SeqControl: Process control for DNA sequencing

Lauren C. Chong, Marco A. Albuquerque, Nicholas J. Harding, Cristian Caloian, Michelle Chan-Seng-Yue, Richard De Borja, Michael Fraser, Robert E. Denroche, Timothy A. Beck, Theodorus Van Der Kwast, Robert G. Bristow, John Douglas Mcpherson, Paul C. Boutros

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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/.

Original languageEnglish (US)
Pages (from-to)1071-1075
Number of pages5
JournalNature Methods
Volume11
Issue number10
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

DNA Sequence Analysis
Area Under Curve
Process control
Throughput
DNA
Quality Control
Paraffin
Formaldehyde
Industrial applications
Quality control
Prostatic Neoplasms
Software
Pipelines
Genes
Genome
Costs and Cost Analysis
Monitoring
Costs
Data Accuracy

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology
  • Medicine(all)

Cite this

Chong, L. C., Albuquerque, M. A., Harding, N. J., Caloian, C., Chan-Seng-Yue, M., De Borja, R., ... Boutros, P. C. (2014). SeqControl: Process control for DNA sequencing. Nature Methods, 11(10), 1071-1075. https://doi.org/10.1038/nmeth.3094

SeqControl : Process control for DNA sequencing. / Chong, Lauren C.; Albuquerque, Marco A.; Harding, Nicholas J.; Caloian, Cristian; Chan-Seng-Yue, Michelle; De Borja, Richard; Fraser, Michael; Denroche, Robert E.; Beck, Timothy A.; Van Der Kwast, Theodorus; Bristow, Robert G.; Mcpherson, John Douglas; Boutros, Paul C.

In: Nature Methods, Vol. 11, No. 10, 01.01.2014, p. 1071-1075.

Research output: Contribution to journalArticle

Chong, LC, Albuquerque, MA, Harding, NJ, Caloian, C, Chan-Seng-Yue, M, De Borja, R, Fraser, M, Denroche, RE, Beck, TA, Van Der Kwast, T, Bristow, RG, Mcpherson, JD & Boutros, PC 2014, 'SeqControl: Process control for DNA sequencing', Nature Methods, vol. 11, no. 10, pp. 1071-1075. https://doi.org/10.1038/nmeth.3094
Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, De Borja R et al. SeqControl: Process control for DNA sequencing. Nature Methods. 2014 Jan 1;11(10):1071-1075. https://doi.org/10.1038/nmeth.3094
Chong, Lauren C. ; Albuquerque, Marco A. ; Harding, Nicholas J. ; Caloian, Cristian ; Chan-Seng-Yue, Michelle ; De Borja, Richard ; Fraser, Michael ; Denroche, Robert E. ; Beck, Timothy A. ; Van Der Kwast, Theodorus ; Bristow, Robert G. ; Mcpherson, John Douglas ; Boutros, Paul C. / SeqControl : Process control for DNA sequencing. In: Nature Methods. 2014 ; Vol. 11, No. 10. pp. 1071-1075.
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