Table 1.
Exon-targeted detection of gene CNVs
| Locia |
Total count (%) |
Conservative/stringentb count (%) |
|
|---|---|---|---|
| All gene CNVs | 397 (14) | 255 (9) | |
| Signal: | gain only | 170 (43) | 97 (38) |
| loss only | 123 (31) | 80 (31) | |
| gain & loss | 104 (26) | 78 (31) | |
| Within SDs | 239 (60) | 163 (64) | |
| Common | 205 (52) | 164 (64) | |
| Whole gene CNV | 166 (6) | 134 (5) | |
| Signal: | gain only | 61 (37) | 50 (37) |
| loss only | 47 (28) | 41 (31) | |
| gain & loss | 58 (35) | 40 (30) | |
| Within SDs | 136 (82) | 96 (72) | |
| Common | 127 (77) | 85 (63) | |
| Single exon | 50 (30) | 30 (22) | |
| Partial gene CNV only | 231 (8) | 121 (4) | |
| Signal: | gain only | 109 (47) | 47 (39) |
| loss only | 76 (33) | 39 (32) | |
| gain & loss | 46 (20) | 35 (29) | |
| Within SDs | 111 (48) | 67 (55) | |
| Common | 95 (41) | 79 (65) | |
| Genes negative for CNV | 2393 (86) | 2535 (91) | |
| Within SDs | 333 (14) | 409 (16) | |
| Total candidates | 2790 | 2790 | |
| Within SDs | 572 (21) | 572 (21) | |
a
Within SDs: =50% of exonic sequence fall within segmental duplications (SD). Common: Detected in >1 individual.
b
Estimate based on retaining one locus per duplication cluster and removing two exon CNVs in large genes (>5 exons) appearing in a single individual as likely false positives; thereby providing a minimal estimate of CNV within our studied individuals.