Noninvasive whole-genome sequencing of a human fetus

Science Translational Medicine

Volumn 4, Issue 137, 2012, Pages

  Kitzman, Jacob O ^a   Snyder, Matthew W ^a   Ventura, Mario ^a,b   Lewis, Alexandra P ^a   Qiu, Ruolan ^a   Simmons, LaVone E ^c   Gammill, Hilary S ^c,d   Rubens, Craig E ^c,e   Santillan, Donna A ^f   Murray, Jeffrey C ^g   Tabor, Holly K ^c,h   Bamshad, Michael J ^a,c   Eichler, Evan E ^a,i   Shendure, Jay ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF BARI   (Italy)

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

^d Fred Hutchinson Cancer Research Center   (United States)

^e Global Alliance to Prevent Prematurity and Stillbirth   (United States)

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

^g UNIVERSITY OF IOWA   (United States)

^h SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

ⁱ HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; FEMALE; FETUS; GENE FREQUENCY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GESTATIONAL AGE; HAPLOTYPE; HETEROZYGOTE; HUMAN; MALE; MATERNAL PLASMA; MOTHER FETUS RELATIONSHIP; MUTATIONAL ANALYSIS; NON INVASIVE PROCEDURE; POINT MUTATION; PREDICTION; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; BLOOD; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; PREGNANCY;

DNA;

DNA; FEMALE; FETUS; GESTATIONAL AGE; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PREGNANCY; PRENATAL DIAGNOSIS;

EID: 84862118837     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.3004323     Document Type: Article

References (25)

