The impact of digital DNA counting technologies on noninvasive prenatal testing

Expert Review of Molecular Diagnostics

Volumn 15, Issue 10, 2015, Pages 1261-1268

  Sun, Kun ^a   Jiang, Peiyong ^a   Chan, Kc Allen ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

cell free fetal DNA; digital PCR; massive parallel sequencing; maternal plasma; NIPT

Indexed keywords

DNA;

ANEUPLOIDY; ARTICLE; CHROMOSOME DISORDER; DIGITAL POLYMERASE CHAIN REACTION SYSTEM; DNA DETERMINATION; DNA SEQUENCE; FETUS; GENOME; GENOME ANALYSIS; HUMAN; MATERNAL PLASMA; MONOGENIC DISORDER; POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION SYSTEM; PREGNANT WOMAN; PRENATAL DIAGNOSIS; PRENATAL SCREENING; BLOOD; CHROMOSOME ABERRATION; COMPUTER ASSISTED DIAGNOSIS; FEMALE; FETAL DISEASES; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR DIAGNOSIS; PREGNANCY;

CHROMOSOME ABERRATIONS; FEMALE; FETAL DISEASES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MOLECULAR DIAGNOSTIC TECHNIQUES; PREGNANCY; PRENATAL DIAGNOSIS; SEQUENCE ANALYSIS, DNA;

EID: 84942297179     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.2015.1084227     Document Type: Article

References (56)

