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

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

	Panel+^a/WGS–^b	Panel–/WGS+	Panel+/WGS+	Panel–/WGS–	PPA [95% CI]	NPA [95% CI]
All compiled	76^c	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%]

^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

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