Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders
Abstract Background Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated....
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-04-01
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| Series: | BMC Medical Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12920-021-00948-5 |
| _version_ | 1819284190607179776 |
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| author | Yan Sun Fengxia Liu Chunna Fan Yaoshen Wang Lijie Song Zhonghai Fang Rui Han Zhonghua Wang Xiaodan Wang Ziying Yang Zhenpeng Xu Jiguang Peng Chaonan Shi Hongyun Zhang Wei Dong Hui Huang Yun Li Yanqun Le Jun Sun Zhiyu Peng |
| author_facet | Yan Sun Fengxia Liu Chunna Fan Yaoshen Wang Lijie Song Zhonghai Fang Rui Han Zhonghua Wang Xiaodan Wang Ziying Yang Zhenpeng Xu Jiguang Peng Chaonan Shi Hongyun Zhang Wei Dong Hui Huang Yun Li Yanqun Le Jun Sun Zhiyu Peng |
| author_sort | Yan Sun |
| collection | DOAJ |
| description | Abstract Background Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. Methods Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. Results In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. Conclusions The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports. |
| first_indexed | 2024-12-24T01:43:26Z |
| format | Article |
| id | doaj.art-622803846148469f9d00a1a29febd601 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-24T01:43:26Z |
| publishDate | 2021-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-622803846148469f9d00a1a29febd6012022-12-21T17:21:57ZengBMCBMC Medical Genomics1755-87942021-04-0114111310.1186/s12920-021-00948-5Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disordersYan Sun0Fengxia Liu1Chunna Fan2Yaoshen Wang3Lijie Song4Zhonghai Fang5Rui Han6Zhonghua Wang7Xiaodan Wang8Ziying Yang9Zhenpeng Xu10Jiguang Peng11Chaonan Shi12Hongyun Zhang13Wei Dong14Hui Huang15Yun Li16Yanqun Le17Jun Sun18Zhiyu Peng19BGI Genomics, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenBGI Genomics, BGI-ShenzhenBGI Genomics, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenBGI Genomics, BGI-ShenzhenBGI-Beijing Clinical Laboratories, BGI-ShenzhenBGI Genomics, BGI-ShenzhenBGI Genomics, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenBGI Genomics, BGI-ShenzhenAbstract Background Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. Methods Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. Results In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. Conclusions The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.https://doi.org/10.1186/s12920-021-00948-5WGSSensitivity and PPVDP and breadth of coverageCNVClinical diagnosis |
| spellingShingle | Yan Sun Fengxia Liu Chunna Fan Yaoshen Wang Lijie Song Zhonghai Fang Rui Han Zhonghua Wang Xiaodan Wang Ziying Yang Zhenpeng Xu Jiguang Peng Chaonan Shi Hongyun Zhang Wei Dong Hui Huang Yun Li Yanqun Le Jun Sun Zhiyu Peng Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders BMC Medical Genomics WGS Sensitivity and PPV DP and breadth of coverage CNV Clinical diagnosis |
| title | Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders |
| title_full | Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders |
| title_fullStr | Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders |
| title_full_unstemmed | Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders |
| title_short | Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders |
| title_sort | characterizing sensitivity and coverage of clinical wgs as a diagnostic test for genetic disorders |
| topic | WGS Sensitivity and PPV DP and breadth of coverage CNV Clinical diagnosis |
| url | https://doi.org/10.1186/s12920-021-00948-5 |
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