Confirmation of linkage to and localization of familial colon cancer risk haplotype on chromosome 9q22

Abstract

Genetic risk factors are important contributors to the development of colorectal cancer. Following the definition of a linkage signal at 9q22-31, we fine mapped this region in an independent collection of colon cancer families. We used a custom array of single-nucleotide polymorphisms (SNP) densely spaced across the candidate region, performing both single-SNP and moving-window association analyses to identify a colon neoplasia risk haplotype. Through this approach, we isolated the association effect to a five-SNP haplotype centered at 98.15 Mb on chromosome 9q. This haplotype is in strong linkage disequilibrium with the haplotype block containing HABP4 and may be a surrogate for the effect of this CD30 Ki-1 antigen. It is also in close proximity to GALNT12, also recently shown to be altered in colon tumors. We used a predictive modeling algorithm to show the contribution of this risk haplotype and surrounding candidate genes in distinguishing between colon cancer cases and healthy controls. The ability to replicate this finding, the strength of the haplotype association (odds ratio, 3.68), and the accuracy of our prediction model (approximately 60%) all strongly support the presence of a locus for familial colon cancer on chromosome 9q.

Figure 1

Haseman-Elston and sibling-pair mean test linkage analysis and fine mapping in the revised original, confirmation and a combined collection of colon neoplasia kindreds. Points on the lines represent the –log p-values of the Haseman-Elston regression test at markers (i.e D9S1820) and intermarker distances (i.e. 9_18) across the region; Black dots represent the –log p-values of the mean allele sharing test at D9S1786. Note that there is no line for the confirmation sample as it contained only affected sibling pairs and was therefore not informative for the Haseman-Elston regression test.

Figure 2

Single SNP Association Analysis across the entire 13.5 cM region.

Figure 3

Moving Window Association Analysis, window size of five SNPs (upper figure) compared to LD in the region (lower figure). Brackets indicate that the level of linkage disequilibrium between the three highest peaks is greater than 0.9.

Figure 4

Sensitivity, Specificity and Accuracy of SVM colon cancer prediction model including only SNPs in regions of significance centered at 92Mb, 98.15Mb, 98.29Mb and 102Mb. The threshold of 0.365 is the point at which the three attributes of interest intersect.

Figure 5

Rankings by predictability A) for SNPs in the four candidate regions centered at 92 megabases (Mb), 98.15Mb, 98.29Mb and 102Mb and B) for SNPs in both the candidate regions and the surrounding candidate genes (ZNF367, HABP4, GABBR2 and GALNT12). The solid box in both A. and B. represents the risk haplotype block at 98.29Mb. The dashed box in B includes the SNPs within HABP4.

Figure 6

LD plot of regions with significant moving-window association results and in linkage disequilibrium with candidate genes for A) cases (N=225) and B) controls (N=248). Solid ovals indicate significant regions, the solid box indicates the risk haplotype at 98.15Mb, brackets indicate genes and dashed ovals highlight regions of LD between the haplotype block containing HABP4 and the four regions of significance.