Table 2.

Summary of the impact of DNA source and eukaryotic DNA enrichment on the accuracy of genetic variant detection from whole-genome sequencing data.

Variant type	Sensitivity	False positive rate
Blood versus non-enriched saliva or buccal
SNVs	Little or no difference	Blood
Indels	Little or no difference	Little or no difference
CNVs (deletions)	Blood	Little or no difference
CNVs (duplications)	Blood	Blood
Enriched versus non-enriched saliva or buccal
SNVs	Little or no difference	Enriched
Indels	Little or no difference	Little or no difference
CNVs (deletions)	Non-enriched	Little or no difference
CNVs (duplications)	Non-enriched	Non-enriched

For each comparison, the better sample type (ie, the one having higher sensitivity or a lower false positive rate) is indicated. Blood and enriched saliva and buccal samples tended to have lower false positive rates for SNVs than non-enriched saliva and buccal samples, but the magnitude of the differences were small except when considering rare SNVs (see text) and exhibited variability across individuals.

CNV, copy number variant; SNV, single nucleotide variant.