Analysis of genetic inheritance in a family quartet by whole-genome sequencing

Science

Volumn 328, Issue 5978, 2010, Pages 636-639

  Roach, Jared C ^a   Glusman, Gustavo ^a   Smit, Arian F A ^a   Huff, Chad D ^a,b   Hubley, Robert ^a   Shannon, Paul T ^a   Rowen, Lee ^a   Pant, Krishna P ^c   Goodman, Nathan ^a   Bamshad, Michael ^d   Shendure, Jay ^e   Drmanac, Radoje ^c   Jorde, Lynn B ^b   Hood, Leroy ^a   Galas, David J ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

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

^c Complete Genomics Inc ^*  (United States)

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

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENEALOGY; GENETIC ANALYSIS; GENETIC RESOURCE; GENETIC VARIATION; GENOME; POLYMORPHISM; SIBLING;

ARTICLE; AUTOSOMAL RECESSIVE DISORDER; AUTOSOMAL RECESSIVE INHERITANCE; CILIARY DYSKINESIA; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; FAMILY; FEMALE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DISORDER; GENETIC RECOMBINATION; HAPLOIDY; HUMAN; HUMAN GENOME; HUMAN RELATION; INHERITANCE; MAJOR CLINICAL STUDY; MALE; MILLER DIEKER SYNDROME; MISSENSE MUTATION; PARENT; PRIORITY JOURNAL; PROGENY; RISK FACTOR; SIBLING; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME SEQUENCING;

ABNORMALITIES, MULTIPLE; ALGORITHMS; ALLELES; AXONEMAL DYNEINS; CILIARY MOTILITY DISORDERS; CROSSING OVER, GENETIC; FEMALE; GENES, DOMINANT; GENES, RECESSIVE; GENETIC ASSOCIATION STUDIES; GENOME, HUMAN; HUMANS; INHERITANCE PATTERNS; LIMB DEFORMITIES, CONGENITAL; MALE; MANDIBULOFACIAL DYSOSTOSIS; MUTATION; NUCLEAR FAMILY; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SYNDROME;

EID: 77951799158     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1186802     Document Type: Article

References (27)

1. R. Drmanac et al., Science 327, 78 (2010).
2. J. C. Roach, C. Boysen, K. Wang, L. Hood, Genomics 26, 345 (1995).
3. G. A. Watterson, Theor. Popul. Bioi 7, 256 (1975).
4. Materials and methods are available as supporting material on Science Online.
5. K. P. Donnelly, Theor. Popul. Biol. 23, 34 (1983).
6. L. Kruglyak, M. J. Daly, M. P. Reeve-Daly, E. S. Lander, Am. J. Hum. Genet. 58, 1347 (1996).
7. G. R. Abecasis, S. S. Cherny, W. O. Cookson, L. R. Cardon, Nat Genet. 30, 97 (2002).
8. P. M. Petkov, K. W. Broman, J. P. Szatkiewicz, K. Paigen, Trends Genet. 23, 539 (2007).
9. Chimpanzee Sequencing and Analysis Consortium, Nature 437, 69 (2005).
10. M. W. Nachman, S. L. Crowell, Genetics 156, 297 (2000).
11. Y. Haile-Selassie, Nature 412, 178 (2001).
12. Y. Haile-Selassie, B. Asfaw, T. D. White, Am. J. Phys. Anthropol. 123, 1 (2004).
13. Y. Haile-Selassie, G. Suwa, T. D. White, Science 303, 1503 (2004).
14. A. L. Deino, L. Tauxe, M. Monaghan, A. Hill, J. Hum. Evol. 42, 117 (2002).
15. M. Brunet et al., Nature 418, 145 (2002).
16. F. C. Chen, W. H. Li, Am. J. Hum. Genet. 68, 444 (2001).
17. R. Burgess, Z. Yang, Mol. Biol. Evol. 25, 1979 (2008).
18. N. Takahata, Jpn. J. Genet. 68, 539 (1993).
19. J. D. Wall, Generics 163, 395 (2003).
20. A. S. Kondrashov, Hum. Mutat 21, 12 (2003).
21. Y. Xue et al., Curr. Biol. 19, 1453 (2009).
22. S. B. Ng et al., Nat. Genet. 42, 30 (2010).
23. H. Olbrich et al., Nat. Genet. 30, 143 (2002).
24. S. B. Ng et al., Nature 461, 272 (2009).
25. M. Choi et al., Proc. Natl Acad. Sci. U.S.A. 106, 190961 (2009).
26. This study was supported by the University of Luxembourg-Institute for Systems Biology Program and by these NIH grants: Center for Systems Biology GM076547 (L.H. and L.R.), RO1GM081083 (A.F.S. and G.G.), R01HL094976 and RZ1HG004749 (J.S.), RC2HG005608 (M.D. and J.S.), and R01HD048895 (M.B.). H. Tabor assisted with ethical review. J. Xing performed the principal components analysis. H. Mefford performed CNV analysis. A. Bigham and K. Buckingham evaluated candidate genes in unrelated individuals. D. Ballinger, A. Sparks, A. Halpern, and G. Nilsen assisted with sequencing and analysis. R. Bressler, S. Dee, and D. Mauldin assisted with bioinformatics. S. Ng and R. Qiu performed the capture array. S. Bloom obtained the resequencing data on the Illumina Genome Analyzer. M. Janer and S. Li performed Sequenom analysis. D. Cox commented on an early version of the manuscript. R. Durbin and D. Altshuler granted permission for our use of 1000 genomes SNP data. CGI employees (R.D. and K.P.) have stock options in the company. J.S. has consulted for CGI. L.H. is a scientific advisor to CGI and holds stock in the company.
27. The dbGAP accessions can be found at www.ncbi.nlm.nih.gov/projects/gap/ cgibin/study.cgi?study-id=phs000244.v1.p1 (accession phs000244. v1.p1).