2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2015
Abstrakt

Jared T. Simpson, Rebecca E. McIntyre, David J. Adams, Richard Durbin. Copy number variant detection in inbred strains from short read sequence data. Bioinformatics, 26(4):565-567. 2010.

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Abstract:

SUMMARY: We have developed an algorithm to detect copy number variants (CNVs) in 
homozygous organisms, such as inbred laboratory strains of mice, from short read 
sequence data. Our novel approach exploits the fact that inbred mice are
homozygous at virtually every position in the genome to detect CNVs using a
hidden Markov model (HMM). This HMM uses both the density of sequence reads
mapped to the genome, and the rate of apparent heterozygous single nucleotide
polymorphisms, to determine genomic copy number. We tested our algorithm on short
read sequence data generated from re-sequencing chromosome 17 of the mouse
strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 
copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the
performance of our algorithm through comparison to CNVs previously identified by 
array-comparative genomic hybridization (array CGH). We performed
quantitative-PCR validation on a subset of the calls that differed from the array
CGH data sets.