From days to hours: Reporting clinically actionable variants from whole genome sequencing

Sumit Middha, Saurabh Baheti, Steven Hart, Jean-Pierre Kocher

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

As the cost of whole genome sequencing (WGS) decreases, clinical laboratories will be looking at broadly adopting this technology to screen for variants of clinical significance. To fully leverage this technology in a clinical setting, results need to be reported quickly, as the turnaround rate could potentially impact patient care. The latest sequencers can sequence a whole human genome in about 24 hours. However, depending on the computing infrastructure available, the processing of data can take several days, with the majority of computing time devoted to aligning reads to genomics regions that are to date not clinically interpretable. In an attempt to accelerate the reporting of clinically actionable variants, we have investigated the utility of a multi-step alignment algorithm focused on aligning reads and calling variants in genomic regions of clinical relevance prior to processing the remaining reads on the whole genome. This iterative workflow significantly accelerates the reporting of clinically actionable variants with no loss of accuracy when compared to genotypes obtained with the OMNI SNP platform or to variants detected with a standard workflow that combines Novoalign and GATK.

Original languageEnglish (US)
Article numbere86803
JournalPLoS One
Volume9
Issue number2
DOIs
StatePublished - Feb 5 2014

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Workflow
Genes
Genome
Technology
genome
Human Genome
Genomics
Clinical laboratories
Single Nucleotide Polymorphism
genomics
Patient Care
patient care
Genotype
Processing
Costs and Cost Analysis
infrastructure
genotype
Costs

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

From days to hours : Reporting clinically actionable variants from whole genome sequencing. / Middha, Sumit; Baheti, Saurabh; Hart, Steven; Kocher, Jean-Pierre.

In: PLoS One, Vol. 9, No. 2, e86803, 05.02.2014.

Research output: Contribution to journalArticle

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