Publication Date:
2010-10-30
Description:
Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020103/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020103/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sudmant, Peter H -- Kitzman, Jacob O -- Antonacci, Francesca -- Alkan, Can -- Malig, Maika -- Tsalenko, Anya -- Sampas, Nick -- Bruhn, Laurakay -- Shendure, Jay -- 1000 Genomes Project -- Eichler, Evan E -- 085532/Wellcome Trust/United Kingdom -- HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120-03/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21030649" target="_blank"〉PubMed〈/a〉
Keywords:
Chromosome Mapping
;
Continental Population Groups/genetics
;
*DNA Copy Number Variations
;
Databases, Nucleic Acid
;
Evolution, Molecular
;
Female
;
Gene Conversion
;
*Gene Dosage
;
*Gene Duplication
;
Gene Frequency
;
Genes, Duplicate
;
*Genetic Variation
;
*Genome, Human
;
Genomics/*methods
;
Genotype
;
Haplotypes
;
Humans
;
Male
;
Polymorphism, Single Nucleotide
;
Sequence Analysis, DNA
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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