Table 2. Description of the different capture designs and number of detected mutations.
| Targeted genes | Design 1 | Design 2 | Design 3 | Number of patients tested | Mutations inducing PTC | Splicing mutationsa | Deleterious missense mutationsb | Potential splicing mutationsc | Potential deleterious missense mutationsd |
|---|---|---|---|---|---|---|---|---|---|
| BRCA1 | x | x | x | 708 | 28 | 3 | 3 | ||
| BRCA2 | x | x | x | 708 | 25 | 7 | 8 | ||
| TP53 | x | x | 468 | 4 | 3e | ||||
| ATM | x | x | x | 708 | 4 | 1 | 1 | 9 | |
| BAP1 | x | x | 379 | ||||||
| BARD1 | x | x | x | 708 | 1 | ||||
| BRIP1 | x | x | x | 708 | |||||
| CDH1 | x | x | x | 708 | 1 | ||||
| CHEK2 | x | x | x | 708 | 3 | 2 | 2 | 8 | |
| MLH1 | x | x | 468 | 2 | |||||
| MLH3 | x | x | 468 | 1 | 1 | ||||
| MRE11A | x | x | x | 708 | 3 | 1 | 1 | ||
| MSH2 | x | x | 468 | 3 | 2 | ||||
| MSH6 | x | x | 468 | 1 | |||||
| NBS1 | x | x | x | 708 | 3 | 4 | 1 | ||
| PALB2 | x | x | x | 708 | 7 | 3 | |||
| PMS1 | x | x | 468 | 1 | 1 | ||||
| PMS2 | x | x | 468 | 1 | 1 | 2 | |||
| PTEN | x | x | x | 708 | |||||
| RAD50 | x | x | x | 708 | 1 | 1 | |||
| RAD51 | x | 139 | |||||||
| RAD51B | x | 139 | 1 | ||||||
| RAD51C | x | x | x | 708 | 2 | 1 | |||
| RAD51D | x | x | 379 | ||||||
| STK11 | x | x | x | 708 | |||||
| XRCC2 | x | 139 | |||||||
| XRCC3 | x | 139 |
Abbreviation: PTC, premature termination codon.
a
Mutations within the canonical AG/GT splice sites, or mutations previously known to induce a splicing defect in BRCA1, BRCA2 and TP53.
b
Published deleterious missense mutations.
c
Variations within the consensus sites inducing a 15% of decrease of the MaxEntScan sore and a 5% decrease of the SpliceSiteFinder except mutations listed in a.
d
Missense mutations with an Align GVGD score >C45 and a MAF in ESP samples <0.01 excluding those in b and excluding published neutral variants.
e
Missense mutations in TP53 reported as ‘probably deleterious' were only filtered against MAF in ESP samples <0.01.