To find sufficient CRC cases with loss of expression of MLH1 not due to germline MLH1 gene mutations, we included all available cases from the C-CFR.
To determine our ability to detect pathogenic mutations, we included one sample from a female patient (S-2) harboring a dominant pathogenic point mutation in the MECP2 gene, (c.538C>T) on the X chromosome.
For rifampicin- and fluoroquinolone-resistance conferring mutations, we included the rifampicin-resistance determining region (RRDR) [ 34] and the quinolone resistance determining region (QRDR) [ 48], respectively, rather than specific positions.
For the replication of the association found when patients were stratified according to the RET mutation status, we included 21 independent HSCR cases bearing RET CDS mutations and 71 control individuals from Mainland China (replication group).
Since one of the parameters we need to infer is the mutation rate θs, we included in the summary statistics the proportion of segregating sites S that is highly informative about this parameter (Watterson 1975).
While in principle our analysis could be confounded by the known correlation between EGFR mutation and erlotinib sensitivity, we included in our analysis several lines that are resistant to erlotinib despite having activating EGFR mutations (H1975, H820, H2279, and H1650), as well as lines with wt EGFR that are sensitive to erlotinib (H292, H358, H1648, and H322).
To increase the power we included mutation data for an additional 73 cases increasing the number of cases from 145 to 218 and a negative association was observed (p = 0.0085, hypergeometric test).
We included mutation results that conferred low-level, intermediate-level and high-level resistance.
However, as some regions (e.g. hot spot regions of drug resistance) can harbour several mutations in close proximity, we included the capability to scan regions of interest for the presence of any (new) mutation.
In addition, due to the altered ratio of FL-PINK1 to ΔN-PINK1 in cells expressing the N-terminal PD-associated mutations C92F, Q115L and R147H, we included the PINK1-C92F mutant protein in our analysis.
