A previous study found that one of the BC susceptibility variants that we analysed, SNP rs3817198 in the 11p15 region (LSP1 gene), displayed POE with BC risk (Kong et al, 2009).
Although we were aware of the variants we were analysing, it seems reasonable to assume that an allele frequency of down to 10% could be routinely detected.
For all putative splice-site variants, we performed further analyses to unequivocally determine their pathogenic effect.
To rank the remaining participants based on variants, we focused our analyses on 27 genes (Table 2) deemed either as actionable by CPIC [ 4], or as important drug targets based on preliminary association data to pharmacological traits [ 3].
Finally, our current analyses do not exclude the possibility that sequence variants in the genes we analysed are associated with low penetrance CRC susceptibility.
Similarly, we found that the majority (77%) of variants were consistent with the Mendelian laws when we analysed those variants that are in common between the exome sequencing and an SNP genotyping array for a trio-case (data not shown).
By comparing the results of analyses that included variants at less than 1% frequency with those of analyses excluding those variants, we assessed the impact of this rule of thumb on inferences regarding patterns of sequence polymorphism.
To further investigate the potential clinical significance of these variants using the likelihood approach, we analysed the tumours arising in carriers of these variants for ER and cytokeratin expression in order to extend the histopathology component of the model and we updated and revised data for the co-inheritance and sequence conservation components of the model.
To confirm that the newly derived variants were not indicative of clonal expansion from very few residual variants present in the cells, we analysed the raw data from the next generation sequencing runs for the HSR-GBM1 cell line and were able to confirm that these variants had not been called.
Furthermore, we analysed the variants using the same models as in the original work by Gaulton et al. [2].
