Next-generation human genetics

Genome Biology

Volumn 12, Issue 9, 2011, Pages

  Shendure, Jay ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COST EFFECTIVENESS ANALYSIS; DATA ANALYSIS SOFTWARE; EDITORIAL; EXOME; GENE MUTATION; GENE SEQUENCE; GENETIC CODE; GENETIC DISORDER; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; HUMAN GENETICS; MENDELIAN DISORDER; PHENOTYPE; SEQUENCE ANALYSIS; DNA SEQUENCE; GENETIC HETEROGENEITY; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; GENOMICS; HUMAN GENOME; MEDICAL GENETICS; METHODOLOGY;

EXOME; GENETIC DISEASES, INBORN; GENETIC HETEROGENEITY; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENETICS, MEDICAL; GENOME, HUMAN; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 80052855150     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-9-408     Document Type: Editorial

References (17)

1. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732. 10.1126/science.1117389, 16081699.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
3. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010, 7:111-118. 10.1038/nmeth.1419, 20111037.
4. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009, 461:272-276. 10.1038/nature08250, 2844771, 19684571.
5. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR. Genome-wide in situ exon capture for selective resequencing. Nat Genet 2007, 39:1522-1527. 10.1038/ng.2007.42, 17982454.
6. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59. 10.1038/nature07517, 2581791, 18987734.
7. Walsh T, Shahin H, Elkan-Miller T, Lee MK, Thornton AM, Roeb W, Abu Rayyan A, Loulus S, Avraham KB, King MC, Kanaan M. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010, 87:90-94. 10.1016/j.ajhg.2010.05.010, 2896776, 20602914.
8. Johnson JO, Mandrioli J, Benatar M, Abramzon Y, Van Deerlin VM, Trojanowski JQ, Gibbs JR, Brunetti M, Gronka S, Wuu J, Ding J, McCluskey L, Martinez-Lage M, Falcone D, Hernandez DG, Arepalli S, Chong S, Schymick JC, Rothstein J, Landi F, Wang YD, Calvo A, Mora G, Sabatelli M, Monsurrò MR, Battistini S, Salvi F, Spataro R, Sola P, Borghero G, et al. ITALSGEN Consortium Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 2010, 68:857-864. 10.1016/j.neuron.2010.11.036, 21145000, ITALSGEN Consortium.
9. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkalo¿lu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 2009, 106:19096-19101. 10.1073/pnas.0910672106, 2768590, 19861545.
10. Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van Lier B, Arts P, Wieskamp N, del Rosario M, van Bon BW, Hoischen A, de Vries BB, Brunner HG, Veltman JA. A de novo paradigm for mental retardation. Nat Genet 2010, 42:1109-1112. 10.1038/ng.712, 21076407.
11. O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, Mackenzie AP, Ng SB, Baker C, Rieder MJ, Nickerson DA, Bernier R, Fisher SE, Shendure J, Eichler EE. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet 2011, 43:585-589. 10.1038/ng.835, 21572417.
12. Girard SL, Gauthier J, Noreau A, Xiong L, Zhou S, Jouan L, Dionne-Laporte A, Spiegelman D, Henrion E, Diallo O, Thibodeau P, Bachand I, Bao JY, Tong AH, Lin CH, Millet B, Jaafari N, Joober R, Dion PA, Lok S, Krebs MO, Rouleau GA. Increased exonic de novo mutation rate in individuals with schizophrenia. Nat Genet 2011, 43:860-863. 10.1038/ng.886, 21743468, 21743468.
13. Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011, 469:539-542. 10.1038/nature09639, 3030920, 21248752.
14. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, Gartner J, Davis S, Stemke-Hale K, Davies MA, Gershenwald JE, Robinson W, Robinson S, Rosenberg SA, Samuels Y. NISC Comparative Sequencing Program Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 2011, 43:442-446. 10.1038/ng.810, 3161250, 21499247, NISC Comparative Sequencing Program.
15. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
17. Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst F, Bergstrom DE, Murray SA, Bult C, Richardson J, Kile B, Gut I, Hager J, Sigurdsson S, Mauceli E, Di Palma F, Lindblad-Toh K, Cunningham ML, Cox TC, Justice MJ, Spector MS, Lowe SW, Albert T, et al. Mutation discovery in mice by whole exome sequencing. Genome Biol 2011,