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An optimization framework for unsupervised identification of rare copy number variation from SNP array data.

Yavas G, Koyutürk M, Ozsoyoğlu M, Gould MP, LaFramboise T.

Genome Biol. 2009;10(10):R119. Epub 2009 Oct 23.PMID: 19849861 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparing CNV detection methods for SNP arrays.

Winchester L, Yau C, Ragoussis J.

Brief Funct Genomic Proteomic. 2009 Sep;8(5):353-66. Epub 2009 Sep 8. Review.PMID: 19737800 [PubMed - indexed for MEDLINE]Related articles

Cokgen: a software for the identification of rare copy number variation from SNP microarrays.

Yavaş G, Koyutürk M, Ozsoyoğlu M, Gould MP, Laframboise T.

Pac Symp Biocomput. 2010:371-82.PMID: 19908389 [PubMed - in process]Related articlesFree article

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D.

Nat Genet. 2008 Oct;40(10):1253-60. Epub 2008 Sep 7.PMID: 18776909 [PubMed - indexed for MEDLINE]Related articlesFree article

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Huang J, Wei W, Chen J, Zhang J, Liu G, Di X, Mei R, Ishikawa S, Aburatani H, Jones KW, Shapero MH.

BMC Bioinformatics. 2006 Feb 21;7:83.PMID: 16504045 [PubMed - indexed for MEDLINE]Related articlesFree article

Major copy proportion analysis of tumor samples using SNP arrays.

Li C, Beroukhim R, Weir BA, Winckler W, Garraway LA, Sellers WR, Meyerson M.

BMC Bioinformatics. 2008 Apr 21;9:204.PMID: 18426588 [PubMed - indexed for MEDLINE]Related articlesFree article

Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes.

Shen F, Huang J, Fitch KR, Truong VB, Kirby A, Chen W, Zhang J, Liu G, McCarroll SA, Jones KW, Shapero MH.

BMC Genet. 2008 Mar 28;9:27.PMID: 18373861 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.

Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, Lee C, Scherer SW, Jones KW, Shapero MH, Huang J, Aburatani H.

Genome Res. 2006 Dec;16(12):1575-84. Epub 2006 Nov 22.PMID: 17122084 [PubMed - indexed for MEDLINE]Related articlesFree article

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.

Yu T, Ye H, Sun W, Li KC, Chen Z, Jacobs S, Bailey DK, Wong DT, Zhou X.

BMC Bioinformatics. 2007 May 3;8:145.PMID: 17477871 [PubMed - indexed for MEDLINE]Related articlesFree article

A genome-wide survey of copy number variations in Han Chinese residing in Taiwan.

Lin CH, Lin YC, Wu JY, Pan WH, Chen YT, Fann CS.

Genomics. 2009 Oct;94(4):241-6. Epub 2009 Jun 25.PMID: 19559783 [PubMed - indexed for MEDLINE]Related articles

Modeling genetic inheritance of copy number variations.

Wang K, Chen Z, Tadesse MG, Glessner J, Grant SF, Hakonarson H, Bucan M, Li M.

Nucleic Acids Res. 2008 Dec;36(21):e138. Epub 2008 Oct 2.PMID: 18832372 [PubMed - indexed for MEDLINE]Related articlesFree article

High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications.

Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'Arcy M, Frackelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield JP, Dabaghyan E, Eckert A, Onyiah CC, Ostapenko S, Otieno FG, Santa E, Shaner JL, Skraban R, Smith RM, Elia J, Goldmuntz E, Spinner NB, Zackai EH, Chiavacci RM, Grundmeier R, Rappaport EF, Grant SF, White PS, Hakonarson H.

Genome Res. 2009 Sep;19(9):1682-90. Epub 2009 Jul 10.PMID: 19592680 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA.

BMC Bioinformatics. 2007 Oct 2;8:368.PMID: 17910767 [PubMed - indexed for MEDLINE]Related articlesFree article

Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

Macconaill LE, Aldred MA, Lu X, Laframboise T.

BMC Genomics. 2007 Jul 3;8:211.PMID: 17608949 [PubMed - indexed for MEDLINE]Related articlesFree article

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer.

Kloth JN, Oosting J, van Wezel T, Szuhai K, Knijnenburg J, Gorter A, Kenter GG, Fleuren GJ, Jordanova ES.

BMC Genomics. 2007 Feb 20;8:53.PMID: 17311676 [PubMed - indexed for MEDLINE]Related articlesFree article

CNV discovery using SNP genotyping arrays.

Yau C, Holmes CC.

Cytogenet Genome Res. 2008;123(1-4):307-12. Epub 2009 Mar 11. Review.PMID: 19287169 [PubMed - indexed for MEDLINE]Related articles

Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling.

Lin CH, Huang MC, Li LH, Wu JY, Chen YT, Fann CS.

Hum Mutat. 2008 Aug;29(8):1055-62.PMID: 18470944 [PubMed - indexed for MEDLINE]Related articles

Global variation in copy number in the human genome.

Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME.

Nature. 2006 Nov 23;444(7118):444-54.PMID: 17122850 [PubMed - indexed for MEDLINE]Related articlesFree article

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA.

Wong KK, Tsang YT, Shen J, Cheng RS, Chang YM, Man TK, Lau CC.

Nucleic Acids Res. 2004 May 17;32(9):e69.PMID: 15148342 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimation and assessment of raw copy numbers at the single locus level.

Bengtsson H, Irizarry R, Carvalho B, Speed TP.

Bioinformatics. 2008 Mar 15;24(6):759-67. Epub 2008 Jan 19.PMID: 18204055 [PubMed - indexed for MEDLINE]Related articlesFree article