Development and validation of next generation sequencing based 35-gene hereditary cancer panel

Table 2 Overview of results for 4820 variants, of which 62 variants had been classified as pathogenic or likely pathogenic in APC, ATM, BRCA1, BRCA2, CDKN2A, MEN1 and PTEN

Gene	Total Variants	True Positives	False Negatives
APC	622	622	0
ATM	176	176	0
BAP1	17	17	0
BARD1	298	298	0
BMPR1A	82	82	0
BRCA1	399	399	0
BRCA2	577	577	0
BRIP1	331	331	0
CDH1	116	116	0
CDK4	0	0	0
CDKN2A	29	29	0
CHEK2	19	19	0
EPCAM	111	111	0
GREM1	31	31	0
MEN1	252	252	0
MITF	4	4	0
MLH1	34	34	0
MRE11	140	140	0
MSH2	104	104	0
MSH6	104	104	0
MUTYH	76	76	0
NBN	260	260	0
PALB2	41	41	0
PMS1	10	10	0
PMS2	362	362	6^a
POLD1	124	124	0
POLE	322	322	0
PTEN	7	7	0
RAD50	10	10	0
RAD51C	10	10	0
RAD51D	55	55	0
SMAD4	0	0	0
STK11	8	8	0
TP53	85	85	0
XRCC2	4	4	0
TOTAL	4820	4820	6^a

^a6 variants at the position Chr7:6013153 in PMS2 is a false negative. But, this is in a pseudogene region and is also a benign variant

ISSN: 1897-4287