1. A. O. H. Nygren, J. Dean, T. J. Jensen, S. Kruse, W. Kwong, D. van den Boom, M. Ehrich, Quantification of fetal DNA by use of methylation-based DNA discrimination. Clin. Chem. 56, 1627-1635 (2010).
2. Y. M. Lo, M. S. Tein, T. K. Lau, C. J. Haines, T. N. Leung, P. M. Poon, J. S. Wainscoat, P. J. Johnson, A. M. Chang, N. M. Hjelm, Quantitative analysis of fetal DNA in maternal plasma and serum: Implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet. 62, 768-775 (1998).
3. Y. M. Lo, J. Zhang, T. N. Leung, T. K. Lau, A. M. Chang, N. M. Hjelm, Rapid clearance of fetal DNA from maternal plasma. Am. J. Hum. Genet. 64, 218-224 (1999).
4. Y. M. Dennis Lo, R. W. K. Chiu, Prenatal diagnosis: Progress through plasma nucleic acids. Nat. Rev. Genet. 8, 71-77 (2007).
5. H. C. Fan, Y. J. Blumenfeld, U. Chitkara, L. Hudgins, S. R. Quake, Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc. Natl. Acad. Sci. U.S.A. 105, 16266-16271 (2008).
6. R. W. K. Chiu, K. C. A. Chan, Y. Gao, V. Y. M. Lau, W. Zheng, T. Y. Leung, C. H. F. Foo, B. Xie, N. B. Y. Tsui, F. M. F. Lun, B. C. Y. Zee, T. K. Lau, C. R. Cantor, Y. M. D. Lo, Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc. Natl. Acad. Sci. U.S.A. 105, 20458-20463 (2008).
7. Y. M. D. Lo, K. C. A. Chan, H. Sun, E. Z. Chen, P. Jiang, F. M. F. Lun, Y. W. Zheng, T. Y. Leung, T. K. Lau, C. R. Cantor, R. W. K. Chiu, Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci. Transl. Med. 2, 61ra91 (2010).
8. D. G. MacArthur, S. Balasubramanian, A. Frankish, N. Huang, J. Morris, K. Walter, L. Jostins, L. Habegger, J. K. Pickrell, S. B. Montgomery, C. A. Albers, Z. D. Zhang, D. F. Conrad, G. Lunter, H. Zheng, Q. Ayub,M. A. DePristo, E. Banks, M. Hu, R. E. Handsaker, J. A. Rosenfeld,M. Fromer, M. Jin, X. J. Mu, E. Khurana, K. Ye, M. Kay, G. I. Saunders, M.-M. Suner, T. Hunt, I. H. A. Barnes, C. Amid, D. R. Carvalho-Silva, A. H. Bignell, C. Snow, B. Yngvadottir, S. Bumpstead, D. N. Cooper, Y. Xue, I. G. Romero; 1000 Genomes Project Consortium, J. Wang, Y. Li, R. A. Gibbs, S. A. McCarroll, E. T. Dermitzakis, J. K. Pritchard, J. C. Barrett, J. Harrow, M. E. Hurles, M. B. Gerstein, C. Tyler-Smith, A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828 (2012).
9. J. O. Kitzman, A. P. MacKenzie, A. Adey, J. B. Hiatt, R. P. Patwardhan, P. H. Sudmant, S. B. Ng, C. Alkan, R. Qiu, E. E. Eichler, J. Shendure, Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat. Biotechnol. 29, 59-63 (2011).
10. L. Ma, Y. Xiao, H. Huang, Q. Wang, W. Rao, Y. Feng, K. Zhang, Q. Song, Direct determination of molecular haplotypes by chromosome microdissection. Nat. Methods 7, 299-301 (2010).
11. H. C. Fan, J. Wang, A. Potanina, S. R. Quake, Whole-genome molecular haplotyping of single cells. Nat. Biotechnol. 29, 51-57 (2011).
12. H. Yang, X. Chen, W. H. Wong, Completely phased genome sequencing through chromosome sorting. Proc. Natl. Acad. Sci. U.S.A. 108, 12- 17 (2011).
13. D. F. Conrad, J. E. M. Keebler, M. A. DePristo, S. J. Lindsay, Y. Zhang, F. Casals, Y. Idaghdour, C. L. Hartl, C. Torroja, K. V. Garimella, M. Zilversmit, R. Cartwright, G. A. Rouleau, M. Daly, E. A. Stone, M. E. Hurles, P. Awadalla; 1000 Genomes Project, Variation in genome-wide mutation rates within and between human families. Nat. Genet. 43, 712-714 (2011).
14. J. C. Roach, G. Glusman, A. F. A. Smit, C. D. Huff, R. Hubley, P. T. Shannon, L. Rowen, K. P. Pant, N. Goodman, M. Bamshad, J. Shendure, R. Drmanac, L. B. Jorde, L. Hood, D. J. Galas, Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636-639 (2010).
15. S. S. Ajay, S. C. J. Parker, H. O. Abaan, K. V. F. Fajardo, E. H. Margulies, Accurate and comprehensive sequencing of personal genomes. Genome Res. 21, 1498-1505 (2011).
16. 1000 Genomes Project Consortium, A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
17. P. D. Stenson, E. V. Ball, K. Howells, A. D. Phillips, M. Mort, D. N. Cooper, The Human Gene Mutation Database: Providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum. Genomics 4, 69- 72 (2009).
18. P. H. Sudmant, J. O. Kitzman, F. Antonacci, C. Alkan, M. Malig, A. Tsalenko, N. Sampas, L. Bruhn, J. Shendure; 1000 Genomes Project, E. E. Eichler, Diversity of human copy number variation and multicopy genes. Science 330, 641-646 (2010).
19. J. Amberger, C. A. Bocchini, A. F. Scott, A. Hamosh, McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 37, D793-D796 (2009).
20. C. J. Bell, D. L. Dinwiddie, N. A. Miller, S. L. Hateley, E. E. Ganusova, J. Mudge, R. J. Langley, L. Zhang, C. C. Lee, F. D. Schilkey, V. Sheth, J. E. Woodward, H. E. Peckham, G. P. Schroth, R. W. Kim, S. F. Kingsmore, Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci. Transl. Med. 3, 65ra4 (2011).
21. G. M. Cooper, J. Shendure, Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12, 628-640 (2011).
22. A. Adey, H. G. Morrison, Asan, X. Xun, J. O. Kitzman, E. H. Turner, B. Stackhouse,A. P. MacKenzie, N. C. Caruccio, X. Zhang, J. Shendure, Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11, R119 (2010).
23. M. A. DePristo, E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire, C. Hartl, A. A. Philippakis, G. del Angel, M. A. Rivas, M. Hanna, A. McKenna, T. J. Fennell, A. M. Kernytsky, A. Y. Sivachenko, K. Cibulskis, S. B. Gabriel, D. Altshuler, M. J. Daly, A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
24. V. Bansal, V. Bafna, HapCUT: An efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24, i153-i159 (2008).
25. International Parkinson Disease Genomics Consortium, M. A. Nalls, V. Plagnol, D. G. Hernandez, M. Sharma, U.-M. Sheerin, M. Saad, J. Simón-Sánchez, C. Schulte, S. Lesage, S. Sveinbjörnsdó ttir, K. Stefánsson, M. Martinez, J. Hardy, P. Heutink, A. Brice, T. Gasser, A. B. Singleton, N. W. Wood, Imputation of sequence variants for identification of genetic risks for Parkinson 's disease: A meta-analysis of genome-wide association studies. Lancet 377, 641-649 (2011).