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Items: 1 to 20 of 58

1.

Detection of structural variants and indels within exome data.

Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, Eichler EE.

Nat Methods. 2011 Dec 18;9(2):176-8. doi: 10.1038/nmeth.1810.

2.

Detection of clinically relevant copy number variants with whole-exome sequencing.

de Ligt J, Boone PM, Pfundt R, Vissers LE, Richmond T, Geoghegan J, O'Moore K, de Leeuw N, Shaw C, Brunner HG, Lupski JR, Veltman JA, Hehir-Kwa JY.

Hum Mutat. 2013 Oct;34(10):1439-48. doi: 10.1002/humu.22387. Epub 2013 Aug 30.

PMID:
23893877
3.

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Narzisi G, O'Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.

Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069. Epub 2014 Aug 17.

4.
5.

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK.

Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. Epub 2012 Feb 2.

6.

Analytical validation of whole exome and whole genome sequencing for clinical applications.

Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE.

BMC Med Genomics. 2014 Apr 23;7:20. doi: 10.1186/1755-8794-7-20.

7.

Modeling read counts for CNV detection in exome sequencing data.

Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1732/1544-6115.1732.xml. doi: 10.2202/1544-6115.1732.

8.

A practical method to detect SNVs and indels from whole genome and exome sequencing data.

Shigemizu D, Fujimoto A, Akiyama S, Abe T, Nakano K, Boroevich KA, Yamamoto Y, Furuta M, Kubo M, Nakagawa H, Tsunoda T.

Sci Rep. 2013;3:2161. doi: 10.1038/srep02161.

9.

Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.

10.

Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.

Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, Handsaker RE, McCarroll SA, O'Donovan MC, Owen MJ, Kirov G, Sullivan PF, Hultman CM, Sklar P, Purcell SM.

Am J Hum Genet. 2012 Oct 5;91(4):597-607. doi: 10.1016/j.ajhg.2012.08.005.

11.

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster.

Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, Robyr D, Bottani A, Antonarakis SE.

Genome Res. 2014 Feb;24(2):349-55. doi: 10.1101/gr.163832.113. Epub 2014 Jan 3.

12.

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER.

Nat Methods. 2009 Sep;6(9):677-81. doi: 10.1038/nmeth.1363. Epub 2009 Aug 9.

13.

A population model for genotyping indels from next-generation sequence data.

Shao H, Bellos E, Yin H, Liu X, Zou J, Li Y, Wang J, Coin LJ.

Nucleic Acids Res. 2013 Feb 1;41(3):e46. doi: 10.1093/nar/gks1143. Epub 2012 Dec 5.

14.

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.

Cantarel BL, Weaver D, McNeill N, Zhang J, Mackey AJ, Reese J.

BMC Bioinformatics. 2014 Apr 12;15:104. doi: 10.1186/1471-2105-15-104.

15.

Sensitive and accurate detection of copy number variants using read depth of coverage.

Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.

Genome Res. 2009 Sep;19(9):1586-92. doi: 10.1101/gr.092981.109. Epub 2009 Aug 5.

16.

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control.

Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y.

Biomed Res Int. 2013;2013:915636. doi: 10.1155/2013/915636. Epub 2013 Nov 4.

17.

Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.

Zhuang Z, Gusev A, Cho J, Pe'er I.

PLoS One. 2012;7(10):e47618. doi: 10.1371/journal.pone.0047618. Epub 2012 Oct 11.

18.

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.

Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.

19.

Estimation of copy number alterations from exome sequencing data.

Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS.

PLoS One. 2012;7(12):e51422. doi: 10.1371/journal.pone.0051422. Epub 2012 Dec 19.

20.

Automating resequencing-based detection of insertion-deletion polymorphisms.

Bhangale TR, Stephens M, Nickerson DA.

Nat Genet. 2006 Dec;38(12):1457-62. Epub 2006 Nov 19.

PMID:
17115056
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