Background
Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. African Americans are disproportionately affected by CRC. Our hypothesis is that driver genes with known and novel mutations have an impact on CRC outcome in this population. Therefore, we investigated the variants’ profiles in a panel of 15 CRC genes.
Patients & Methods
Colorectal specimens (n=140) were analyzed by targeted exome sequencing using an Ion Torrent platform. Detected variants were validated in 36 samples by Illumina sequencing. The novel status of the validated variants was determined by comparison to publicly available databases. Annotated using ANNOVAR and
in-silico
functional analysis of these variants were performed to determine likely pathogenic variants.
Results
Overall, 121 known and novel variants were validated:
APC
(27%),
AMER1
(3%)
, ARID1
(7%),
MSH3
(12%),
MSH6
(10%),
BRAF
(4%),
KRAS
(6%),
FBXW7
(4%),
PIK3CA
(6%),
SMAD4
(5%),
SOX9
(2%),
TCF7L2
(2%),
TGFBR2
(5%),
TP53
(7%). From these validated variants, 12% were novel in 8 genes
(AMER1, APC, ARID1A, BRAF, MSH6, PIK3CA, SMAD4,
and
TCF7L2
). Of the validated variants, 23% were non-synonymous, 14% were stopgains, 24% were synonymous and 39% were intronic variants.
Conclusion
We here report the specifics of variants’ profiles of African Americans with colorectal lesions. Validated variants showed that Tumor Suppressor Genes (TSGs)
APC
and
ARID1
and DNA Mismatch repair (MMR) genes
MSH3
and
MSH6
are the genes with the highest numbers of validated variants. Oncogenes
KRAS and PIK3CA
are also altered and likely participate in the increased proliferative potential of the mutated colonic epithelial cells in this population.