Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- And informatics-based approach

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Hall, Megan P ^a   Hill, Matthew ^a   Zimmermann, Bernhard ^a   Sigurjonsson, Styrmir ^a   Westemeyer, Margaret ^a   Saucier, Jennifer ^a   Demko, Zachary ^a   Rabinowitz, Matthew ^a  

^a NATERA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ADULT; ANEUPLOIDY; ARTICLE; CASE CONTROL STUDY; CHROMOSOME 13; CHROMOSOME 18; CHROMOSOME 21; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; DNA ISOLATION; DNA SEQUENCE; FEMALE; FETUS; GENE AMPLIFICATION; GENE DOSAGE; GENE IDENTIFICATION; GENETIC SCREENING; HUMAN; INFORMATION SCIENCE; MATERNAL BLOOD; MAXIMUM LIKELIHOOD METHOD; MULTIPLEX POLYMERASE CHAIN REACTION; NON INVASIVE PROCEDURE; PRENATAL SCREENING; SINGLE NUCLEOTIDE POLYMORPHISM; TRISOMY 13; X CHROMOSOME; Y CHROMOSOME; ALGORITHM; BIOLOGY; CHROMOSOME DISORDERS; GENETICS; PREGNANCY; PRENATAL DIAGNOSIS; PROCEDURES; TRISOMY;

ALGORITHMS; CASE-CONTROL STUDIES; CHROMOSOME DISORDERS; CHROMOSOMES, HUMAN, PAIR 13; COMPUTATIONAL BIOLOGY; FEMALE; GENETIC TESTING; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; PRENATAL DIAGNOSIS; TRISOMY;

EID: 84900537983     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096677     Document Type: Article

References (49)