1. Lo YMD, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet 1997; 350 (9076): 485-7
2. Lo YMD, Hjelm NM, Fidler C, et al. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. N Engl J Med 1998; 339 (24): 1734-8
3. Scheffer PG, van der Schoot CE, Page-Christiæns GC, de Haas M. Noninvasive fetal blood group genotyping of rhesus D, c, E and of K in alloimmunised pregnant women: evaluation of a 7-year clinical experience. BJOG 2011; 118 (11): 1340-8
4. Van der Schoot CE, Soussan AA, Koelewijn J, et al. Non-invasive antenatal RHD typing. Transfus Clin Biol 2006; 13 (1-2): 53-7
5. Finning K, Martin P, Summers J, et al. Effect of high throughput RHD typing of fetal DNA in maternal plasma on use of anti-RhD immunoglobulin in RhD negative pregnant women: prospective feasibility study. BMJ 2008; 336 (7648): 816-18
6. Muller SP, Bartels I, Stein W, et al. The determination of the fetal D status from maternal plasma for decision making on Rh prophylaxis is feasible. Transfusion 2008; 48 (11): 2292-301
7. Saito H, Sekizawa A, Morimoto T, et al. Prenatal DNA diagnosis of a single-gene disorder from maternal plasma [letter] [In Process Citation]. Lancet 2000; 356 (9236): 1170
8. Amicucci P, Gennarelli M, Novelli G, Dallapiccola B. Prenatal diagnosis of myotonic dystrophy using fetal DNA obtained from maternal plasma. Clin Chem 2000; 46 (2): 301-2
9. Gonzalez-Gonzalez MC, Trujillo MJ, Rodriguez de Alba M, et al. Huntington disease-unaffected fetus diagnosed from maternal plasma using QF-PCR. Prenat Diagn 2003; 23 (3): 232-4
10. Sykes PJ, Neoh SH, Brisco MJ, et al. Quantitation of targets for PCR by use of limiting dilution. Biotechniques 1992; 13 (3): 444-9
11. Kalinina O, Lebedeva I, Brown J, Silver J. Nanoliter scale PCR with TaqMan detection. Nucleic Acids Res 1997; 25 (10): 1999-2004
12. Vogelstein B, Kinzler KW. Digital PCR. Proc Natl Acad Sci USA 1999; 96 (16): 9236-41
13. Lo YMD, Lun FMF, Chan KCA, et al. Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc Natl Acad Sci USA 2007; 104 (32): 13116-21
14. Lun FMF, Chiu RWK, Chan KCA, et al. Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. Clin Chem 2008; 54 (10): 1664-72
15. Chang YH, Lee GB, Huang FC, et al. Integrated polymerase chain reaction chips utilizing digital microfluidics. Biomed Microdevices 2006; 8 (3): 215-25
16. Ottesen EA, Hong JW, Quake SR, Leadbetter JR. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 2006; 314 (5804): 1464-7
17. Beer NR, Hindson BJ, Wheeler EK, et al. On-chip, real-time, single-copy polymerase chain reaction in picoliter droplets. Anal Chem 2007; 79 (22): 8471-5
18. Nakano M, Komatsu J, Matsuura S, et al. Single-molecule PCR using water-in-oil emulsion. J Biotechnol 2003; 102 (2): 117-24
19. Chan KCA, Ding C, Gerovassili A, et al. Hypermethylated RASSF1A in maternal plasma: a universal fetal DNA marker that improves the reliability of noninvasive prenatal diagnosis. Clin Chem 2006; 52 (12): 2211-18
20. Lo YMD, Tein MS, Lau TK, et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet 1998; 62 (4): 768-75
21. Lun FMF, Tsui NBY, Chan KCA, et al. Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma. Proc Natl Acad Sci USA 2008; 105 (50): 19920-5
22. El Karoui N, Zhou W, Whittemore AS. Getting more from digital SNP data. Stat Med 2006; 25 (18): 3124-33
23. Tsui NB, Kadir RA, Chan KC, et al. Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood 2011; 117 (13): 3684-91
24. Gu W, Koh W, Blumenfeld YJ, et al. Noninvasive prenatal diagnosis in a fetus at risk for methylmalonic acidemia. Genet Med 2014; 16 (7): 564-7
25. Lo YMD, Chan KCA, Sun H, et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2010; 2 (61): 61ra91
26. Lam KW, Jiang P, Liao GJ, et al. Noninvasive prenatal diagnosis of monogenic diseases by targeted massively parallel sequencing of maternal plasma: application to beta-thalassemia. Clin Chem 2012; 58 (10): 1467-75
27. New MI, Tong YK, Yuen T, et al. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab 2014; 99 (6): E1022-30
28. Ge H, Huang X, Li X, et al. Noninvasive prenatal detection for pathogenic CNVs: the application in alpha-thalassemia. PLoS One 2013; 8 (6): e67464
29. Ma D, Ge H, Li X, et al. Haplotype-based approach for noninvasive prenatal diagnosis of congenital adrenal hyperplasia by maternal plasma DNA sequencing. Gene 2014; 544 (2): 252-8
30. Yoo SK, Lim BC, Byeun J, et al. Noninvasive prenatal diagnosis of Duchenne muscular dystrophy: comprehensive genetic diagnosis in carrier, proband, and fetus. Clin Chem 2015; 61 (6): 829-37
31. Liao GJ, Lun FM, Zheng YW, et al. Targeted massively parallel sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles. Clin Chem 2011; 57 (1): 92-101
32. Chim SSC, Jin S, Lee TY, et al. Systematic search for placental DNA-methylation markers on chromosome 21: toward a maternal plasma-based epigenetic test for fetal trisomy 21. Clin Chem 2008; 54 (3): 500-11
33. Chim SSC, Tong YK, Chiu RWK, et al. Detection of the placental epigenetic signature of the maspin gene in maternal plasma. Proc Natl Acad Sci USA 2005; 102 (41): 14753-8
34. Chiu RWK, Chan KCA, Gao Y, et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 2008; 105 (51): 20458-63
35. Chiu RWK, Akolekar R, Zheng YW, et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011; 342: c7401
36. Chen EZ, Chiu RW, Sun H, et al. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 2011; 6 (7): e21791
37. Palomaki GE, Deciu C, Kloza EM, et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med 2012; 14 (3): 296-305
38. Palomaki GE, Kloza EM, Lambert-Messerlian GM, et al. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med 2011; 13 (11): 913-20
39. Zhang H, Gao Y, Jiang F, et al. Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146 958 pregnancies. Ultrasound Obstet Gynecol 2015; 45 (5): 530-8
40. Nicolaides KH, Syngelaki A, Ashoor G, et al. Noninvasive prenatal testing for fetal trisomies in a routinely screened first-trimester population. Am J Obstet Gynecol 2012; 207 (5): 374 e371-6
41. Liao GJ, Chan KC, Jiang P, et al. Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 2012; 7 (5): e38154
42. Zimmermann B, Hill M, Gemelos G, et al. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenat Diagn 2012; 32 (13): 1233-41
43. Yu SC, Jiang P, Choy KW, et al. Noninvasive prenatal molecular karyotyping from maternal plasma. PLoS One 2013; 8 (4): e60968
44. Zhao C, Tynan J, Ehrich M, et al. Detection of fetal subchromosomal abnormalities by sequencing circulating cell-free DNA from maternal plasma. Clin Chem 2015; 61 (4): 608-16
45. Chen S, Ge H, Wang X, et al. Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing. Genome Med 2013; 5 (2): 18
46. Fan HC, Gu W, Wang J, et al. Non-invasive prenatal measurement of the fetal genome. Nature 2012; 487 (7407): 320-4
47. Kitzman JO, Snyder MW, Ventura M, et al. Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med 2012; 4 (137): 137ra176
48. Pettit KE, Hull AD, Korty L, et al. The utilization of circulating cell-free fetal DNA testing and decrease in invasive diagnostic procedures: an institutional experience. J Perinatol 2014; 34 (10): 750-3
49. Chan KCA, Jiang P, Zheng YW, et al. Cancer genome scanning in plasma: Detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem 2013; 59: 211-24
50. Chan KC, Jiang P, Chan CW, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA 2013; 110 (47): 18761-8
51. Jiang P, Chan CW, Chan KC, et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc Natl Acad Sci USA 2015; 112 (11): E1317-25
52. Chan KCA. Scanning for cancer genomic changes in plasma: toward an era of personalized blood-based tumor markers. Clin Chem 2013; 59 (11): 1553-5
53. Chan KCA, Jiang P, Chan CWM, et al. Noninvasive detection of cancer-associated genomewide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA 2013; 110 (47): 18761-8
54. Zheng YWL, Chan KCA, Sun H, et al. Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. Clin Chem 2012; 58 (3): 549-58
55. American College of O, Gynecologists Committee on G. Committee Opinion No. 545: Noninvasive prenatal testing for fetal aneuploidy. Obstet Gynecol 2012; 120 (6): 1532-4
56. Hudecova I, Sahota D, Heung MM, et al. Maternal plasma fetal DNA fractions in pregnancies with low and high risks for fetal chromosomal aneuploidies. PLoS One 2014; 9 (2): e88484