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For: 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. ACTA ACUST UNITED AC 2009;25:2283-5. [PMID: 19542151 DOI: 10.1093/bioinformatics/btp373] [Citation(s) in RCA: 980] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
951
Wang W, Wei Z, Lam TW, Wang J. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep 2011;1:55. [PMID: 22355574 PMCID: PMC3216542 DOI: 10.1038/srep00055] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 07/25/2011] [Indexed: 01/30/2023]  Open
952
Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, Cattonaro F, Morgante M. Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011;67:736-45. [PMID: 21554453 DOI: 10.1111/j.1365-313x.2011.04627.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
953
Missirian V, Comai L, Filkov V. Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics 2011. [PMID: 21756356 DOI: 10.1186/1471‐2105‐12‐287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
954
Missirian V, Comai L, Filkov V. Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics 2011;12:287. [PMID: 21756356 PMCID: PMC3150297 DOI: 10.1186/1471-2105-12-287] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 07/14/2011] [Indexed: 11/17/2022]  Open
955
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 JYJ, Tong AHY, 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;43:860-3. [PMID: 21743468 DOI: 10.1038/ng.886] [Citation(s) in RCA: 295] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/15/2011] [Indexed: 12/17/2022]
956
Margraf RL, Durtschi JD, Dames S, Pattison DC, Stephens JE, Voelkerding KV. Variant identification in multi-sample pools by illumina genome analyzer sequencing. J Biomol Tech 2011;22:74-84. [PMID: 21738440 PMCID: PMC3121147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
957
Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L. Discovery of rare mutations in populations: TILLING by sequencing. PLANT PHYSIOLOGY 2011;156:1257-68. [PMID: 21531898 PMCID: PMC3135940 DOI: 10.1104/pp.110.169748] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 04/28/2011] [Indexed: 05/19/2023]
958
Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 2011;107:1-15. [PMID: 21139633 PMCID: PMC3186121 DOI: 10.1038/hdy.2010.152] [Citation(s) in RCA: 642] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 09/10/2010] [Accepted: 11/02/2010] [Indexed: 11/09/2022]  Open
959
Hornsey M, Loman N, Wareham DW, Ellington MJ, Pallen MJ, Turton JF, Underwood A, Gaulton T, Thomas CP, Doumith M, Livermore DM, Woodford N. Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J Antimicrob Chemother 2011;66:1499-503. [PMID: 21565804 DOI: 10.1093/jac/dkr168] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
960
Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics 2011;12:267. [PMID: 21714929 PMCID: PMC3148209 DOI: 10.1186/1471-2105-12-267] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 06/29/2011] [Indexed: 12/15/2022]  Open
961
Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 2011;12:231. [PMID: 21663684 PMCID: PMC3212839 DOI: 10.1186/1471-2105-12-231] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 06/11/2011] [Indexed: 11/10/2022]  Open
962
Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LCS, Kiang AS, Campbell M, Weinstock GM, Koboldt DC, Ding L, Fulton RS, Sodergren EJ, Allman D, Millington-Ward S, Palfi A, McKee A, Blanton SH, Slifer S, Konidari I, Farrar GJ, Daiger SP, Humphries P. A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. Eur J Hum Genet 2011;19:1074-81. [PMID: 21654732 DOI: 10.1038/ejhg.2011.86] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
963
Erlich Y. Blood ties: chimerism can mask twin discordance in high-throughput sequencing. Twin Res Hum Genet 2011;14:137-43. [PMID: 21425895 DOI: 10.1375/twin.14.2.137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
964
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. Nat Genet 2011. [PMID: 21478889 DOI: 10.1038/ng.806.a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
965
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. Nat Genet 2011;43:491-8. [PMID: 21478889 PMCID: PMC3083463 DOI: 10.1038/ng.806] [Citation(s) in RCA: 8233] [Impact Index Per Article: 588.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 03/17/2011] [Indexed: 02/07/2023]
966
Erlich Y, Edvardson S, Hodges E, Zenvirt S, Thekkat P, Shaag A, Dor T, Hannon GJ, Elpeleg O. Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res 2011;21:658-64. [PMID: 21487076 DOI: 10.1101/gr.117143.110] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
967
HIRD SARAHM, BRUMFIELD ROBBT, CARSTENS BRYANC. PRG matic : an efficient pipeline for collating genome‐enriched second‐generation sequencing data using a ‘provisional‐reference genome’. Mol Ecol Resour 2011;11:743-8. [DOI: 10.1111/j.1755-0998.2011.03005.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
968
Legendre M, Santini S, Rico A, Abergel C, Claverie JM. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. Virol J 2011;8:99. [PMID: 21375749 PMCID: PMC3058096 DOI: 10.1186/1743-422x-8-99] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/04/2011] [Indexed: 11/30/2022]  Open
