SNP-based non-invasive prenatal testing detects sex chromosome aneuploidies with high accuracy

Prenatal Diagnosis

Volumn 33, Issue 7, 2013, Pages 643-649

  Samango Sprouse, Carole ^a,c   Banjevic, Milena ^b   Ryan, Allison ^b   Sigurjonsson, Styrmir ^b   Zimmermann, Bernhard ^b   Hill, Matthew ^b   Hall, Megan P ^b   Westemeyer, Margaret ^b   Saucier, Jennifer ^b   Demko, Zachary ^b   Rabinowitz, Matthew ^b  

^a GEORGE WASHINGTON UNIVERSITY SCHOOL OF MEDICINE AND HEALTH SCIENCES   (United States)

^b NATERA INC   (United States)

^c Neurodevelopmental Diagnostic Center for Young Children   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME 13; CHROMOSOME 18; CHROMOSOME 21; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DNA ISOLATION; GENE LOCUS; GENE SEQUENCE; HUMAN; KARYOTYPE 45,X; KARYOTYPE 47,XXY; KARYOTYPE 47,XYY; MATERNAL PLASMA; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEX CHROMOSOME ABERRATION; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; Y CHROMOSOME;

ANEUPLOIDY; CHROMOSOMES, HUMAN, X; CHROMOSOMES, HUMAN, Y; DNA; FEMALE; GENETIC TESTING; GESTATIONAL AGE; HUMANS; MALE; MONOSOMY; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; PRENATAL DIAGNOSIS; SENSITIVITY AND SPECIFICITY; SEX CHROMOSOME ABERRATIONS; TRISOMY;

EID: 84880041032     PISSN: 01973851     EISSN: 10970223     Source Type: Journal    
DOI: 10.1002/pd.4159     Document Type: Article

References (47)

