PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Research Abstract Details 

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PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Abstract Text:

Kai Wang,Mingyao Li,Dexter Hadley,Rui Liu,Joseph Glessner,Struan F A Grant,Hakon Hakonarson,Maja Bucan,Kai Wang,Mingyao Li,Dexter Hadley,Rui Liu,Joseph Glessner,Struan F A Grant,Hakon Hakonarson,Maja Bucan,

Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs, and the pedigree information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average, we detected approximately 27 CNVs for each individual with a median size of approximately 12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction of CNVs in offspring not detected in parents (CNV-NDPs) was 3.3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping.

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Publishing Authors By Initials

K Wang,M Li,D Hadley,R Liu,J Glessner,SF Grant,H Hakonarson,M Bucan,K Wang,M Li,D Hadley,R Liu,J Glessner,SF Grant,H Hakonarson,M Bucan,

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PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Genome research

VOLUME: 17

Page Numbers: 1665-74

Journal Abbreviation: Genome Res.

ISSN: 1088-9051

DAY: 5

MONTH: 10

YEAR: 2007

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Information

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LANGUAGE: eng

NlmUniqueID: 9518021

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Grant and Affiliation Information for PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

AFFILIATION: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

Country: United States

AGENCY: United States NIMH

GRANT: R01 MH604687

ACRONYM: MH

MEDLINETA: Genome Res

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