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Table 2 Accuracy of variant calling across genomic contexts and variant types in patient samples

From: Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

  Panel+a/WGS–b Panel–/WGS+ Panel+/WGS+ Panel–/WGS– PPA [95% CI] NPA [95% CI]
All compiled 76c 201 29,475 45,847,148 99.74% [99.68–99.81%] 100% [100–100%]
P/LP variants only 0 0 145 28,474,503 100% [100–100%] 100% [100–100%]
SNVs only 23 6 28,710 45,848,108 99.92% [99.87–99.97%] 100% [100–100%]
Insertions only 9 8 225 29,887,204 96.20% [94.30–98.00%] 100% [100–100%]
Deletions only 33 12 540 42,170,158 94.24% [92.65–95.83%] 100% [100–100%]
Segmental duplications 12 2 2119 38,466,267 99.44% [99.10–99.78%] 100% [100–100%]
Known pseudogenes 9 74 1075 45,676,596 99.17% [98.60–99.73%] 100% [100–100%]
Low mappability regions 18 12 1069 36,912,107 98.34% [97.84–98.85%] 100% [100–100%]
Low complexity regions 24 69 956 38,072,735 97.55% [96.35–98.75%] 100% [100–100%]
Low GC regions 6 12 197 14,792,575 97.04% [95.87–98.22%] 100% [100–100%]
High GC regions 0 0 23 3,891,553 100% [100–100%] 100% [100–100%]
Heterozygous variants only 75 147 18,295 45,858,382 99.59% [98.48–99.70%] 100% [100–100%]
Homozygous variants only 1 83 11,180 45,865,561 99.99% [99.97–100%] 100% [100–100%]
  1. a+ indicates that a variant was present on the panel or the corresponding whole genome sequencing (WGS) sample. b– indicates that a variant was not present on the panel or the corresponding WGS sample. cSubsequent to the investigational device exemption (IDE) submission, additional review indicated that this number should in fact be a total of 21 panel positive, but WGS negative variants distributed across the various subcategories (some variants were missannotated in the original tables). However, to reflect what was actually submitted as part of the IDE, the original number is listed here. The impact on overall performance measures is small. PPA positive percent agreement, CI confidence interval, NPA negative percent agreement, P/LP pathogenic/likely pathogenic, SNVs single-nucleotide variants