Personalized copy number and segmental duplication maps using next-generation sequencing. Export

@article{citeulike:5687044, abstract = {Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology.}, author = {Alkan, Can and Kidd, Jeffrey M. and Marques-Bonet, Tomas and Aksay, Gozde and Antonacci, Francesca and Hormozdiari, Fereydoun and Kitzman, Jacob O. and Baker, Carl and Malig, Maika and Mutlu, Onur and Sahinalp, S. Cenk and Gibbs, Richard A. and Eichler, Evan E.}, citeulike-article-id = {5687044}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng.437}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng.437}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19718026}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19718026}, day = {30}, doi = {10.1038/ng.437}, issn = {1546-1718}, journal = {Nature genetics}, keywords = {cnv, nextgen, segmental\_duplication}, month = {October}, number = {10}, pages = {1061--1067}, posted-at = {2009-09-02 12:04:21}, priority = {4}, publisher = {Nature Publishing Group}, title = {Personalized copy number and segmental duplication maps using next-generation sequencing.}, url = {http://dx.doi.org/10.1038/ng.437}, volume = {41}, year = {2009} }

TY - JOUR ID - citeulike:5687044 L3 - citeulike-article-id:5687044 N2 - Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology. IS - 10 JF - Nature genetics SN - 1546-1718 EP - 1067 TI - Personalized copy number and segmental duplication maps using next-generation sequencing. PB - Nature Publishing Group VL - 41 SP - 1061 KW - cnv KW - nextgen KW - segmental_duplication AU - Alkan, Can AU - Kidd, Jeffrey AU - Marques-Bonet, Tomas AU - Aksay, Gozde AU - Antonacci, Francesca AU - Hormozdiari, Fereydoun AU - Kitzman, Jacob AU - Baker, Carl AU - Malig, Maika AU - Mutlu, Onur AU - Sahinalp, Cenk AU - Gibbs, Richard AU - Eichler, Evan PY - 2009/10/30/ UR - http://dx.doi.org/10.1038/ng.437 ER -