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).
| Concordant | Unique to sample type 1 | Unique to sample type 2 | Concordant | Unique to sample type 1 | Unique to sample type 2 | Concordant | Unique to sample type 1 | Unique to sample type 2 | ||
| Sample type 1 | Sample type 2 | [1 kb, 5 kb) | [5 kb,10 kb) | [10 kb,…) | ||||||
| Deletions | ||||||||||
| HuRef blood 1 | HuRef blood 2 | 127 | 41 (3/3) | 35 (2/3) | 66 | 7 (3/3) | 2 (2/2) | 31 | 0 (0/0) | 1 (1/1) |
| Blood | Non-enriched saliva | 463 | 244 (32/32) | 117 (23/23) | 222 | 64 (29/29) | 14 (13/13) | 147 | 15 (12/12) | 4 (3/4) |
| Blood | Non-enriched buccal | 460 | 247 (35/35) | 107 (19/19) | 248 | 38 (23/23) | 13 (10/10) | 149 | 13 (11/11) | 9 (7/9) |
| Enriched saliva | Non-enriched saliva | 359 | 100 (18/18) | 220 (22/23) | 190 | 37 (21/21) | 47 (19/19) | 123 | 7 (7/7) | 28 (8/9) |
| Enriched buccal | Non-enriched buccal | 209 | 18 (14/14) | 360 (36/37) | 104 | 7 (6/7) | 154 (34/34) | 71 | 12 (4/9) | 88 (23/24) |
| Duplications | ||||||||||
| HuRef blood 1 | HuRef blood 2 | 28 | 2 (1/2) | 10 (1/3) | 17 | 3 (2/3) | 2 (1/2) | 32 | 2 (0/2) | 3 (0/3) |
| Blood | Non-enriched saliva | 107 | 34 (10/21) | 17 (6/15) | 49 | 13 (6/13) | 3 (1/3) | 150 | 9 (1/8) | 14 (0/12) |
| Blood | Non-enriched buccal | 105 | 36 (7/21) | 31 (5/22) | 48 | 14 (7/14) | 10 (2/10) | 146 | 13 (0/10) | 11 (1/10) |
| Enriched saliva | Non-enriched saliva | 85 | 12 (5/10) | 39 (7/19) | 33 | 6 (3/6) | 18 (7/12) | 123 | 27 (1/17) | 42 (4/22) |
| Enriched buccal | Non-enriched buccal | 49 | 3 (0/3) | 84 (12/36) | 22 | 1 (1/1) | 40 (12/27) | 110 | 33 (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
, 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.
