Reducing INDEL errors in whole-genome and exome sequencing

نویسندگان

  • Han Fang
  • Giuseppe Narzisi
  • Jason A. O’Rawe
  • Yiyang Wu
  • Julie Rosenbaum
  • Michael Ronemus
  • Ivan Iossifov
  • Michael C. Schatz
  • Gholson J. Lyon
چکیده

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Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data

Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are ...

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Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome...

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This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whol...

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The Challenge of Small-Scale Repeats for Indel Discovery

Repetitive sequences are abundant in the human genome. Different classes of repetitive DNA sequences, including simple repeats, tandem repeats, segmental duplications, interspersed repeats, and other elements, collectively span more than 50% of the genome. Because repeat sequences occur in the genome at different scales they can cause various types of sequence analysis errors, including in alig...

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تاریخ انتشار 2014