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Measuring coverage and accuracy of whole-exome sequencing in clinical context

Abstract

Purpose

To evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors.

Methods

Blood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio.

Results

Mean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability. For the two vendors with mean depth of coverage >120 ×, analytic positive predictive values (aPPVs) exceeded 99.1% for single-nucleotide variants and homozygous indels, and sensitivities were 98.9–99.9%; however, heterozygous indels showed lower accuracy and sensitivity. Among the trios, FNRs in the offspring were 0.07–0.62% at well-covered variants concordantly called in both parents.

Conclusion

The current standard of 120 × coverage for clinical WES may be insufficient for consistent breadth of coverage across the exome. Ordering clinicians and researchers would benefit from vendors’ reports that estimate sensitivity and aPPV, including depth of coverage across the exome.

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Acknowledgments

This work was supported by the Boston Children’s Hospital Precision Link initiative. S.W.K. was supported, in part, by a grant from the National Institutes of Health (R01MH107205).

Author information

Disclosure

The authors declare no conflict of interest.

Correspondence to Sek Won Kong MD.

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Keywords

  • breadth of coverage
  • depth of coverage
  • false negatives
  • pharmacogenomics
  • whole-exome sequencing

Further reading

Figure 1: Variability in breadth of coverage for the American College of Medical Genetics and Genomics (ACMG) 56 genes and 63 pharmacogenes among the nine individuals.
Figure 2: Analytical positive predictive value and sensitivity of variant calls from each vendor.
Figure 3: Vendor-specific false-negative rates in trio.