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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Copy number variation in inbred and wild mice

ABSTRACT: Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs. 3-5 males from 13 inbred strains and 21 Mus musculus caught in various geographic locations were compared to a single C57BL/6J individual by array comparative genome hybridisation.

ORGANISM(S): Mus spretus

SUBMITTER: Charlotte Henrichsen

PROVIDER: E-GEOD-24424 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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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Copy number variation in inbred and wild mice

Project description:Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs.

2010-12-31 | GSE24424 | GEO

Validation and copy number variation in inbred and wild mice

Project description:This SuperSeries is composed of the following subset Series: GSE24424: Copy number variation in inbred and wild mice GSE24640: Validation of a subset of copy number variants from GSE24424 by aCGH Refer to individual Series

2010-12-31 | E-GEOD-24643 | biostudies-arrayexpress

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2010-12-31 | E-GEOD-24640 | biostudies-arrayexpress

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2010-06-30 | E-GEOD-2597 | biostudies-arrayexpress

A high resolution map of segmental DNA copy number variation in the mouse genome

Project description:Submicroscopic (< 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study twenty-one well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays (oligo-aCGH) to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21-2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. 21 strains of mouse were assayed for copy number changes. Seven strains were assayed at least twice. DNA was extracted from tail for all strains. For two strains spleen DNA was also assayed on separate chips. C57BL/6 was used as the reference sample in all experiments.

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CGH analysis of haploid ES cells

Project description:DNA samples of haploid ES cells and control DNA were compared to genomic DNA of the C57B/6 inbred mouse strain on a NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9), (GPL10989) this analysis was performed to analyse copy number variations in haploid mouse ES cells from different genetic backgrounds. Male C57/B6 DNA was used as control. To identify CNVs based on the different genetic background control experiments comparing DNA from the inbred CBA and a mixed transgeneic mouse strain were performed.

2011-07-22 | E-GEOD-30749 | biostudies-arrayexpress

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

Project description:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1,000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385,000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH, and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM’s performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of less than 10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2-5 kb, and 1 kb, respectively. Keywords: CNV detection algorithm development and assessment All four samples in this series are hybridizations of genomic DNA from inbred mouse strains 129X1/SvJ versus C57BL6/J. The experiments were performed at increasing resolutions (one 385K, two 2.1M, and one 3.1M).

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