清中的游离的婴儿DNA来检测是婴儿的染色体异常【10-14】。 其中最常见的是对唐氏综合征的无创检测【15-20】。 唐氏综合征(Down syndrome)又被称为21三体综合征(trisomy 21), 是最常见的严重出生缺陷病, 在美国有35万唐氏综合征的病人,而在全球范围内的唐氏的发病率和症状也都很相似。除了唐氏综合征,还有其他的染色体异常, 包括13三体综合征(trisomy 13, 又称Patau Syndrome), 18三体综合征(trisomy 18, 又称Edward Syndrome),特纳综合征 (Turner Syndrome, 又称45,X)和较为罕见的全套染色体三体综合征(Triploidy)。
对于这些染色体遗传病的无创检测, 已经有了相当的临床病例积累【21-30】。 无创产检的检测方法主要是PCR和测序,包括大规模平行测序等二代测序方法【6-8, 31-33】。 从现有文献提供的数据看, 无创产检的系统和传统方法相比, 除了风险的降低, 它的检出率(DR, detection rate)和假阳性率(FPR, false positive rate)也明显优于传统方法。 至此,无创产检在安全性、灵敏度、特异性上全方位超越了传统方法,已经进入了临床诊疗指南【34-35】,成为主流的检测方法。基于无创产检的检测产品, 也陆续在法规上得到获得批准。
除了对染色体异常的检测, 无创产检的还提供了更前沿的产检项目, 包括全基因组分析、全转录组分析、全甲基化组分析、组织来源分析等【36-39】。 这些前沿的虽然还是停留在研发阶段, 没有进入法规, 但也引领了未来的无创产检以致整个液体活检的方向。
产检是有标准答案的平台
无创产检为开发液体活检的方法和产品,提供了一个完美的平台。 这个平台的最大的优势,在于这个平台能够提供标准答案。
在无创方法之前, 产检是通过羊水穿刺或绒毛检查来完成, 用这些传统方法来检测染色体异常,是有完整的方法学和大量的临床积累的【40-46】。 这些传统方法为无创方法提供了参照系,提供了标准答案。 产检的标准答案是体现在这个几个方面。
第一,明确的时间表;
第二,清楚定义的检测目标;
第三,异源系统。
无论是第一孕期还是第二孕期, 染色体异常的出现时机、概率、位点、游离DNA水平等, 都有明确的期待范围【47-54】。 所以任何新的产检方法, 包括已经开发的无创检测,还有未来的产检方法, 只要和现有方法比对, 就可以计算出检出率和假阳性率,相对准确地对新方法的优劣做出鉴别。 相当来说,肿瘤的出现或者复发,没有明确的时间表, 突变位点众多, 它是没有标准答案的, 如果要计算出检出率等参数,其过程也更为复杂,这样开发新检测方法的成本和时间要求就更高。 作为异源系统, 产检提供了明确而简便的异源系统, 每一份婴儿的DNA都有特征DNA(比如Y染色体DNA), 而肿瘤的高度异质性和突变率决定了它作为异源系统,是非常复杂的。 可以这样认为,如果没有无创产检在近年的技术推动, 液体活检领域到现在还只能是在黑暗中充满希望地摸索着。
综合地看, 无创产检作为液体活检的先行领域,开创了重要的概念和方法学, 对液体活检的整个领域做出了非常积极的推动作用。 从市场规模和未来发展前景看,产检只是液体活检的一个很小的部分,但是它作为液体活检的试验田的在未来将持续发挥重要作用。
参考文献
1 |
Nawroz H et al. Microsatellite alterations in serum DNA of head and neck cancer patients. Nat Med. 1996 Sep;2(9):1035-7. |
2 |
Chen XQ et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat Med. 1996 Sep;2(9):1033-5. |
3 |
Leon SA et al. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977 Mar;37(3):646-50. |
4 |
Ziegler A et al. Circulating DNA: a new diagnostic gold mine? Cancer Treat Rev. 2002 Oct;28(5):255-71. |
5 |
Lui YY et al. Circulating DNA in plasma and serum: biology, preanalytical issues and diagnostic applications. Clin Chem Lab Med. 2002 Oct;40(10):962-8. |
6 |
Lo YM et al. Noninvasive prenatal diagnosis: from dream to reality. Clin Chem. 2015 Jan;61(1):32-7. |
7 |
Avent ND et al. Cell-free fetal DNA in the maternal serum and plasma: current and evolving applications. Curr Opin Obstet Gynecol. 2009 Apr;21(2):175-9. |
8 |
Puszyk WM et al. Noninvasive prenatal diagnosis of aneuploidy using cell-free nucleic acids in maternal blood: promises and unanswered questions. Prenat Diagn. 2008 Jan;28(1):1-6. |
9 |
Lo YM et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997 Aug 16;350(9076):485-7. |
10 |
Lo YM et al. Noninvasive prenatal detection of fetal chromosomal aneuploidies by maternal plasma nucleic acid analysis: a review of the current state of the art. BJOG. 2009 Jan;116(2):152-7. |
11 |
Dondorp W et al. Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening. Eur J Hum Genet. 2015 Nov;23(11):1592. |
12 |
de Jong A et al. Non-invasive prenatal diagnosis for aneuploidy: toward an integral ethical assessment. Hum Reprod. 2011 Nov;26(11):2915-7. |
13 |
Chiu RW et al. Noninvasive prenatal diagnosis empowered by high-throughput sequencing. Prenat Diagn. 2012 Apr;32(4):401-6. |
14 |
