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Items: 1 to 20 of 100

1.

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.

Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T.

Genome Biol. 2011 Sep 28;12(9):R93. doi: 10.1186/gb-2011-12-9-r93.

2.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

3.

Quantification of rare allelic variants from pooled genomic DNA.

Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD.

Nat Methods. 2009 Apr;6(4):263-5. doi: 10.1038/nmeth.1307. Epub 2009 Mar 1.

4.

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.

5.

Comparison of solution-based exome capture methods for next generation sequencing.

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J.

Genome Biol. 2011 Sep 28;12(9):R94. doi: 10.1186/gb-2011-12-9-r94.

6.

The functional spectrum of low-frequency coding variation.

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project.

Genome Biol. 2011 Sep 14;12(9):R84. doi: 10.1186/gb-2011-12-9-r84.

7.

Deep sequencing to reveal new variants in pooled DNA samples.

Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PE, Tops CM, Breuning MH, van Ommen GJ, den Dunnen JT, Devilee P, Hes FJ.

Hum Mutat. 2009 Dec;30(12):1703-12. doi: 10.1002/humu.21122.

PMID:
19842214
8.

Evaluation of variant detection software for pooled next-generation sequence data.

Huang HW; NISC Comparative Sequencing Program, Mullikin JC, Hansen NF.

BMC Bioinformatics. 2015 Jul 29;16:235. doi: 10.1186/s12859-015-0624-y.

9.

Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing.

ElSharawy A, Warner J, Olson J, Forster M, Schilhabel MB, Link DR, Rose-John S, Schreiber S, Rosenstiel P, Brayer J, Franke A.

BMC Genomics. 2012 Sep 20;13:500. doi: 10.1186/1471-2164-13-500.

10.

Efficient identification of rare variants in large populations: deep re-sequencing the CRP locus in the CARDIA study.

Chen CT, McDavid AN, Kahsai OJ, Zebari AS, Carlson CS.

Nucleic Acids Res. 2013 Apr;41(7):e85. doi: 10.1093/nar/gkt092. Epub 2013 Feb 13.

11.

SNP calling by sequencing pooled samples.

Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.

BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.

12.

Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing.

Cao CC, Li C, Huang Z, Ma X, Sun X.

Genet Epidemiol. 2013 Dec;37(8):820-30. doi: 10.1002/gepi.21769. Epub 2013 Oct 28.

13.

Rare variant discovery and calling by sequencing pooled samples with overlaps.

Wang W, Yin X, Soo Pyon Y, Hayes M, Li J.

Bioinformatics. 2013 Jan 1;29(1):29-38. doi: 10.1093/bioinformatics/bts645. Epub 2012 Oct 27.

14.

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.

Berglund EC, Lindqvist CM, Hayat S, Övernäs E, Henriksson N, Nordlund J, Wahlberg P, Forestier E, Lönnerholm G, Syvänen AC.

BMC Genomics. 2013 Dec 5;14:856. doi: 10.1186/1471-2164-14-856.

15.
16.

Accurate detection and genotyping of SNPs utilizing population sequencing data.

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA.

Genome Res. 2010 Apr;20(4):537-45. doi: 10.1101/gr.100040.109. Epub 2010 Feb 11.

17.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.

18.

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

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, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA.

Science. 2010 Jan 1;327(5961):78-81. doi: 10.1126/science.1181498. Epub 2009 Nov 5.

19.

A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Bansal V.

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214. Erratum in: Bioinformatics. 2016 Oct 15;32(20):3213.

20.

iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array.

Zhou J, Tantoso E, Wong LP, Ong RT, Bei JX, Li Y, Liu J, Khor CC, Teo YY.

Bioinformatics. 2014 Jun 15;30(12):1714-20. doi: 10.1093/bioinformatics/btu107. Epub 2014 Feb 23.

PMID:
24567545

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