Noninvasive fetal genome sequencing: A primer

Prenatal Diagnosis

Volumn 33, Issue 6, 2013, Pages 547-554

  Snyder, Matthew W ^a   Simmons, LaVone E ^b   Kitzman, Jacob O ^a   Santillan, Donna A ^c   Santillan, Mark K ^c   Gammill, Hilary S ^b,d   Shendure, Jay ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF IOWA HOSPITALS AND CLINICS   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FETAL CELL FREE DNA; UNCLASSIFIED DRUG;

DNA DETERMINATION; FETUS; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; NON INVASIVE PROCEDURE; NONINVASIVE FETAL WHOLE GENOME SEQUENCING; PLASMA; PREGNANT WOMAN; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; REVIEW;

DNA; FEMALE; FETUS; GENETIC TESTING; GENOME, HUMAN; HUMANS; PREGNANCY; PRENATAL DIAGNOSIS; PROFESSIONAL PRACTICE; SEQUENCE ANALYSIS, DNA; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84878144399     PISSN: 01973851     EISSN: 10970223     Source Type: Journal    
DOI: 10.1002/pd.4097     Document Type: Review

References (46)

1. Merkatz IR, Nitowsky HM, Macri JN, Johnson WE. An association between low maternal serum alpha-fetoprotein and fetal chromosomal abnormalities. Am J Obstet Gynecol 1984;148:886-94.
2. ACOG Committee on Practice Bulletins. ACOG Practice Bulletin No. 77: screening for fetal chromosomal abnormalities. Obstet Gynecol 2007;109:217-27.
3. Lapaire O, Holzgreve W, Oosterwijk JC, et al. Georg Schmorl on trophoblasts in the maternal circulation. Placenta 2007;28:1-5.
4. Schröder J, la Chapelle De A. Fetal lymphocytes in the maternal blood. Blood 1972;39:153-62.
5. Herzenberg LA, Bianchi DW, Schröder J, et al. Fetal cells in the blood of pregnant women: detection and enrichment by fluorescence-activated cell sorting. Proc Natl Acad Sci USA 1979;76:1453-5.
6. Lo YM. Noninvasive prenatal diagnosis using fetal cells in maternal blood. Methods Mol Med 1996;5:237-44.
7. Bianchi DW, Simpson JL, Jackson LG, et al. Fetal gender and aneuploidy detection using fetal cells in maternal blood: analysis of NIFTY I data. Prenat Diagn 2002;22:609-15.
8. Lo YMD, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet 1997;350:485-7.
9. Shendure J, Aiden EL. The expanding scope of DNA sequencing. Nat Biotechnol 2012;30:1084-94.
10. American College of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 545: noninvasive prenatal testing for fetal aneuploidy. Obstet Gynecol 2012;120:1532-4.
11. Reddy UM, Page GP, Saade GR, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med 2012;367:2185-93.
12. Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012;367:2175-84.
13. 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;2:61ra91.
14. Kitzman JO, Snyder MW, Ventura M, et al. Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med 2012;4:137ra76.
15. Fan HC, Gu W, Wang J, et al. Non-invasive prenatal measurement of the fetal genome. Nature 2012;487:320-4.
16. Tjoa ML, Cindrova-Davies T, Spasic-Boskovic O, et al. Trophoblastic oxidative stress and the release of cell-free feto-placental DNA. Am J Pathol 2006;169:400-4.
17. Fan HC, Blumenfeld YJ, Chitkara U, et al. Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. Clin Chem 2010;56:1279-86.
18. Poon LLM, Leung TN, Lau TK, et al. Differential DNA methylation between fetus and mother as a strategy for detecting fetal DNA in maternal plasma. Clin Chem 2002; 48:35-41.
19. Jiang P, Chan KCA, Liao GJW, et al. FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics 2012;28:2883-90.
20. Kitzman JO, MacKenzie AP, Adey A, et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol 2011;29:59-63.
21. Peters BA, Kermani BG, Sparks AB, et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 2012;487:190-5.
22. Yang H, Chen X, Wong WH. Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci USA 2011;108:12-7.
23. Ma L, Xiao Y, Huang H, et al. Direct determination of molecular haplotypes by chromosome microdissection. Nat Meth 2010;7:299-301.
24. Fan HC, Wang J, Potanina A, Quake SR. Whole-genome molecular haplotyping of single cells. Nat Biotechnol 2010;29:51-7.
25. Kong A, Frigge ML, Masson G, et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 2012;488:471-5.
26. Bell CJ, Dinwiddie DL, Miller NA, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011;3:65ra4-65ra4.
27. Ng SB, Turner EH, Robertson PD, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009;461:272-6.
28. O'Roak BJ, Vives L, Fu W, et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012;338:1619-22.
29. American College of Obstetricians and Gynecologists. ACOG Practice Bulletin No. 88, December 2007. Invasive prenatal testing for aneuploidy. Obstet Gynecol 2007;110:1459-67.
30. Kalousek DK, Dill FJ. Chromosomal mosaicism confined to the placenta in human conceptions. Science 1983;221:665-7.
31. 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 2012. doi:10.1002/pd.4024
32. 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;17:801-20.
33. Carroll SG, Davies T, Kyle PM, et al. Fetal karyotyping by chorionic villus sampling after the first trimester. Br J Obstet Gynaecol 1999;106:1035-40.
34. Engel E. A fascination with chromosome rescue in uniparental disomy: Mendelian recessive outlaws and imprinting copyrights infringements. Eur J Hum Genet 2006;14:1158-69.
35. Inbar-Feigenberg M, Choufani S, Cytrynbaum C, et al. Mosaicism for genome-wide paternal uniparental disomy with features of multiple imprinting disorders: diagnostic and management issues. Am J Med Genet 2012;161:13-20.
36. Filges I, Kang A, Klug V, et al. aCGH on chorionic villi mirrors the complexity of fetoplacental mosaicism in prenatal diagnosis. Prenat Diagn 2011;31:473-8.
37. Stetten G, Escallon CS, South ST, et al. Reevaluating confined placental mosaicism. Am J Med Genet 2004;131A:232-9.
38. Vago L, Perna SK, Zanussi M, et al. Loss of mismatched HLA in leukemia after stem-cell transplantation. N Engl J Med 2009;361:478-88.
39. Choate KA, Lu Y, Zhou J, et al. Mitotic recombination in patients with ichthyosis causes reversion of dominant mutations in KRT10. Science 2010;330:94-7.
40. Nelson JL. The otherness of self: microchimerism in health and disease. Trends Immunol 2012;33:421-7.
41. Tabor HK, Murray JC, Gammill HS, et al. Non-invasive fetal genome sequencing: opportunities and challenges. Am J Med Genet 2012.doi:10.1002/ajmg.a.35545
42. Fan HC, Blumenfeld YJ, Chitkara U, et al. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA 2008;105(42):16266-71.
43. 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.
44. Tynan JA, Angkachatchai V, Ehrich M, et al. Multiplexed analysis of circulating cell-free fetal nucleic acids for noninvasive prenatal diagnostic RHD testing. Am J Obstet Gynecol 2011;204(3):251.e1-e6.
45. 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.
46. Srinivasan A, Bianchi DW, Huang H, et al. Noninvasive Detection of Fetal Subchromosome Abnormalities via Deep Sequencing of Maternal Plasma. Am J Hum Genet 2013; 1-10.