Metcalfe A et al. Beyond Trisomy 21: Additional Chromosomal Anomalies Detected through Routine Aneuploidy Screening. J Clin Med. 2014 Apr 8;3(2):388-415. |
15 |
Sifakis S et al. Noninvasive prenatal diagnosis of Down syndrome: current knowledge and novel insights. J Perinat Med. 2012 Feb 13;40(4):319-27. |
16 |
Patterson D et al. Down syndrome and genetics - a case of linked histories. Nat Rev Genet. 2005 Feb;6(2):137-47. |
17 |
Goodliffe JW et al. Absence of Prenatal Forebrain Defects in the Dp(16)1Yey/+ Mouse Model of Down Syndrome. J Neurosci. 2016 Mar 9;36(10):2926-44. |
18 |
Vassy C et al. From a genetic innovation to mass health programmes: the diffusion of Down's Syndrome prenatal screening and diagnostic techniques in France. Soc Sci Med. 2006 Oct;63(8):2041-51. |
19 |
Chiang HH et al. Informed choice of pregnant women in prenatal screening tests for Down's syndrome. J Med Ethics. 2006 May;32(5):273-7. |
20 |
Favre R et al. What about informed consent in first-trimester ultrasound screening for Down syndrome? Fetal Diagn Ther. 2008;23(3):173-84. |
21 |
Bianchi DW et al. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol. 2012 May;119(5):890-901. |
22 |
Chiu RW et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20458-63. |
23 |
Bianchi DW et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014 Feb 27;370(9):799-808. |
24 |
Chiu RW et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ. 2011 Jan 11;342:c7401. |
25 |
Stumm M et al. Diagnostic accuracy of random massively parallel sequencing for non-invasive prenatal detection of common autosomal aneuploidies: a collaborative study in Europe. Prenat Diagn. 2014 Feb;34(2):185-91. |
26 |
Tong YK et al. Noninvasive prenatal detection of fetal trisomy 18 by epigenetic allelic ratio analysis in maternal plasma: Theoretical and empirical considerations. Clin Chem. 2006 Dec;52(12):2194-202. |
27 |
Walsh JM et al. Fetal aneuploidy detection by maternal plasma DNA sequencing: a technology assessment. Prenat Diagn. 2013 Jun;33(6):514-20. |
28 |
Cheng SH et al. Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: feasibility assessment. Clin Chem. 2015 Oct;61(10):1305-6. |
29 |
Dondorp W et al. Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening. Summary and recommendations. Eur J Hum Genet. 2015 Apr 1. |
30 |
Liang D et al. Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing. Prenat Diagn. 2013 May;33(5):409-15. |
31 |
Chitty LS et al. Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA. Cold Spring Harb Perspect Med. 2015 Jul 17;5(9):a023085. |
32 |
Wong FC et al. Prenatal Diagnosis Innovation: Genome Sequencing of Maternal Plasma. Annu Rev Med. 2016;67:419-32. |
33 |
Song Y et al. Noninvasive prenatal testing of fetal aneuploidies by massively parallel sequencing in a prospective Chinese population. Prenat Diagn. 2013 Jul;33(7):700-6. |
34 |
Chitayat D et al. Prenatal screening for fetal aneuploidy in singleton pregnancies. J Obstet Gynaecol Can. 2011 Jul;33(7):736-50. |
35 |
ACOG Committee on Practice Bulletins. et al. ACOG Practice Bulletin No. 77: screening for fetal chromosomal abnormalities. Obstet Gynecol. 2007 Jan;109(1):217-27. |
36 |
