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).
| 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 is the number of CNVs verified as correct by visual inspection and 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.