Table 1

SNV- and indel-detection concordance between blood samples and non-enriched saliva or buccal samples and between enriched saliva or buccal samples and the corresponding non-enriched samples, for filtered variants detected anywhere in the genome.

ConcordantUnique to sample type 1Unique to sample type 2ConcordantUnique to sample type 1Unique to sample type 2
Sample type 1Sample type 2          Known          Novel
SNVs
 HuRef blood 1HuRef blood 294.83.61.652.439.58.1
 BloodNon-enriched saliva96.41.71.856.614.029.4
 BloodNon-enriched buccal96.12.01.949.714.935.4
 Enriched salivaNon-enriched saliva96.81.61.656.717.026.4
 Enriched buccalNon-enriched buccal96.11.82.148.816.334.9
Indels
 HuRef blood 1HuRef blood 287.45.96.765.414.220.3
 BloodNon-enriched saliva87.05.97.163.416.620.0
 BloodNon-enriched buccal86.46.47.263.416.220.3
 Enriched salivaNon-enriched saliva87.16.26.763.318.917.7
 Enriched buccalNon-enriched buccal86.46.67.064.518.017.4
  • Concordances are shown for known variants (those present in gnomAD) and novel variants. Numbers represent the percentage of variants in that category; for instance, of all known SNVs detected in either the non-enriched or the enriched buccal samples from a given individual, 96.1% were detected in both non-enriched and enriched, 1.8% were detected only in enriched, and 2.1% were detected only in non-enriched. HuRef blood 1 and HuRef blood 2 refer to replicates sequenced from the same blood-derived DNA sample and represent a baseline level of concordance; all other values were aggregated across the four study participants. For individual-specific data, see online supplementary file 3.

  • SNV, single nucleotide variant.