Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM: Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes. Science. 2012,
Google Scholar
Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zollner S, Whittaker JC, Chissoe SL, Novembre J: An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people. Science. 2012, 337: 100-104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olson MV: Human genetic individuality. Annual review of genomics and human genetics. 2012, 13: 1-27.
Article
CAS
PubMed
Google Scholar
Bearn AG: Archibald Garrod and the individuality of Man. 1993, Oxford, New York: Clarendon Press; Oxford University Press,
Google Scholar
Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT: A public resource facilitating clinical use of genomes. Proceedings of the National Academy of Sciences of the United States of America. 2012, 109: 11920-11927.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drmanac R: The advent of personal genome sequencing. Genetics in medicine : official journal of the American College of Medical Genetics. 2011, 13: 188-190. 10.1097/GIM.0b013e31820f16e6.
Article
Google Scholar
Rosenfeld JA, Mason CE, Smith TM: Limitations of the human reference genome for personalized genomics. PLoS One. 2012, 7: e40294-
Article
CAS
PubMed
PubMed Central
Google Scholar
Reumers J, De Rijk P, Zhao H, Liekens A, Smeets D, Cleary J, Van Loo P, Van Den Bossche M, Catthoor K, Sabbe B, Despierre E, Vergote I, Hilbush B, Lambrechts D, Del-Favero J: Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nature biotechnology. 2012, 30: 61-68.
Article
CAS
Google Scholar
Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M: Detecting and annotating genetic variations using the HugeSeq pipeline. Nature biotechnology. 2012, 30: 226-229.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam HY, Clark MJ, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M: Performance comparison of whole-genome sequencing platforms. Nature biotechnology. 2012, 30: 78-82.
Article
CAS
PubMed Central
Google Scholar
Comparing Performance Data - Taking a Different Perspective.http://www.completegenomics.com/blog/Comparing-Performance-Data--Taking-a-Different-Perspective--140765443.html
Cliff Reid on CG vs Illumina.http://mendeliandisorder.blogspot.com/2012/03/cliff-reid-on-cg-vs-illumina.html
Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics. 2011, 12: 443-451.
Article
CAS
PubMed
PubMed Central
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: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010, 327: 78-81.
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.
Article
CAS
PubMed
Google Scholar
Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, Pant KP, Ebert JC, Brownley A, Morenzoni M, Karpinchyk V, Martin B, Ballinger DG, Drmanac R: Computational techniques for human genome resequencing using mated gapped reads. Journal of computational biology : a journal of computational molecular cell biology. 2012, 19: 279-292. 10.1089/cmb.2011.0201.
Article
CAS
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760.
Article
CAS
PubMed
PubMed Central
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics. 2011, 43: 491-498.
Article
CAS
PubMed
PubMed Central
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.
Article
PubMed
PubMed Central
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.
Article
CAS
PubMed
Google Scholar
Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K: SNP detection for massively parallel whole-genome resequencing. Genome research. 2009, 19: 1124-1132.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Yang H, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. Genome research. 2010, 20: 265-272.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE: The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics. 2009, 26: 38-45.
Article
PubMed
Google Scholar
Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H: SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic acids research. 2011, 39: e132-
Article
CAS
PubMed
PubMed Central
Google Scholar
SNP & Variation Suite (Version 7.6.10) [Software].http://www.goldenhelix.com
Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010, 38: e164-
Article
PubMed
PubMed Central
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
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.
Article
CAS
PubMed
PubMed Central
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ: Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010, 328: 636-639.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P: Variation in genome-wide mutation rates within and between human families. Nature genetics. 2011, 43: 712-714.
Article
CAS
PubMed
PubMed Central
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
PubMed Central
Google Scholar
Lee H, Schatz MC: Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score. Bioinformatics. 2012,
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 research. 2010, 20: 1297-1303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li R, Li Y, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program. Bioinformatics. 2008, 24: 713-714.
Article
CAS
PubMed
Google Scholar
Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009, 25: 1966-1967.
Article
CAS
PubMed
Google Scholar
Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data. Human genomics. 2010, 4: 271-277.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lyon GJ, Wang K: Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome medicine. 2012, 4: 58-
Article
PubMed
PubMed Central
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. American journal of human genetics. 2011, 89: 28-43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mullaney JM, Mills RE, Pittard WS, Devine SE: Small insertions and deletions (INDELs) in human genomes. Human Molecular Genetics. 2010, 19: R131-R136.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R: Mapping copy number variation by population-scale genome sequencing. Nature. 2011, 470: 59-65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE: An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research. 2006, 16: 1182-1190.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE: Natural genetic variation caused by small insertions and deletions in the human genome. Genome Research. 2011, 21: 830-839.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1, 092 human genomes. Nature. 2012, 491: 56-65.
Article
PubMed
Google Scholar
Krawitz P, Rodelsperger C, Jager M, Jostins L, Bauer S, Robinson PN: Microindel detection in short-read sequence data. Bioinformatics. 2010, 26: 722-729.
Article
CAS
PubMed
Google Scholar
Neuman JA, Isakov O, Shomron N: Analysis of insertion‚deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in Bioinformatics. 2012,
Google Scholar
O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE: Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012, 485: 246-250.
Article
PubMed
PubMed Central
Google Scholar
Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, Stepansky A, Troge J, Andrews P, Bekritsky M, Pradhan K, Ghiban E, Kramer M, Parla J, Demeter R, Fulton LL, Fulton RS, Magrini VJ, Ye K, Darnell JC, Darnell RB: De novo gene disruptions in children on the autistic spectrum. Neuron. 2012, 74: 285-299.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y: Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012, 485: 242-245.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Gunel M, Roeder K, Geschwind DH, Devlin B, State MW: De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012, 485: 237-241.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu B, Ionita-Laza I, Roos JL, Boone B, Woodrick S, Sun Y, Levy S, Gogos JA, Karayiorgou M: De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nature genetics. 2012
Google Scholar
Chahrour MH, Yu TW, Lim ET, Ataman B, Coulter ME, Hill RS, Stevens CR, Schubert CR, Greenberg ME, Gabriel SB, Walsh CA: Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism. PLoS genetics. 2012, 8: e1002635-
Article
CAS
PubMed
PubMed Central
Google Scholar
Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R: Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature. 2012, 487: 190-195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS genetics. 2011, 7: e1002280-
Article
CAS
PubMed
PubMed Central
Google Scholar
Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP: SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010, 26: 730-736.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR: Low-coverage sequencing: implications for design of complex trait association studies. Genome research. 2011, 21: 940-951.
Article
CAS
PubMed
PubMed Central
Google Scholar
Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D: Phasing of many thousands of genotyped samples. American journal of human genetics. 2012, 91: 238-251.
Article
CAS
PubMed
PubMed Central
Google Scholar
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR: Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature genetics. 2012, 44: 955-959.
Article
CAS
PubMed
PubMed Central
Google Scholar
Howie B, Marchini J, Stephens M: Genotype imputation with thousands of genomes. G3. 2011, 1: 457-470.
Article
PubMed
PubMed Central
Google Scholar
Browning BL, Browning SR: A fast, powerful method for detecting identity by descent. American journal of human genetics. 2011, 88: 173-182.
Article
CAS
PubMed
PubMed Central
Google Scholar
Browning SR, Browning BL: Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. American journal of human genetics. 2007, 81: 1084-1097.
Article
CAS
PubMed
PubMed Central
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 research. 2012, 40: 2426-2431.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gigerenzer G: Calculated risks : how to know when numbers deceive you. 2002, New York: Simon & Schuster,
Google Scholar