Refinement of the associations between risk of colorectal cancer and polymorphisms on chromosomes 1q41 and 12q13.13

Abstract

In genome-wide association studies (GWASs) of colorectal cancer, we have identified two genomic regions in which pairs of tagging-single nucleotide polymorphisms (tagSNPs) are associated with disease; these comprise chromosomes 1q41 (rs6691170, rs6687758) and 12q13.13 (rs7163702, rs11169552). We investigated these regions further, aiming to determine whether they contain more than one independent association signal and/or to identify the SNPs most strongly associated with disease. Genotyping of additional sample sets at the original tagSNPs showed that, for both regions, the two tagSNPs were unlikely to identify a single haplotype on which the functional variation lay. Conversely, one of the pair of SNPs did not fully capture the association signal in each region. We therefore undertook more detailed analyses, using imputation, logistic regression, genealogical analysis using the GENECLUSTER program and haplotype analysis. In the 1q41 region, the SNP rs11118883 emerged as a strong candidate based on all these analyses, sufficient to account for the signals at both rs6691170 and rs6687758. rs11118883 lies within a region with strong evidence of transcriptional regulatory activity and has been associated with expression of PDGFRB mRNA. For 12q13.13, a complex situation was found: SNP rs7972465 showed stronger association than either rs11169552 or rs7136702, and GENECLUSTER found no good evidence for a two-SNP model. However, logistic regression and haplotype analyses supported a two-SNP model, in which a signal at the SNP rs706793 was added to that at rs11169552. Post-GWAS fine-mapping studies are challenging, but the use of multiple tools can assist in identifying candidate functional variants in at least some cases.

Figure 1.

Individual SNP associations in the 1q41 region. Association testing was performed in SNPtest using typed and imputed genotypes from the three GWAS series (UK1, Scotland1 and VQ58) and displayed using SNAP (http://www.broadinstitute.org/mpg/snap/). The X-axis shows position on chromosome 1 and the Y-axis, −log10(P) from the per allele association test. The most strongly associated SNP, rs11118883, is shown as a large diamond, and the colours of other data points reflect the LD between that SNP and rs11118883. The smaller diamond points indicate genotyped SNPs and the triangles indicate imputed SNPs. The blue line represents recombination rates.

Figure 2.

GENECLUSTER output for the 1q41 region. The upper left panel compares the Bayes factors (BFs) for models in which the association signals at rs6691170 and 6687758 are derived from either one functional SNP (red) or two functional SNPs (green). Recombination rates are also shown as a red line. The upper right panel shows the log₁₀(BF) at the focal position—the site of the highest log₁₀(BF), here chr1:220,129,000 bases—under one- and two-SNP models. The lower right panel shows reconstructed genealogies for UK1, Scotland1 and VQ58 combined, based on each individual's genotypes in the region from the Illumina Hap300/370/550 panels and HapMap2 data. The most likely positions of SNP origins under the one-SNP model (blue, rs11577023) and two-SNP model (green and red) are shown. These result in counts of cases and controls and relative risks as indicated in the upper right panel. The lower left panel shows haplotypes (rows) and SNPs (columns). Note that the region analysed extends for several Mb flanking rs6691170 and 6687758; although no signal reaches nominal significance at log₁₀(BF) = 4, there is some evidence of a second independent region of 1q associated with CRC at ∼218.2 Mb, as we have reported previously. The importance of rs11577023 was supported by the Margarita analysis in which it was the second most strongly associated with disease (P = 3.59 × 10⁻⁴).

Figure 3.

Individual SNP associations in the 12q13.13 region. Legend is as for Figure 1.

Figure 4.

LD and main haplotypes at SNPs with best evidence of association on 12q13.13. Note that in this Haploview output from HapMap3 data, the alleles at rs706793 are shown on the opposite strand (that is G/A rather than C/T as used in the rest of this manuscript).

Figure 5.

GENECLUSTER output for the 12q13.13 region. The legend is as for Figure 2, except that the focal position is Chr12:48,849,000 and the double peak of association at ∼48.85 and 49.45 Mb should be noted. The top SNP (blue dot) under the one-SNP model is the imputed SNP rs3184122. The top-genotyped SNP in the GENECLUSTER analysis was rs7138945, which was the SNP with the second-best association signal in Margarita (P = 1.14 × 10⁻⁵).