Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants

  • Kim, Kyung (Department of Biomedical Informatics, Ajou University School of Medicine) ;
  • Seong, Moon-Woo (Department of Laboratory Medicine, Seoul National University Hospital College of Medicine) ;
  • Chung, Won-Hyong (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Park, Sung Sup (Department of Laboratory Medicine, Seoul National University Hospital College of Medicine) ;
  • Leem, Sangseob (Department of Biomedical Informatics, Ajou University School of Medicine) ;
  • Park, Won (Department of Functional Genomics, Korea University of Science and Technology) ;
  • Kim, Jihyun (Department of Biomedical Informatics, Ajou University School of Medicine) ;
  • Lee, KiYoung (Department of Biomedical Informatics, Ajou University School of Medicine) ;
  • Park, Rae Woong (Department of Biomedical Informatics, Ajou University School of Medicine) ;
  • Kim, Namshin (Department of Functional Genomics, Korea University of Science and Technology)
  • Received : 2015.04.08
  • Accepted : 2015.05.28
  • Published : 2015.06.30
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Abstract

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

Keywords

References

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