Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J: Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011, 12: 745-755. 10.1038/nrg3031.
Article
CAS
PubMed
Google Scholar
Ku CS, Naidoo N, Pawitan Y: Revisiting Mendelian disorders through exome sequencing. Hum Genet. 2011, 129: 351-370. 10.1007/s00439-011-0964-2.
Article
PubMed
Google Scholar
Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R: Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol. 2012, 71: 5-14. 10.1002/ana.22647.
Article
CAS
PubMed
Google Scholar
Lyon GJ, Wang K: Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012, 4: 58-10.1186/gm359.
Article
PubMed Central
PubMed
Google Scholar
Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ: Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet. 2011, 89: 28-43. 10.1016/j.ajhg.2011.05.017.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007, 17: 1665-1674. 10.1101/gr.6861907.
Article
PubMed Central
CAS
PubMed
Google Scholar
Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K: Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res. 2008, 36: e126-10.1093/nar/gkn556.
Article
PubMed Central
PubMed
Google Scholar
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, et al: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010, 327: 78-81. 10.1126/science.1181498.
Article
CAS
PubMed
Google Scholar
Roach JC, Boysen C, Wang K, Hood L: Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics. 1995, 26: 345-353. 10.1016/0888-7543(95)80219-C.
Article
CAS
PubMed
Google Scholar
Guo Y, Shen Y, Lyon GJ, Wang K: SeqMule: an automated pipeline for whole genome/exome vari-ants generation. Submitted. 2013, [http://seqmule.usc.edu]
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10: R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012, 9: 357-359. 10.1038/nmeth.1923.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009, 25: 1966-1967. 10.1093/bioinformatics/btp336.
Article
CAS
PubMed
Google Scholar
Li R, Li Y, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program. Bioinformatics. 2008, 24: 713-714. 10.1093/bioinformatics/btn025.
Article
CAS
PubMed
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25: 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L: VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009, 25: 2283-2285. 10.1093/bioinformatics/btp373.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K: Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med. 2011, 12: 41-55.
PubMed Central
PubMed
Google Scholar
Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010, 38: e164-10.1093/nar/gkq603.
Article
PubMed Central
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25: 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
PubMed
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010, 28: 511-515. 10.1038/nbt.1621.
Article
PubMed Central
CAS
PubMed
Google Scholar
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol. 2011, 29: 24-26. 10.1038/nbt.1754.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ: Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010, 42: 30-35. 10.1038/ng.499.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J: Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010, 42: 790-793. 10.1038/ng.646.
Article
PubMed Central
CAS
PubMed
Google Scholar
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, et al: A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012, 335: 823-828. 10.1126/science.1215040.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang PJ, Page DC: Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. Hum Mol Genet. 2002, 11: 2341-2346. 10.1093/hmg/11.19.2341.
Article
CAS
PubMed
Google Scholar
Yamanaka K, Ishikawa H, Megumi Y, Tokunaga F, Kanie M, Rouault TA, Morishima I, Minato N, Ishimori K, Iwai K: Identification of the ubiquitin-protein ligase that recognizes oxidized IRP2. Nat Cell Biol. 2003, 5: 336-340. 10.1038/ncb952.
Article
CAS
PubMed
Google Scholar
Heinrich V, Stange J, Dickhaus T, Imkeller P, Kruger U, Bauer S, Mundlos S, Robinson PN, Hecht J, Krawitz PM: The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process. Nucleic Acids Res. 2012, 40: 2426-2431. 10.1093/nar/gkr1073.
Article
PubMed Central
CAS
PubMed
Google Scholar
Benjamini Y, Speed TP: Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012, 40: e72-10.1093/nar/gks001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sirmaci A, Edwards YJ, Akay H, Tekin M: Challenges in whole exome sequencing: an example from hereditary deafness. PLoS ONE. 2012, 7: e32000-10.1371/journal.pone.0032000.
Article
PubMed Central
CAS
PubMed
Google Scholar
Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Gibbs RA, Hurles ME, McVean GA: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
CAS
PubMed
Google Scholar
Boisson B, Laplantine E, Prando C, Giliani S, Israelsson E, Xu Z, Abhyankar A, Israël L, Trevejo-Nunez G, Bogunovic D, Cepika AM, MacDuff D, Chrabieh M, Hubeau M, Bajolle F, Debré M, Mazzolari E, Vairo D, Agou F, Virgin HW, Bossuyt X, Rambaud C, Facchetti F, Bonnet D, Quartier P, Fournet JC, Pascual V, Chaussabel D, Notarangelo LD, Puel A, et al: Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency. Nat Immunol. 2012, 13: 1178-1186. 10.1038/ni.2457.
Article
PubMed Central
CAS
PubMed
Google Scholar