Table 2.
BAP1 alterations and co-existing genomic alterations, TMB and MSI status in patients with advanced BAP1 - altered MPM.
| Patients | BAP1 alteration | Somatic/germline nature of BAP1 alteration | Co-existing genomic alterations | TMB, muts/Mb | MSI |
|---|---|---|---|---|---|
| #1 | BAP1 Q684 | NA | CDKN2A/B loss; NOTCH3 R1893 |
4 | MS-stable |
| #2 | BAP1 F660fs*32 | NA The sample failed the copy BAP1 number quality metrics for SGZ calling, whereas somatic/germline calling was still unavailable with manual review |
MLL2 splice site 14382+1G>T | NA | NA |
| #3 | BAP1 loss exons 9-17 | NA Somatic/germline calling is not available for copy number alteration events |
NF2 W74; CDKN2A p16INK4a R80* and p14ARF P94L; CREBBP complex rearrangement |
3 | MS-stable |
| #4 | BAP1 E198fs*45 | NA The sample failed the copy number quality metrics for SGZ calling, whereas somatic/germline calling was still unavailable with manual review |
DNMT3A D529fs*16 | NA | NA |
| #5 | BAP1 splice site 375+2T>C | NA | HGF amplification; CDKN2A/B loss; PBRM1 deletion exons 8-12 |
5 | MS-stable |
| #6 | BAP1 loss exons 13-17 | NA Somatic/germline calling is not available for copy number alteration events |
TP53 splice site 9209_993+70del153 | 1 | MS-stable |
| #7 | BAP1 loss | NA Somatic/germline calling is not available for copy numberalteration events |
KDM6A loss; PBRM1 loss exons 23-30 | NA | NA |
| #8 | BAP1 copy number loss | NA Somatic/germline calling is not available for copy number stable alteration events |
PBRM1 copy number loss | 0.8 | MS-stable |
BAP1, BRCA1 associated protein-1; MSI, microsatellite instability; mut/Mb, mutations per megabase; NA, not determined; TMB, tumor mutational burden.