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Methods and strategies for analyzing copy number variation using DNA microarrays.

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TLDR
Current challenges involve developing methods not only for detecting and cataloging CNVs in human populations at increasingly higher resolution but also for determining the association of CNVs with biological function, recent human evolution, and common and complex human disease.
Abstract
The association of DNA copy-number variation (CNV) with specific gene function and human disease has been long known, but the wide scope and prevalence of this form of variation has only recently been fully appreciated. The latest studies using microarray technology have demonstrated that as much as 12% of the human genome and thousands of genes are variable in copy number, and this diversity is likely to be responsible for a significant proportion of normal phenotypic variation. Current challenges involve developing methods not only for detecting and cataloging CNVs in human populations at increasingly higher resolution but also for determining the association of CNVs with biological function, recent human evolution, and common and complex human disease.

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Journal ArticleDOI

Coming of age: ten years of next-generation sequencing technologies

TL;DR: These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.
Journal ArticleDOI

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

TL;DR: PennCNV, a hidden Markov model (HMM) based approach, is presented for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data, demonstrating the feasibility of whole-genome fine-mapping ofCNVs via high- density SNP genotypesing.
Journal ArticleDOI

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

TL;DR: By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, it is estimated that at least 11% of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier.
Journal ArticleDOI

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

TL;DR: This work demonstrates the analysis, individually and as mixtures, of 95 bacterial artificial chromosome clones that cover the 4.7-Mb human major histocompatibility complex region and obtains accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length.
References
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Journal ArticleDOI

A haplotype map of the human genome

John W. Belmont, +232 more
TL;DR: A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.
Journal ArticleDOI

Detection of large-scale variation in the human genome.

TL;DR: This article identified 255 loci across the human genome that contain genomic imbalances among unrelated individuals, and revealed that half of these regions overlap with genes, and many coincide with segmental duplications or gaps in human genome assembly.
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