Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants
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 adeq...
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| Format: | Article |
| Language: | English |
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BioMed Central
2015-06-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-13-31.pdf |
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| author | Kyung Kim Moon-Woo Seong Won-Hyong Chung Sung Sup Park Sangseob Leem Won Park Jihyun Kim KiYoung Lee Rae Woong Park Namshin Kim |
| author_facet | Kyung Kim Moon-Woo Seong Won-Hyong Chung Sung Sup Park Sangseob Leem Won Park Jihyun Kim KiYoung Lee Rae Woong Park Namshin Kim |
| author_sort | Kyung Kim |
| collection | DOAJ |
| description | 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 ~200×. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of 120×. 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×. Moreover, the phenomena were consistent across the breast cancer samples. |
| format | Article |
| id | doaj-art-552e9c6ed5f14e26b43822f6a983f2e1 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2015-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-552e9c6ed5f14e26b43822f6a983f2e12025-02-02T23:07:46ZengBioMed CentralGenomics & Informatics1598-866X2234-07422015-06-01132313910.5808/GI.2015.13.2.31159Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic VariantsKyung Kim0Moon-Woo Seong1Won-Hyong Chung2Sung Sup Park3Sangseob Leem4Won Park5Jihyun Kim6KiYoung Lee7Rae Woong Park8Namshin Kim9Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.Department of Laboratory Medicine, Seoul National University Hospital College of Medicine, Seoul 110-799, Korea.Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.Department of Laboratory Medicine, Seoul National University Hospital College of Medicine, Seoul 110-799, Korea.Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.Department of Functional Genomics, Korea University of Science and Technology, Daejeon 305-806, Korea.Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 443-749, Korea.Department of Functional Genomics, Korea University of Science and Technology, 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 ~200×. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of 120×. 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×. Moreover, the phenomena were consistent across the breast cancer samples.http://genominfo.org/upload/pdf/gni-13-31.pdfclinical applicationdiagnostic variantexome sequencinggenetic variationhigh-throughput nucleotide sequence variantsequencing |
| spellingShingle | Kyung Kim Moon-Woo Seong Won-Hyong Chung Sung Sup Park Sangseob Leem Won Park Jihyun Kim KiYoung Lee Rae Woong Park Namshin Kim Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants Genomics & Informatics clinical application diagnostic variant exome sequencing genetic variation high-throughput nucleotide sequence variant sequencing |
| title | Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants |
| title_full | Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants |
| title_fullStr | Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants |
| title_full_unstemmed | Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants |
| title_short | Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants |
| title_sort | effect of next generation exome sequencing depth for discovery of diagnostic variants |
| topic | clinical application diagnostic variant exome sequencing genetic variation high-throughput nucleotide sequence variant sequencing |
| url | http://genominfo.org/upload/pdf/gni-13-31.pdf |
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