Characterizing coverage and accuracy of clinical WGS as a diagnostic test for genetic disorders

Purpose: To evaluate the coverage and accuracy of clinical whole genome sequencing as a diagnostic test for monogenic disorders. Methods: All the samples underwent WGS using MGISEQ-2000. The performance of NA12878, NA24631, NA24694 and NA24695 and YH cell line were measured for sensitivity, PPV (analytical positive predictive value), coverage of depth and breadth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern in the Chinese trios. Results: With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was >99.25% and >99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. However, even with a mean depth of ~150X, the sensitivity and PPV is still not 100%. We observed a substantial variation in the detection rate of CNVs across different tools. With a mean depth of ~40X, NA12878-2 showed the highest CNV detection rate of more than 89.66% in our new CNV call set using BreakDancer. In general, the breadth of coverage for disease-associated genes and CNV syndromes increased with mean depth. For the American College of Medical Genetics and Genomics 59 genes, 100% of genes covered at 10X required a mean depth of more than 90X for NA12878. Among the Chinese trios, FNRs in the offspring were 0.52% and 3.64% for SNP and indel detection at well-covered variants. Conclusion: The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and the identification of most CNVs. Clinical scientists should know 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.