1. Carey JC (2010) Trisomy 18 and Trisomy 13 Syndromes. In: Cassidy SB, Allanson JE, editors. Management of Genetic Syndromes. Hoboken, NJ: John Wiley & Sons, Inc.
2. Lakovschek IC, Streubel B, Ulm B (2011) Natural outcome of trisomy 13, trisomy 18, and triploidy after prenatal diagnosis. American Journal of Medical Genetics, Part A 155: 2626-2633.
3. Crider KS, Olney RS, Cragan JD (2008) Trisomies 13 and 18: Population prevalences, characteristics, and prenatal diagnosis, metropolitan Atlanta, 1994-2003. American Journal of Medical Genetics, Part A 146A: 820-826. (Pubitemid 351499785)
4. Parker MJ, Budd JL, Draper ES, Young ID (2003) Trisomy 13 and trisomy 18 in a defined population: epidemiological, genetic and prenatal observations. Prenatal Diagnosis 23: 856-860. (Pubitemid 37279874)
5. Forrester MB, Merz RD (2003) First-year mortality rates for selected birth defects, Hawaii, 1986-1999. American Journal of Medical Genetics, Part A 119A: 311-318. (Pubitemid 37063861)
6. Vendola C, Canfield M, Daiger SP, Gambello M, Hashmi SS, et al. (2010) Survival of Texas infants born with trisomies 21, 18, and 13. American Journal of Medical Genetics, Part A 152A: 360-366.
7. Egan JF, Benn P, Borgida AF, Rodis JF, Campbell WA, et al. (2000) Efficacy of screening for fetal Down syndrome in the United States from 1974 to 1997. Obstetrics and Gynecology 96: 979-985.
8. Buyse ML (1990) Birth Defects Encyclopedia. Cambridge, MA: Blackwell Scientific Publications.
9. Griffith CB, Vance GH, Weaver DD (2009) Phenotypic variability in trisomy 13 mosaicism: two new patients and literature review. American Journal of Medical Genetics, Part A 149A: 1346.
10. Pont SJ, Robbins JM, Bird TM, Gibson JB, Cleves MA, et al. (2006) Congenital malformations among liveborn infants with trisomies 18 and 13. American Journal of Medical Genetics, Part A 140: 1749-1756. (Pubitemid 44148236)
11. Patau K, Smith DW, Therman E, Inhorn SL, Wagner HP (1960) Multiple congenital anomaly caused by an extra autosome. Lancet 275: 790-793.
12. Hassold TJ, Jacobs PA (1984) Trisomy in man. Annual Review of Genetics 18: 69-97.
13. Baty BJ, Blackburn BL, Carey JC (1994) Natural history of trisomy 18 and trisomy 13: I. Growth, physical assessment, medical histories, survival, and recurrence risk. American Journal of Medical Genetics, Part A 49: 175-188. (Pubitemid 24018129)
14. Mankinen CB, Sears JW (1976) Trisomy 13 in a female over 5 years of age. Journal of Medical Genetics 13: 157-161.
15. Cowen JM, Walker S, Harris F (1979) Trisomy 13 and extended survival. Journal of Medical Genetics 16: 155-157. (Pubitemid 9164913)
16. Redheendran R, Neu RL, Bannerman RM (1981) Long survival in trisomy-13-syndrome: 21 cases including prolonged survival in two patients 11 and 19 years old. American Journal of Medical Genetics, Part A 8: 167-172. (Pubitemid 11075560)
17. Boyd PA, Lindenbaum RH, Redman C (1987) Pre-eclampsia and trisomy 13: a possible association. Lancet 2: 425-427.
18. Spencer K, Nicolaides KH (2002) A first trimester trisomy 13/trisomy 18 risk algorithm combining fetal nuchal translucency thickness, maternal serum free beta-hCG and PAPP-A. Prenatal Diagnosis 22: 877-879. (Pubitemid 35175986)
19. (2007) ACOG Practice Bulletin No. 88, December 2007. Invasive prenatal testing for aneuploidy. Obstet Gynecol 110: 1459-1467.
20. Palomaki GE, Deciu C, Kloza EM, Lambert-Messerlian GM, Haddow JE, et al. (2012) DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med 14: 296-305.
21. Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, et al. (2011) DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med 13: 913-920.
22. Bianchi DW, Platt LD, Goldberg JD, Abuhamad AZ, Sehnert AJ, et al. (2012) Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol 119: 890-901.
23. Sparks AB, Struble CA, Wang ET, Song K, Oliphant A (2012) 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 206: 319. e311-319.
24. Sparks AB, Wang ET, Struble CA, Barrett W, Stokowski R, et al. (2012) Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenat Diagn 32: 3-9.
25. Ashoor G, Syngelaki A, Wagner M, Birdir C, Nicolaides KH (2012) Chromosome-selective sequencing of maternal plasma cell-free DNA for first-trimester detection of trisomy 21 and trisomy 18. Am J Obstet Gynecol 206: 322. e321-325.
26. Ashoor G, Syngelaki A, Wang E, Struble C, Oliphant A, et al. (2013) Trisomy 13 detection in the first trimester of pregnancy using a chromosome-selective cell-free DNA analysis method. Ultrasound Obstet Gynecol 41: 21-25.
27. Chen EZ, Chiu RW, Sun H, Akolekar R, Chan KC, et al. (2011) Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 6: e21791.
28. Zimmermann B, Hill M, Gemelos G, Demko Z, Banjevic M, et al. (2012) Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenat Diagn 32: 1233-1241.
29. Nicolaides KH, Syngelaki A, Gil M, Atanasova V, Markova D (2013) Validation of targeted sequencing of single-nucleotide polymorphisms for non-invasive prenatal detection of aneuploidy of chromosomes 13, 18, 21, X, and Y. Prenat Diagn 33: 575-579.
30. Samango-Sprouse C, Banjevic M, Ryan A, Sigurjonsson S, Zimmermann B, et al. (2013) SNP-based non-invasive prenatal testing detects sex chromosome aneuploidies with high accuracy. Prenat Diagn 33: 643-649.
31. Zimmermann B, Hill M, Lacroute P, Dodd M (2013) Highly multiplex PCR methods and compositions. Unites States: Natera, Inc.
32. Rabinowitz M, Gemelos G, Banjevic M, Ryan A, Demko Z, et al. (2012) Methods for non-invasive prenatal ploidy calling. In: World Intellectual Property Organization IB, editor. G06F 19/22 (2011.01) G01N 33/48 (2006.01) ed. United States.
33. Zimmermann B, Hill M, Lacroute P, Dodd M (2013) Highly multiplexed PCR methods and compositions. In: Office USP, editor. C12Q 1/68 (2006.01) ed. United States.
34. Rabinowitz M, Banjevic M, Demko Z, Johnson DS (2013) Method for determining the number of copies of a chromosome in the genome of a target individual using genetic data from genetically related individuals. In: Office USP, editor. United States.
35. Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 29: 308-311. (Pubitemid 32054478)
36. Norton ME, Brar H, Weiss J, Karimi A, Laurent LC, et al. (2012) 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 207: 137. e131-138.
37. Mazloom AR, Dzakula Z, Oeth P, Wang H, Jensen T, et al. (2013) Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell-free DNA from maternal plasma. Prenat Diagn 33: 591-597.
38. Nicolaides KH, Syngelaki A, Ashoor G, Birdir C, Touzet G (2012) Noninvasive prenatal testing for fetal trisomies in a routinely screened first-trimester population. Am J Obstet Gynecol 207: 374. e371-376.
39. Rasmussen SA, Wong LYC, Yang QY, May KM, Friedman JM (2003) Population-based analysis of mortality in trisomy 13 and trisomy 18. Pediatrics 111: 777-784.
40. Tsukada K, Imataka G, Suzumura H, Arisaka O (2012) Better prognosis in newborns with trisomy 13 who received intensive treatments: a retrospective study of 16 patients. Cell Biochemistry and Biophysics 63: 191-198.
41. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR (2008) Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A 105: 16266-16271.
42. Chiu RW, Sun H, Akolekar R, Clouser C, Lee C, et al. (2010) Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of trisomy 21. Clin Chem 56: 459-463.
43. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41: 1061-1067.
44. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.
45. Liao GJ, Chan KC, Jiang P, Sun H, Leung TY, et al. (2012) Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 7: e38154.
46. Wegrzyn P, Faro C, Falcon O, Peralta CF, Nicolaides KH (2005) Placental volume measured by three-dimensional ultrasound at 11 to 13+6 weeks of gestation: relation to chromosomal defects. Ultrasound Obstet Gynecol 26: 28-32. (Pubitemid 41537008)
47. McFadden DE, Kalousek DK (2005) Two different phenotypes of fetuses with chromosomal triploidy: Correlation with parental origin of the extra haploid set. American Journal of Medical Genetics, Part A 38: 535-538.
48. Nicolaides K, Syngelaki A, Gil M, Quezada M, Zinevich Y (2013) Prenatal Detection of Fetal Triploidy from Cell-Free DNA Testing in Maternal Blood. Fetal Diagnosis and Therapy.
49. Choi H, Lau TK, Jiang FM, Chan MK, Zhang HY, et al. (2013) Fetal aneuploidy screening by maternal plasma DNA sequencing: 'false positive' due to confined placental mosaicism. Prenat Diagn 33: 198-200.