1. Nielsen J, Wohlert M. Chromosome abnormalities found among 34, 910 newborn children: results from a 13-year incidence study in Arhus, Denmark. Hum Genet 1991;87:81-3.
2. Ranke MB, Saenger P. Turner's syndrome. Lancet 2001;358:309-14.
3. Kagan KO, Avgidou K, Molina FS, et al. Relation between increased fetal nuchal translucency thickness and chromosomal defects. Obstet Gynecol 2006;107:6-10.
4. Saenger P. Turner's syndrome. New Engl J Med 1996;335:1749-54.
5. Samango-Sprouse CA, Sadeghin T, Mitchell FL, et al. Positive effects of short course androgen therapy on the neurodevelopmental outcome in boys with 47, XXY syndrome at 36 and 72 months of age. Am J Med Genet A 2013;161(3):501-8.
6. Samango-Sprouse CA, Gropman AL, Sadeghin T, et al. Effects of short-course androgen therapy on the neurodevelopmental profile of infants and children with 49, XXXXY syndrome. Acta Paediatr 2011;100:861-5.
7. Simpson JL, Elias S. Fetal cells in maternal blood: overview and historical perspective. Ann N Y Acad Sci 1994;7:1-8.
8. Kazakov VI, Bozhkov VM, Linde VA, et al. Extracellular DNA in the blood of pregnant women. Tsitologia 1995;37:232-6.
9. Lo YM, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet 1997;350:485-7.
10. Fan HC, Blumenfeld YJ, Chitkara U, et al. Non-invasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA 2008;105:266-71.
11. Chiu RW, Chan KC, Gao Y, et al. Non-invasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 2008;105:20458-63.
12. Ehrich M, Deciu C, Zwiefelhofer T, et al. Non-invasive 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.e1-205.e11.
13. 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;57:92-101.
14. 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;13:913-20.
15. Chen EZ, Chiu RW, Sun H, et al. Non-invasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 2011;6(7):e21791.
16. 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;57:1042-49.
17. 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. doi:10.1038/gim.2011.73.
18. Bianchi DW, Platt LD, Goldberg JD. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol 2012;119:890-901.
19. 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;32:1-7.
20. Sparks AB, Struble CA, Wang ET, et al. Non-invasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. Am J Ob Gyn 2012;206:319e.1-9.
21. Ashoor G, Syngelaki A, Wagner M, et al. Chromosome-selective sequencing of maternal plasma cell-free DNA for first-trimester detection of trisomy 21 and trisomy 18. Am J Ob Gyn 2012;206:322.e1-5.
22. Chiu RW, Sun H, Akolekar R, et al. Maternal plasma DNA analysis with massively parallel sequencing by ligations for non-invasive prenatal diagnosis of trisomy 21. Clin Chem 2010;56:459-63.
23. Jiang F, Ren J, Chen F, et al. Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies. BMC Med Genomics 2012;5:57.
24. Ashoor G, Syngelaki A, Wang E, et al. Trisomy 13 detection in the first trimester of pregnancy using a chromosome-selective cell-free DNA analysis method. Ultrasound Obstet Gynecol 2013;41:21-5.
25. Futch T, Spinosa J, Bhatt S, et al. Initial clinical laboratory experience in noninvasive prenatal testing for fetal aneuploidy from maternal plasma DNA samples. Prenat Diagn 2013.doi:10.1002/pd.4123.
26. Mazloom AR, Džakula Ž, Wang H, et al. Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell-free DNA from maternal plasma. Prenat Diagn 2013. doi:10.1002/pd4127.
27. Alkan C, Kidd JM, Marques-Bonet T, et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 2009;41:1061-7.
28. Dohm JC, Lottaz C, Borodina T, et al. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acid Res 2008;36(16):e105.
29. Johnson DS, Gemelos G, Baner J, et al. Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-h protocol. Hum Reprod 2010; 25:1066-75.
30. Rabinowitz M, Gemelos G, Banjevic M et al. Methods for non-invasive prenatal ploidy calling. World Intellectual Property Organization Patent application WO/2011/146632; November 24, 2011.
31. Rabinowitz M, Gemelos G, Banjevic M, et al. Methods for non-invasive prenatal ploidy calling. World Intellectual Property Organization, patent application WO/2012/108920; August 16, 2012.
32. 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 Diag 2012;32:1-9.
33. Nicolaides KH, Syngelaki A, Gil M, Atanasova V, Markova D. 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 2013;33(6):575-9.
34. Nicolaides KH. Routine screening by maternal blood of DNA. Advances in Fetal Medicine Meeting; December 2013; London, UK.
35. http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/ProjHapmap.shtml
36. Sherry ST, Ward MH, Kholodov M, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308-11.
37. Simpson JL, Samango-Sprouse C. Prenatal diagnosis and 47, XXY. Am J Med Genet C Semin Med Genet 2013;163C:64-70.
38. Linglart A, Cabrol S, Berlier P, et al. Growth hormone treatment before the age of 4 years prevents short stature in young girls with Turner syndrome. Eur J Endocrinol 2011;164:891-7.
39. Bondy CA. Care of girls and women with Turner syndrome: a guideline of the Turner Syndrome Study Group. J Clin Endocrinol Metab 2007;92:10-25.
40. Hanton L, Axelrod L, Bakalov V, Bondy CA. The importance of estrogen replacement in young women with Turner syndrome. J Womens Health 2003;12:971-7.
41. Ferlin A, Zuccarello D, Zuccarello B, et al. Genetic alterations associated with cryptorchidism. JAMA 2008;300:2271-6.
42. Mehta A, Paduch DA. Klinefelter syndrome: an argument for early aggressive hormonal and fertility management. Fertil Steril 2012;98(5):274-83.
43. Liao GJ, Chan KC, Jiang P, et al. Non-invasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targets massively parallel sequencing of maternal plasma DNA. PLoS One 2012;7:e38154.
44. Chadwick B, Willard HF. Histone H2A variants and the inactive X chromosome: identification of a second macroH2A variant. Human Mol Genet 2001;10:1101-13.
45. Costanzi C, Pehrson JR. Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 1998;393:599-601.
46. Chadwick BP, Willard HF. A novel chromatin proteins, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol 2001;152:375-84.
47. Bischoff FZ, Lewis DE, Simpson JL. Cell-free fetal DNA in maternal blood: kinetics, source and structure. Hum Reprod Update 2005;11:59-67.