Investigating the Source Mutations for Inherited Colorectal Cancer

5% of Colorectal Cancer has an inherited source

Colorectal cancer is the third most-common cancer worldwide, with over 130,000 new cases in the United States in 2014 alone. About 5% of these cases are inherited in an autosomal dominant fashion, and the two major types of these inherited disease cases are called familial adenomatous polyposis and hereditary non-polyposis colorectal cancer (HNPCC).

Hereditary non-polyposis colorectal cancer is divided into two forms: one with a hallmark defective DNA mismatch repair genes, which lead to microsatellite instability, and the other set of HNPCC which do not have mutations in these DNA repair genes. Accounting for 40-50% of this hereditary cancer, this type is called “Familial Colorectal Cancer Type X” (FCCTX), as the genes associated with its inheritance were yet to be identified.

Using multiple technologies including digital PCR to investigate

Using a variety of genomic analysis platforms, Schultz, Sill and collaborators used six samples from an affected pedigree to identify the gene or genes involved. (Of the six samples, five were affected and one unaffected putative carrier.) First using a whole-genome SNP genotyping microarray and linkage analysis, four shared regions were identified but none of them had cancer-associated genes in these regions.

After whole-exome sequencing (WES) on four affected samples, the researchers combined linkage analysis with their WES and filtered for heterozygous, non-synonymous protein-coding or splice-site variants with a minor allele frequency of <1%. All putative variants were confirmed by Sanger sequencing.

A single consistent variant in the SEMA4A gene

Only one variant were shared among the four samples, which was a V78M mutation in the SEMA4A gene, and is absent from dbSNP137, the 1000 Genomes Project database, and the National Heart, Lung and Blood Institute Exome Variant Server.

Investigating additional samples of known affected samples and suspected carriers with the V78M mutation in the SEMA4A gene, they looked for copy-number variation using array hybridization microarrays and loss of heterozygosity (LOH) analysis using Sanger sequencing.  They verified the copy number / LOH data using the QuantStudio 3D^® Digital PCR System for either the wild-type (V78) or mutant (M78) allele.

In order to gain insight on the population genetics of this mutation, the Ion AmpliSeq™ Cancer Hotspot Panel v2 and the Ion Proton™ System were used to look at potential ‘cooperating’ cancer-associated mutations in the mutated SEMA4A samples that revealed several protein-coding changes. Also an associated allele in the same SEMA4A gene (P682S) was shown via TaqMan^TM analysis to be significantly enriched for in 47 unrelated FCCTX samples compared to non-cancer controls.

 

Reference:

Schulz E, Klampfl P, Holzapfel S, Janecke AR, Ulz P, Renner W, Kashofer K, Nojima S, Leitner A, Zebisch A, Wölfler A, Hofer S, Gerger A, Lax S, Beham-Schmid C, Steinke V, Heitzer E, Geigl JB, Windpassinger C, Hoefler G, Speicher MR, Richard Boland C, Kumanogoh A, Sill H. Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X. Nat Commun. 5:5191 (2014)

doi: 10.1038/ncomms6191