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Author Kato, Mamoru ♦ Kawaguchi, Takahisa ♦ Ishikawa, Shumpei ♦ Umeda, Takayoshi ♦ Nakamichi, Reiichiro ♦ Shapero, Michael H. ♦ Jones, Keith W. ♦ Nakamura, Yusuke ♦ Aburatani, Hiroyuki ♦ Tsunoda, Tatsuhiko
Source CiteSeerX
Content type Text
File Format PDF
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Copy Number Variation ♦ Population-genetic Nature ♦ Human Genome ♦ Bi-allelic Ld ♦ Population Frequency ♦ Cnv Snp Link-age Disequilibrium ♦ Genetic Locus ♦ Segmental Duplication ♦ Kilo-base Scale ♦ Integer Copy Number ♦ Integer Copy Number Allele ♦ Universal Genetic Variation ♦ Probabilistic Theory ♦ Previous Conflict-ing Report ♦ Multi-allelic Cnvs ♦ High Population Differentiation ♦ Simple Genetic Analysis ♦ High-density Microarrays ♦ Several Cnv Region ♦ Cnv Allele ♦ Two-copy Allele ♦ Ld Increase ♦ Deletion-allele Frequency ♦ Cnv Snp Haplo-types ♦ Snp Snp Ld ♦ Genomic Sequence
Abstract Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000–4000 CNVs (4– 6 % of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV–SNP haplo-types. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV–SNP link-age disequilibrium (LD) for 500–900 bi- and multi-allelic CNVs per population revealed that previous conflict-ing reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP–SNP LD, whereas the multi-allelic
Educational Role Student ♦ Teacher
Age Range above 22 year
Educational Use Research
Education Level UG and PG ♦ Career/Technical Study
Publisher Date 2009-01-01