Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Validation of a subset of copy number variants from GSE24424 by aCGH

ABSTRACT: This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%. We interrogated a total of 4,420 individual CNVs and their flanks predicted in 17 individuals from the GSE24424 dataset by rehybridizing their DNAs on a high-resolution custom CGH array (median probe spacing 350 bp).

ORGANISM(S): Mus musculus

SUBMITTER: Charlotte Henrichsen

PROVIDER: E-GEOD-24640 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Segmental copy number variation shapes tissue transcriptomes.

Henrichsen Charlotte N CN Vinckenbosch Nicolas N Zöllner Sebastian S Chaignat Evelyne E Pradervand Sylvain S Schütz Frédéric F Ruedi Manuel M Kaessmann Henrik H Reymond Alexandre A

Nature genetics 20090308 4

Copy number variation (CNV) is a key source of genetic diversity, but a comprehensive understanding of its phenotypic effect is only beginning to emerge. We have generated a CNV map in wild mice and classical inbred strains. Genome-wide expression data from six major organs show not only that expression of genes within CNVs tend to correlate with copy number changes, but also that CNVs influence the expression of genes in their vicinity, an effect that extends up to half a megabase. Genes within ...[more]

PMID: 19270705

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Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.

Dataset Information

Validation of a subset of copy number variants from GSE24424 by aCGH

Publications

Segmental copy number variation shapes tissue transcriptomes.

Similar Datasets

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