Other mutation types such as insertions, deletions, copy number alterations, truncating and silent mutations were not considered in this analysis.
While our approach is unable to detect some mutation types, such as large deletions, the results suggest that germline mutations in these three genes have no major contribution to PJS.
To demonstrate its applicability, the mutational catalogues of the 21 breast cancer genomes were extended to include double nucleotide substitutions, indels at microhomologies, indels at mono/polynucleotide repeats, and even a complex mutation type such as kataegis.
The types of p53 mutations (mainly GC → AT transitions) further suggest a role of ROS, which are known to favour such mutation types (Moraes et al, 1990; Feig et al, 1994; Purmal et al, 1994; Jenkins et al, 2001).
Neither is the mdx mutation directly involved in the control of mandibular development, nor does it belong to the gene mutation types that promote canalization such as HSP90 [ 35].
Several studies suggest that cellular effects of VDR may be associated with MAPK signaling pathways, especially KRAS mutation in several cancer types such as breast and colorectal cancers [ 48, 49].
If HIV-1 were adapting to the most common HLA alleles in the human population, one could argue that the current HIV-1 consensus sequence in the Caucasian population should contain more CTL escape mutations for common HLA types, such as HLA-B35, than for rare HLA types, such as HLA-B57, B58 and B27.
Nonetheless, several ARS/AIMPs showed relatively high frequency of missense/in-frame indel mutations in several cancer types, such as endometrium and prostate cancers (average relative frequencies = 0.78 and 0.74, respectively).
Indeed, the PI3K sequencing of human tumor tissues samples revealed PIK3CA somatic mutations in different cancer types such as lung (4%), breast (8%), gastric (25%), brain (27%), and colon (32%).
We can also integrate different data types, such as mutation, expression, and proteomic data.
Loss-of-function mutations in the demethylating enzyme TET2 have been previously associated to CIMP in leukemia, and our results reveal recurrence of this mutation in CIMP+ for other types such as UCEC and READ.