Tsui NB et al. Non-invasive prenatal detection of fetal trisomy 18 by RNA-SNP allelic ratio analysis using maternal plasma SERPINB2 mRNA: a feasibility study. Prenat Diagn. 2009 Nov;29(11):1031-7. |
37 |
New MI et al. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab. 2014 Jun;99(6):E1022-30. |
38 |
Sun K et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):E5503-12 |
39 |
Wong AI et al. Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications. Trends Mol Med. 2015 Feb;21(2):98-108. |
40 |
Benn PA et al. Maternal serum screening for birth defects: results of a Connecticut regional program. Conn Med. 1996 Jun;60(6):323-7. |
41 |
Burton BK et al. A prospective trial of prenatal screening for Down syndrome by means of maternal serum alpha-fetoprotein, human chorionic gonadotropin, and unconjugated estriol. Am J Obstet Gynecol. 1993 Sep;169(3):526-30. |
42 |
Orlandi F et al. First-trimester screening for fetal aneuploidy: biochemistry and nuchal translucency. Ultrasound Obstet Gynecol. 1997 Dec;10(6):381-6. |
43 |
Spencer K et al. The influence of ethnic origin on first trimester biochemical markers of chromosomal abnormalities. Prenat Diagn. 2000 Jun;20(6):491-4. |
44 |
Stenhouse EJ et al. First-trimester combined ultrasound and biochemical screening for Down syndrome in routine clinical practice. Prenat Diagn. 2004 Oct;24(10):774-80. |
45 |
Spencer K et al. One stop clinic for assessment of risk for fetal anomalies: a report of the first year of prospective screening for chromosomal anomalies in the first trimester. BJOG. 2000 Oct;107(10):1271-5. |
46 |
Scott F et al. Prospective evaluation of a first trimester screening program for Down syndrome and other chromosomal abnormalities using maternal age, nuchal translucency and biochemistry in an Australian population. Aust N Z J Obstet Gynaecol. 2004 Jun;44(3):205-9. |
47 |
Alamillo CM et al. Nearly a third of abnormalities found after first-trimester screening are different than expected: 10-year experience from a single center. Prenat Diagn. 2013 Mar;33(3):251-6. |
48 |
Hörmansdörfer C et al. Age-independent first trimester screening for Down syndrome: analysis of three modified software programs with 6,508 pregnancies. Arch Gynecol Obstet. 2011 Apr;283(4):749-54. |
49 |
Kagan KO et al. Screening for trisomy 18 by maternal age, fetal nuchal translucency, free beta-human chorionic gonadotropin and pregnancy-associated plasma protein-A. Ultrasound Obstet Gynecol. 2008 Sep;32(4):488-92. |
50 |
Karadzov-Orlic N et al. Improved diagnostic accuracy by using secondary ultrasound markers in the first-trimester screening for trisomies 21, 18 and 13 and Turner syndrome. Prenat Diagn. 2012 Jul;32(7):638-43. |
51 |
Marttala J et al. Screening and outcome of chromosomal abnormalities other than trisomy 21 in Northern Finland. Acta Obstet Gynecol Scand. 2011 Aug;90(8):885-9. |
52 |
Merz E et al. A new approach to calculating the risk of chromosomal abnormalities with first-trimester screening data. Ultraschall Med. 2008 Dec;29(6):639-45. |
53 |
Ranta JK et al. First trimester biochemistry at different maternal ages. Clin Chem Lab Med. 2011 Nov 24;50(3):549-55. |
54 |
Kazerouni NN et al. Triple-marker prenatal screening program for chromosomal defects. Obstet Gynecol. 2009 Jul;114(1):50-8. |