Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing

  • Alkan C
  • Kidd J
  • Marques-bonet T
 et al. 
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Abstract

Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable due to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads allowing 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 73–87 genes will be on average copy-number variable between two human genomes and find that these genic differences overwhelmingly correspond to segmental duplications (OR=135; p

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Authors

  • Can Alkan

  • Jeffrey M Kidd

  • Tomas Marques-bonet

  • Gozde Aksay

  • Fereydoun Hormozdiari

  • Jacob O Kitzman

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