Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management

European Journal of Human Genetics

Volumn 23, Issue 10, 2015, Pages 1286-1293

  Bayindir, Baran ^a,b   Dehaspe, Luc ^a   Brison, Nathalie ^a   Brady, Paul ^a   Ardui, Simon ^a   Kammoun, Molka ^a   Van Der Veken, Lars ^c   Lichtenbelt, Klaske ^c   Van Den Bogaert, Kris ^a   Van Houdt, Jeroen ^a   Peeters, Hilde ^a   Van Esch, Hilde ^a   De Ravel, Thomy ^a   Legius, Eric ^a   Devriendt, Koen ^a   Vermeesch, Joris R ^a  

^a UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^b UNIVERSITY OF PAVIA   (Italy)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANEUPLOIDY; ARTICLE; AUTOSOMAL DISORDER; CHORION VILLUS SAMPLING; CHROMOSOME 13; CHROMOSOME 15; CHROMOSOME 16; CHROMOSOME 18; CHROMOSOME 21; CHROMOSOME 7; FALSE POSITIVE RESULT; FETAL ANEUPLOIDY; FETUS KARYOTYPING; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; MICROARRAY ANALYSIS; NON INVASIVE PROCEDURE; PIPELINE ANALYSIS; PREDICTIVE VALUE; PREGNANCY; PREGNANT WOMAN; PRENATAL SCREENING; PRIORITY JOURNAL; RETROSPECTIVE STUDY; SENSITIVITY AND SPECIFICITY; TRISOMY 13; TRISOMY 18; TRISOMY 21; UNIPARENTAL DISOMY; VALIDATION STUDY; CHROMOSOME ABERRATION; CHROMOSOME DISORDER; DOWN SYNDROME; FEMALE; FETUS; GENETIC SCREENING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN CHROMOSOME; PATHOLOGY; PLACENTA; PRENATAL DIAGNOSIS; PROCEDURES; TRISOMY;

ANEUPLOIDY; CHROMOSOME ABERRATIONS; CHROMOSOME DISORDERS; CHROMOSOMES, HUMAN; CHROMOSOMES, HUMAN, PAIR 18; DOWN SYNDROME; FEMALE; FETUS; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PLACENTA; PREGNANCY; PRENATAL DIAGNOSIS; RETROSPECTIVE STUDIES; TRISOMY;

EID: 84944161591     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.282     Document Type: Article

References (52)

