期刊
NATURE METHODS
卷 11, 期 10, 页码 1071-1075出版社
NATURE PORTFOLIO
DOI: 10.1038/NMETH.3094
关键词
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资金
- Prostate Cancer Canada
- Ontario Institute for Cancer Research - Government of Ontario
- Genome Canada through a Large-Scale Applied Project
- Prostate Cancer Canada - November Foundation [RS2014-01]
- Terry Fox Research Institute New Investigator Award
- Canadian Institutes of Health Research New Investigator Award
As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at http://labs.oicr.on.ca/Boutros-lab/software/SeqControl/.
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