A method to quantify cell-free fetal DNA fraction in maternal plasma using next generation sequencing: Its application in non-invasive prenatal chromosomal aneuploidy detection

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Xu, Xu Ping ^a   Gan, Hai Yan ^b   Li, Fen Xia ^b   Tian, Qi ^c   Zhang, Jun ^c   Liang, Rong Liang ^a   Li, Ming ^a   Yang, Xue Xi ^a   Wu, Ying Song ^a  

^a SOUTHERN MEDICAL UNIVERSITY   (China)

^b Guangzhou Darui Biotechnology Co Ltd   (China)

^c SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL FREE FETAL DNA; DNA; DNA FRAGMENT; UNCLASSIFIED DRUG;

ADULT; ANEUPLOIDY; ARTICLE; BLOOD SAMPLING; CHROMOSOME 13; CHROMOSOME 18; CHROMOSOME 21; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; GESTATIONAL AGE; HUMAN; MAJOR CLINICAL STUDY; MATERNAL AGE; MATERNAL PLASMA; NEXT GENERATION SEQUENCING; PRENATAL SCREENING; PROCESS DEVELOPMENT; QUANTITATIVE ANALYSIS; TRISOMY 13; TRISOMY 18; TRISOMY 21; VALIDATION STUDY; Y CHROMOSOME; CHROMOSOME DISORDERS; FETUS; GENETICS; HIGH THROUGHPUT SEQUENCING; MALE; PREGNANCY; PRENATAL DIAGNOSIS; PROCEDURES; YOUNG ADULT;

ADULT; ANEUPLOIDY; CHROMOSOME DISORDERS; FEMALE; FETUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; PREGNANCY; PRENATAL DIAGNOSIS; YOUNG ADULT;

EID: 84955301956     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0146997     Document Type: Article

References (37)

1. Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997; 350(9076):485-487 PMID: 9274585
2. Chiu RW, Akolekar R, Zheng YW, Leung TY, Sun H, Chan KC, et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ. 2011;342:c7401. doi: 10.1136/bmj.c7401 PMID: 21224326
3. Jeon YJ, Zhou Y, Li Y, Guo Q, Chen J, Quan S, et al. The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform. PLoS One. 2014; 9(10):e110240. doi: 10.1371/journal.pone.0110240 PMID: 25329639
4. Bianchi DW, Parker RL, Wentworth J, Madankumar R, Saffer C, Das AF, et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014; 370(9):799-808. doi: 10.1056/NEJMoa1311037 PMID: 24571752
5. Tsui NB, Kadir RA, Chan KC, Chi C, Mellars G, Tuddenham EG, et al. Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood. 2011; 117 (13):3684-3691. doi: 10.1182/blood-2010-10-310789 PMID: 21263151
6. Niba ET, Tran VK, Tuan-Pham LA, Vu DC, Nguyen NK, Ta VT, et al. Validation of ambiguous MLPA results by targeted next-generation sequencing discloses a nonsense mutation in the DMD gene. Clin Chim Acta. 2014; 436:155-159. doi: 10.1016/j.cca.2014.05.018 PMID: 24892813
7. Liao GJ, Lun FM, Zheng YW, Chan KC, Leung TY, Lau TK, 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. doi: 10.1373/clinchem.2010.154336 PMID: 21078840
8. Finning K, Martin P, Summers J, Massey E, Poole G, Daniels G. 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):816-818. doi: 10.1136/bmj.39518.463206.25 PMID: 18390496
9. Jiang P, Chan KC, Liao GJ, Zheng YW, Leung TY, Chiu RW, et al. FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics. 2012; 28(22):2883-2890. doi: 10.1093/bioinformatics/bts549 PMID: 22962347
10. Hudecova I, Sahota D, Heung MM, Jin Y, Lee WS, Leung TY, et al. Maternal plasma fetal DNA fractions in pregnancies with low and high risks for fetal chromosomal aneuploidies. PLoS One. 2014; 9(2):e88484. doi: 10.1371/journal.pone.0088484 PMID: 24586333
11. Chiu RW, Poon LL, Lau TK, Leung TN, Wong EM, Lo YM. Effects of blood-processing protocols on fetal and total DNA quantification in maternal plasma. Clin Chem. 2001; 47(9):1607-1613. PMID: 11514393
12. Zeybek YG, Gunel T, Benian A, Aydinli K, Kaleli S. Clinical evaluations of cell-free fetal DNA quantities in pre-eclamptic pregnancies. J Obstet Gynaecol Res. 2013; 39(3):632-640. doi: 10.1111/j.1447-0756.2012.02011.x PMID: 23107423
13. Chan KC, Zhang J, Hui AB, Wong N, Lau TK, Leung TN, et al. Size distributions of maternal and fetal DNA in maternal plasma. Clin Chem. 2004; 50(1):88-92. PMID: 14709639
14. Lun FM, Chiu RW, Chan KC, Leung TY, Lau TK, Lo YM. Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. Clin Chem. 2008; 54(10):1664-1672. doi: 10.1373/clinchem.2008.111385 PMID: 18703764
15. Nygren AO, Dean J, Jensen TJ, Kruse S, Kwong W, van den Boom D, et al. Quantification of fetal DNA by use of methylation-based DNA discrimination. Clin Chem. 2010; 56(10):1627-1635. doi: 10.1373/clinchem.2010.146290 PMID: 20729299
16. Manokhina I, Singh TK, Penaherrera MS, Robinson WP. Quantification of cell-free DNA in normal and complicated pregnancies: overcoming biological and technical issues. PLoS One. 2014; 9(7):e101500. doi: 10.1371/journal.pone.0101500 PMID: 24987984
17. Ehrich M, Deciu C, Zwiefelhofer T, Tynan JA, Cagasan L, Tim R, et al. Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting. Am J Obstet Gynecol. 2011; 204(3):201-205.
18. Palomaki GE, Deciu C, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, 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. doi: 10.1038/gim.2011.73 PMID: 22281937
19. McCullough RM, Almasri EA, Guan X, Geis JA, Hicks SC, Mazloom AR, et al. Non-invasive prenatal chromosomal aneuploidy testing - clinical experience: 100,000 clinical samples. PLoS One. 2014; 9 (10):e109173. doi: 10.1371/journal.pone.0109173 PMID: 25289665
20. Committee Opinion No. 545: Noninvasive prenatal testing for fetal aneuploidy. Obstet Gynecol. 2012; 120(6):1532-1534. doi: 10.1097/01.AOG.0000423819.85283.f4 PMID: 23168792
21. Gregg AR, Gross SJ, Best RG, Monaghan KG, Bajaj K, Skotko BG, et al. ACMG statement on noninvasive prenatal screening for fetal aneuploidy. Genet Med. 2013; 15(5):395-398. doi: 10.1038/gim.2013.29 PMID: 23558255
22. Benn P, Borell A, Chiu R, Cuckle H, Dugoff L, Faas B, et al. Position statement from the Aneuploidy Screening Committee on behalf of the Board of the International Society for Prenatal Diagnosis. Prenat Diagn. 2013; 33(7):622-629. doi: 10.1002/pd.4139 PMID: 23616385
23. Yu SC, Chan KC, Zheng YW, Jiang P, Liao GJ, Sun H, et al. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proc Natl Acad Sci U S A. 2014; 111(23):8583-8588. doi: 10.1073/pnas.1406103111 PMID: 24843150
24. Norton ME, Brar H, Weiss J, Karimi A, Laurent LC, Caughey AB, et al. Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am J Obstet Gynecol. 2012; 207(2):131-137.
25. Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, Ehrich M, et al. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med. 2011; 13(11):913-920.
26. Tsui NB, Jiang P, Chow KC, Su X, Leung TY, Sun H, et al. High resolution size analysis of fetal DNA in the urine of pregnant women by paired-end massively parallel sequencing. PLoS One. 2012; 7(10): e48319. doi: 10.1371/journal.pone.0048319 PMID: 23118982
27. Chan KC, Zhang J, Hui AB, Wong N, Lau TK, Leung TN, et al. Size distributions of maternal and fetal DNA in maternal plasma. Clin Chem. 2004; 50(1):88-92. PMID: 14709639
28. Yu SC, Chan KC, Zheng YW, Jiang P, Liao GJ, Sun H, et al. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proc Natl Acad Sci U S A. 2014; 111(23):8583-8588. doi: 10.1073/pnas.1406103111 PMID: 24843150
29. Yu SC, Lee SW, Jiang P, Leung TY, Chan KC, Chiu RW, et al. High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing. Clin Chem. 2013; 59(8):1228-1237. doi: 10.1373/clinchem.2013.203679 PMID: 23603797
30. Han R, Zhong W, Zhao J, Zhang L, Xia Y, Wang H, et al. Comparison of EGFR mutation status in paired pre- and post-chemotherapy serum for advanced pulmonary adenocarcinoma. Zhongguo Fei Ai Za Zhi. 2011; 14(2):127-131. doi: 10.3779/j.issn.1009-3419.2011.02.04 PMID: 21342642
31. Chiu RW, Chan KC, Gao Y, Lau VY, Zheng W, Leung TY, 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; 105(51):20458-20463. doi: 10.1073/pnas.0810641105 PMID: 19073917
32. Ashoor G, Syngelaki A, Poon LC, Rezende JC, Nicolaides KH. Fetal fraction in maternal plasma cell-free DNA at 11-13 weeks' gestation: relation to maternal and fetal characteristics. Ultrasound Obstet Gynecol. 2013; 41(1):26-32. doi: 10.1002/uog.12331 PMID: 23108725
33. Shi X, Zhang Z, Cram DS, Liu C. Feasibility of noninvasive prenatal testing for common fetal aneuploidies in an early gestational window. Clin Chim Acta. 2015; 439:24-28. doi: 10.1016/j.cca.2014.09.032 PMID: 25286007
34. Norton ME, Brar H, Weiss J, Karimi A, Laurent LC, Caughey AB, et al. Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am J Obstet Gynecol. 2012; 207(2):131-137.
35. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. Clin Chem. 2010; 56(8):1279-1286. doi: 10.1373/clinchem.2010.144188 PMID: 20558635
36. Nicolaides KH. Screening for fetal aneuploidies at 11 to 13 weeks. Prenat Diagn. 2011; 31(1):7-15. doi: 10.1002/pd.2637 PMID: 21210475
37. Ashoor G, Poon L, Syngelaki A, Mosimann B, Nicolaides KH. Fetal fraction in maternal plasma cell-free DNA at 11-13 weeks' gestation: effect of maternal and fetal factors. Fetal Diagn Ther. 2012; 31(4):237-243. doi: 10.1159/000337373 PMID: 22572044