Skip to main content

Table 1 List of genes with positive samples tested in the validation study

From: Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

Gene Total samples tested With Known SNVs With Known Indels With Known CNVs
Exons Tested N Exons Tested N N
APC 14 4,8,16 9 5,16 4 1
ATM 1 - - 10 1 -
BAP1 1 - - 8 1 -
BMPR1A 1 - - - - 1
BRCA1 48 2,3,4,6,10,12,13,17,20,23 13 2,3,7,8,10,14,15,16,19,23 23 12
BRCA2 38 3,4,9,11,12,14,18,23,27 12 5,10,11,14,15,17 21 5
CDH1 12 1,3,5,7,10,14 7 8,10,12,15 4 1
CDKN2A 2 2 2 - - -
CHEK2 1 11 1 - - -
EGFR 1 20 1 - - -
EPCAM 1 - - - - 1
FH 5 1,8 2 7,8 2 1
MLH1 26 1,4,7,12,14,19 7 1,2,9,10,11,12,16,19 16 3
MSH2 44 2,3,5,6,7,8,10,12 21 6,7,12,13 6 17
MSH6 10 - - 4,5,6,8,9,10 10 -
MUTYH 10 2,7,10,12,13,15,16 8 10,14 2 -
PALB2 5 4,7,9 3 - - 2
PTEN 4 1,5 3 3 1 -
RB1 2 12 1 22 1 -
SMAD4 2 - - 10,12 2 -
STK11 2 5 1 1 1 -
TP53 3 2,3,10 3 - - -
TOTAL 233   94   95 44
  1. 5 samples tested were known to be positive for more than 1 germline variant. These mutations included: 1) MSH6 and MLH1 frameshift indels, 2) MSH2 and EPCAM large deletions, 3) MUTYH frameshift indel and p.Y179C missense mutation, 4) MSH2 large deletion and p.P616R missense mutation and 5) APC frameshift indel and p.L1129S