Table 3

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 common CNVs (those with >1% frequency in MSSNG parents32).

ConcordantUnique to
sample type 1
Unique to
sample type 2
ConcordantUnique to
sample type 1
Unique to
sample type 2
ConcordantUnique to
sample type 1
Unique to
sample type 2
Sample type 1Sample type 2[1 kb, 5 kb)[5 kb,10 kb)[10 kb,…)
Deletions
 HuRef blood 1HuRef blood 212741 (3/3)35 (2/3)667 (3/3)2 (2/2)310 (0/0)1 (1/1)
 BloodNon-enriched saliva463244 (32/32)117 (23/23)22264 (29/29)14 (13/13)14715 (12/12)4 (3/4)
 BloodNon-enriched buccal460247 (35/35)107 (19/19)24838 (23/23)13 (10/10)14913 (11/11)9 (7/9)
 Enriched salivaNon-enriched saliva359100 (18/18)220 (22/23)19037 (21/21)47 (19/19)1237 (7/7)28 (8/9)
 Enriched buccalNon-enriched buccal20918 (14/14)360 (36/37)1047 (6/7)154 (34/34)7112 (4/9)88 (23/24)
Duplications
 HuRef blood 1HuRef blood 2282 (1/2)10 (1/3)173 (2/3)2 (1/2)322 (0/2)3 (0/3)
 BloodNon-enriched saliva10734 (10/21)17 (6/15)4913 (6/13)3 (1/3)1509 (1/8)14 (0/12)
 BloodNon-enriched buccal10536 (7/21)31 (5/22)4814 (7/14)10 (2/10)14613 (0/10)11 (1/10)
 Enriched salivaNon-enriched saliva8512 (5/10)39 (7/19)336 (3/6)18 (7/12)12327 (1/17)42 (4/22)
 Enriched buccalNon-enriched buccal493 (0/3)84 (12/36)221 (1/1)40 (12/27)11033 (0/22)46 (5/19)
  • The ‘concordant’ columns contain the number of CNVs detected in both sample type 1 and sample type 2. The ‘unique to sample type 1’ columns contain the total number of CNVs detected in sample type 1 but not sample type 2, followed by an expression of the form Embedded Image, where X is the number of CNVs verified as correct by visual inspection and Y is the total number inspected (and analogously for the ‘unique to sample type 2’ columns). For example, 209 common deletions between 1 and 5 kb were detected in both the enriched buccal sample and the non-enriched buccal sample in the same individual, while 18 were detected only in the enriched buccal sample and 360 were detected only in the non-enriched buccal sample. Of the 37 deletions detected only in non-enriched buccal samples that were checked by visual confirmation, 36 were classified as true. 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 counts were aggregated across the four study participants. For individual-specific data, see online supplementary file 3.

  • CNV, copy number variant.