CNV

From SNPedia

Copy Number Variations are relatively large changes in the genome. this article provides an approachable introduction to the topic.

dbVAR is the NCBI database of structural variations. It's overview is a more technical survery. It uses nsv### identifiers. These are comparable to either the rs### or perhaps the ss###.

the Database of Genomic Variants at http://projects.tcag.ca/variation/ is an upstream resource, but becuase it identifies based on coordinates not names.

http://www.nature.com/nature/journal/v461/n7265/fig_tab/nature08494_T2.html shows some CNVs linked to diseases.

identical twins seem to have differences in CNVs. sciencedaily

near minute 34 of this video James Watson discusses Copy Number Polymorphisms related to autism

[PMID 18204055] extracts CNVs from microarray data

[PMID 17189289] demonstrates the importance of CNVs relative to SNPs

[PMID 17206864] A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome.

[PMID 17122084] Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.

PDF Poster Determination of Genomic Copy Number Variation (CNV) using the SNPLex Genotyping System (can't direct link)

SNP and CNV variation correlated with altered activity in almost 900 and 240 genes, respectively. The HapMap has been invaluable in detecting variants involved in many diseases and these results suggest that the CNV index will prove similarly useful.

"The remarkable finding was that there is such little overlap in the genes found by using the two indices," commented Dr Matthew Hurles, also a leader of the project at the Wellcome Trust Sanger Institute. "Only about 10% of the activity variants associated with a CNV were also associated with a SNP.

"This suggests that we must include CNV studies in our searches for genetic variation associated with disease or we will be missing a lot of the important genetic effects."

The results show that at least 10-20% of heritable variation in gene activity is due to CNVs. The team found associations that included previously known examples, such as UGT2B17, which has been associated with Prostate cancer, proving that the new approach works well. [1]

[PMID 17289997] SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap.

[PMID 17280605] a paper which appears to link CNVs to Breast Cancer

[PMID 17529978] FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity.

DEFB4 Beta-defensin gene CNV is correlated to both Crohn's disease (if you have too few copies) and psoriasis (if you have too many copies)

[PMID 17921354] software. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

[PMID 17910767] discusses several packages for determining CNVs in microarray data