1. Lo YM, Corbetta NChamberlain PF et al: Presence of fetal DNA in maternal plasma and serum. Lancet 1997; 350: 485-487.
2. Chiu RW, Chan KC, 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: 20458-20463.
3. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR: Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA 2008; 105: 16266-16271.
4. Ashoor G, Syngelaki A, Wagner M, Birdir C, Nicolaides KH: Chromosome-selective sequencing of maternal plasma cell-free DNA for first-trimester detection of trisomy 21 and trisomy 18. Am J Obstet Gynecol 2012; 206: 322-325.
5. Bianchi DW, Platt LD, Goldberg JD, Abuhamad AZ, Sehnert AJ, Rava RP: Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol 2012; 119: 890-901.
6. Chiu RW, Akolekar R, Zheng YW et al: Non-invasive prenatal assessment of trisomy
7. by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011; 342: c7401.
8. Dan S, Wang W, Ren J et al: Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn 2012; 32: 1225-1232.
9. Ehrich M, Deciu C, Zwiefelhofer T 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: 205-211.
10. Nicolaides KH, Syngelaki A, Ashoor G, Birdir C, Touzet G: Noninvasive prenatal testing for fetal trisomies in a routinely screened first-trimester population. Am J Obstet Gynecol 2012; 207: 374-376.
11. Norton ME, Brar H, Weiss J 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: 137-138.
12. 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: 296-305.
13. 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: 913-920.
14. Sehnert AJ, Rhees B, Comstock D et al: Optimal detection of fetal chromosomal abnormalities by massively parallel DNA sequencing of cell-free fetal DNA from maternal blood. Clin Chem 2011; 57: 1042-1049.
15. Sparks AB, Struble CA, Wang ET, Song K, Oliphant A: Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. Am J Obstet Gynecol 2012; 206: 319.
16. Sparks AB, Wang ET, Struble CA et al: Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenat Diagn 2012; 32: 3-9.
17. Bianchi DW, Parker RL, Wentworth J et al: DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med 2014; 370: 799-808.
18. Chiu RW, Cantor CR, Lo YM: Non-invasive prenatal diagnosis by single molecule counting technologies. Trends Genet 2009; 25: 324-331.
19. Fan HC, Quake SR: Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics. PLoS One 2010; 5: e10439.
20. Yeang CH, Ma GC, Hsu HW et al: Genome-wide normalized score: a novel algorithm to detect fetal trisomy 21 during non-invasive prenatal testing. Ultrasound Obstet Gynecol 2014; 44: 25-30.
21. Straver R, Sistermans EA, Holstege H, Visser A, Oudejans CB, Reinders MJ: WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme. Nucleic Acids Res 2014; 42: e31.
22. Yao H, Zhang L, Zhang H et al: Noninvasive prenatal genetic testing for fetal aneuploidy detects maternal trisomy X. Prenat Diagn 2012; 32: 1114-1116.
23. Osborne CM, Hardisty E, Devers P et al: Discordant noninvasive prenatal testing results in a patient subsequently diagnosed with metastatic disease. Prenat Diagn 2013; 33: 609-611.
24. Choi H, Lau TK, Jiang FM et al: Fetal aneuploidy screening by maternal plasma DNA sequencing: 'false positive' due to confined placental mosaicism. Prenat Diagn 2013; 33: 198-200.
25. Futch T, Spinosa J, Bhatt S, de FE, Rava RP, Sehnert AJ: Initial clinical laboratory experience in noninvasive prenatal testing for fetal aneuploidy from maternal plasma DNA samples. Prenat Diagn 2013; 33: 569-574.
26. Gao Y, Stejskal D, Jiang F, Wang W: False-negative trisomy 18 non-invasive prenatal test result due to 48,XXX,+18 placental mosaicism. Ultrasound Obstet Gynecol 2014; 43: 477-478.
27. Hahnemann JM, Vejerslev LO: Accuracy of cytogenetic findings on chorionic villus sampling (CVS)-diagnostic consequences of CVS mosaicism and non-mosaic discrepancy in centres contributing to EUCROMIC 1986-1992. Prenat Diagn 1997; 17: 801-820.
28. Hahnemann JM, Vejerslev LO: European collaborative research on mosaicism in CVS (EUCROMIC)-fetal and extrafetal cell lineages in 192 gestations with CVS mosaicism involving single autosomal trisomy. Am J Med Genet 1997; 70: 179-187.
29. Hall AL, Drendel HM, Verbrugge JL et al: Positive cell-free fetal DNA testing for trisomy
30. reveals confined placental mosaicism. Genet Med 2013; 15: 729-732.
31. Lau TK, Jiang FM, Stevenson RJ et al: Secondary findings from non-invasive prenatal testing for common fetal aneuploidies by whole genome sequencing as a clinical service. Prenat Diagn 2013; 33: 602-608.
32. Mao J, Wang T, Wang BJ et al: Confined placental origin of the circulating cell free fetal DNA revealed by a discordant non-invasive prenatal test result in a trisomy 18 pregnancy. Clin Chim Acta 2014; 433C: 190-193.
33. Mennuti MT, Cherry AM, Morrissette JJ, Dugoff L: Is it time to sound an alarm about false-positive cell-free DNA testing for fetal aneuploidy? Am J Obstet Gynecol 2013; 209: 415-419.
34. Pan M, Li FT, Li Y et al: Discordant results between fetal karyotyping and non-invasive prenatal testing by maternal plasma sequencing in a case of uniparental disomy 21 due to trisomic rescue. Prenat Diagn 2013; 33: 598-601.
35. Srebniak MI, Diderich KE, Noomen P, Dijkman A, de VF, Opstal DV: Abnormal NIPT results concordant with the karyotype of the cytotrophoblast, but not reflecting the abnormal fetal karyotype. Ultrasound Obstet Gynecol. 2014; 44: 109-111.
36. Wang Y, Zhu J, Chen Y et al: Two cases of placental T21 mosaicism: challenging the detection limits of non-invasive prenatal testing. Prenat Diagn 2013; 33: 1207-1210.
37. Brady PD, Delle CB, Christenhusz G et al: A prospective study of the clinical utility of prenatal chromosomal microarray analysis in fetuses with ultrasound abnormalities and an exploration of a framework for reporting unclassified variants and risk factors. Genet Med 2013; 16469-476.
38. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-1760.
39. McKenna A, Hanna M, Banks E et al: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
40. Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK: False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics 2011; 27: 2144-2146.
41. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M: An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57-74.
42. Chen EZ, Chiu RW, Sun H et al: Noninvasive prenatal diagnosis of fetal trisomy
43. and trisomy 13 by maternal plasma DNA sequencing. PLoS One 2011; 6: e21791.
44. Rava RP, Srinivasan A, Sehnert AJ, Bianchi DW: Circulating fetal cell-free DNA fractions differ in autosomal aneuploidies and monosomy X. Clin Chem 2014; 60: 243-250.
45. Srinivasan A, Bianchi DW, Huang H, Sehnert AJ, Rava RP: Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma. Am J Hum Genet. 2013; 92: 167-176.
46. Yu SC, Jiang P, Choy KW et al: Noninvasive prenatal molecular karyotyping from maternal plasma. PLoS One 2013; 8: e60968.
47. Chen S, Lau TK, Zhang C et al: A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenat Diagn 2013; 33: 584-590.
48. Peters D, Chu T, Yatsenko SA et al: Noninvasive prenatal diagnosis of a fetal microdeletion syndrome. N Engl J Med 2011; 365: 1847-1848.
49. Jensen TJ, Dzakula Z, Deciu C, van den Boom D, Ehrich M: Detection of microdeletion 22q11.2 in a fetus by next-generation sequencing of maternal plasma. Clin Chem 2012; 58: 1148-1151.
50. Lau TK, Cheung SW, Lo PS et al: Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center. Ultrasound Obstet Gynecol 2014; 43: 254-264.
51. Chu T, Yeniterzi S, Rajkovic A et al: High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm. Prenat Diagn 2014; 34: 469-477.
52. Verweij EJ, de Boer MA, Oepkes D: Non-invasive prenatal testing for trisomy 13; more harm than good? Ultrasound Obstet Gynecol. 2014; 44: 112-114.