Table 1.
Results of splicing assay
| Gene | Variant | Source RNA | Variant frequency | (predicted) RNA effect | Result |
|---|---|---|---|---|---|
| A. Variants known to result in splicing | |||||
| MLH1 | c.(453+1_454-1)_(545+1_546-1)dela | FFPE, CRC45 | NAb | r.? | Genomic exon deletion shown in RNAc |
| MLH1 | c.791-1G>Ca | Cell line | 50% | r.791_884del | Aberrant splicing as reported |
| MLH1 | c.793C>Ta | FFPE, CRC63 | NA | r.791_884del (major), WT (minor) | Unable to isolate nucleic acid |
| MLH1 | c.1731G>A | FFPE, CRC51 | 35% | r.1668_1731del | No MMR RNA expression detected |
| MSH2 | c.1511-2A>Ga | Cell line | 80% | r.1510_1511ins1511-1 | Aberrant splicing as reportedd |
| MSH6 | c.3801+1_3801+5dela | FFPE, Pol67 | NA | r.3647_3801del | Aberrant splicing as reportedc |
| APC | c.1548G>A | FFPE, Pol68 | 28% | r.1409_1548del | Aberrant splicing as reportedc |
| BRCA1 | c.213-12A>G | FFPE, EC74 | 93% | r.212_213ins213-12_213-1 | Aberrant splicing as reportedc |
| B. Variants predicted to result in splicing | |||||
| MLH1 | c.885-2A>G | FFPE, CRC45 | 57% | r.(885_889del)e | No MMR RNA expression detected |
| MLH1 | c.2104-1G>C | FFPE, EC55 | 36% | r.(2104_2105del)e | Only WT product |
| APC | c.834+2T>A | FFPE, Pol60 | 12% | r.(830_834del)e | Aberrant splicing as predicted |
| APC | c.1959-1G>A | FFPE, Pol67 | 40% | r.(1959del)e | Aberrant splicing as predicted |
| BRCA1 | c.212+3A>T | FFPE, OC46 | 54% | r.(191_212del)e | Aberrant splicing as predictedc |
Source RNA shows cell line or formalin-fixed paraffin-embedded (FFPE) tissue block, with type of tumour and age of onset
CRC colorectal cancer, EC endometrial cancer, OC ovarian cancer, Pol polyps, WT wildtype, nt nucleotides, NA not assessed
aGermline variants. Variants were detected with Sanger sequencingPlease check if the term "r.?" is ok in Table 1.yes, this is correct
bLOH was detected in the tumour
cNo WT product detected
dAberrant product only detected after formalin fixation of the cells. Genbank reference sequences NM_000249.2 (MLH1), NM_000251.2 (MSH2), NM_000179.2 (MSH6), NM_000038.5 (APC) and NM_007294.3 (BRCA1) were used
ePredicted RNA effect is based on nearest cryptic splice site, which could possibly act as a new 3′ or 5′ splice site