Genomics Inform.  2015 Jun;13(2):31-39. 10.5808/GI.2015.13.2.31.

Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants

  • 1Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.
  • 2Department of Biomedical Science, Graduate School, Ajou University, Suwon 443-749, Korea.
  • 3Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
  • 4Department of Laboratory Medicine, Seoul National University Hospital College of Medicine, Seoul 110-799, Korea.
  • 5Department of Functional Genomics, Korea University of Science and Technology, Daejeon 305-806, Korea.
  • 6Epigenomics Research Center, Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.


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 ~200x. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of 120x. 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 120x. Moreover, the phenomena were consistent across the breast cancer samples.


clinical application; diagnostic variant; exome sequencing; genetic variation; high-throughput nucleotide sequence variant; sequencing

MeSH Terms

Breast Neoplasms
Genetic Variation
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