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Copy number variation of individual cattle genomes using next-generation sequencing

Author:
Bickhart, Derek K., Hou, Yali, Schroeder, Steven G., Alkan, Can, Cardone, Maria Francesca, Matukumalli, Lakshmi K., Song, Jiuzhou, Schnabel, Robert D., Ventura, Mario, Taylor, Jeremy F., Garcia, Jose Fernando, Van Tassell, Curtis P., Sonstegard, Tad S., Eichler, Evan E., Liu, George E.
Source:
Genome Research 2012 v.22 no.4 pp. 778-790
ISSN:
1088-9051
Subject:
Angus, Hereford, Holstein, Nellore, cattle, chromosome mapping, fluorescence in situ hybridization, gene dosage, genes, genetic variation, polymerase chain reaction, sequence analysis, surveys
Abstract:
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ~55.6-Mbp sequence--476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, ?(2) test; P-value
Handle:
10113/56916