969
Lupton MK, Proitsi P, Danillidou M, Tsolaki M, Hamilton G, Wroe R, Pritchard M, Lord K, Martin BM, Kloszewska I, Soininen H, Mecocci P, Vellas B, Harold D, Hollingworth P, Lovestone S, Powell JF. Deep sequencing of the Nicastrin gene in pooled DNA, the identification of genetic variants that affect risk of Alzheimer's disease. PLoS One 2011;6:e17298. [PMID: 21364883 PMCID: PMC3045431 DOI: 10.1371/journal.pone.0017298] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/27/2011] [Indexed: 11/18/2022]  Open
970
Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics 2011;27:865-6. [PMID: 21278191 DOI: 10.1093/bioinformatics/btr032] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
971
Bowne SJ, Sullivan LS, Koboldt DC, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch DG, Wheaton DH, Heckenlively JR, Liu Q, Pierce EA, Weinstock GM, Daiger SP. Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing. Invest Ophthalmol Vis Sci 2011;52:494-503. [PMID: 20861475 DOI: 10.1167/iovs.10-6180] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
972
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlötterer C. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 2011;6:e15925. [PMID: 21253599 PMCID: PMC3017084 DOI: 10.1371/journal.pone.0015925] [Citation(s) in RCA: 421] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/30/2010] [Indexed: 11/19/2022]  Open
973
Vallania FLM, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 2010;20:1711-8. [PMID: 21041413 DOI: 10.1101/gr.109157.110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
974
Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R. Dindel: accurate indel calls from short-read data. Genome Res 2010;21:961-73. [PMID: 20980555 DOI: 10.1101/gr.112326.110] [Citation(s) in RCA: 323] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
975
Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics 2010;26:i318-24. [PMID: 20529923 PMCID: PMC2881398 DOI: 10.1093/bioinformatics/btq214] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
976
Collins SC, Bray SM, Suhl JA, Cutler DJ, Coffee B, Zwick ME, Warren ST. Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males. Am J Med Genet A 2010;152A:2512-20. [PMID: 20799337 PMCID: PMC2946449 DOI: 10.1002/ajmg.a.33626] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
977
Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood 2010;116:5316-26. [PMID: 20876853 DOI: 10.1182/blood-2010-05-285395] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
978
Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010;11:685-96. [PMID: 20847746 DOI: 10.1038/nrg2841] [Citation(s) in RCA: 778] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
979
Ding L, Wendl MC, Koboldt DC, Mardis ER. Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet 2010;19:R188-96. [PMID: 20843826 DOI: 10.1093/hmg/ddq391] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
980
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. [PMID: 20644199 DOI: 10.1101/gr.107524.110.20] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
981
Margraf RL, Durtschi JD, Dames S, Pattison DC, Stephens JE, Mao R, Voelkerding KV. Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development. J Biomol Tech 2010;21:126-140. [PMID: 20808642 PMCID: PMC2922832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
982
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. [PMID: 20644199 DOI: 10.1101/gr.107524.110.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
983
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;20:1297-303. [PMID: 20644199 DOI: 10.1101/gr.107524.110] [Citation(s) in RCA: 18669] [Impact Index Per Article: 1244.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
984
Koboldt DC, Ding L, Mardis ER, Wilson RK. Challenges of sequencing human genomes. Brief Bioinform 2010;11:484-98. [PMID: 20519329 DOI: 10.1093/bib/bbq016] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
985
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 2010;11:473-83. [PMID: 20460430 DOI: 10.1093/bib/bbq015] [Citation(s) in RCA: 419] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
986
Huss M. Introduction into the analysis of high-throughput-sequencing based epigenome data. Brief Bioinform 2010;11:512-23. [PMID: 20457755 DOI: 10.1093/bib/bbq014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
987
Robison K. Application of second-generation sequencing to cancer genomics. Brief Bioinform 2010;11:524-34. [DOI: 10.1093/bib/bbq013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
988
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res 2009;20:273-80. [PMID: 20019143 DOI: 10.1101/gr.096388.109] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
989
Johnson ML, Lara N, Kamel MA. How genomics has informed our understanding of the pathogenesis of osteoporosis. Genome Med 2009;1:84. [PMID: 19735586 PMCID: PMC2768991 DOI: 10.1186/gm84] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
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