Discovery of common and rare genetic risk variants for colorectal cancer

Abstract

To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10^-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.

Figure 1. Conditionally independent association signals at the BMP2 locus.

Regional association plot showing the unconditional −log₁₀(P-value) for the association with CRC risk in the combined meta-analysis of up to 125,478 individuals, as a function of genomic position (Build 37) for each variant in the region. The lead variants are indicated by a diamond symbol and its positions are indicated by dashed vertical lines. The color-labeling and shape of all other variants indicate the lead variant with which they are in strongest LD. The two new genome-wide significant signals are indicated by an asterisk.

Figure 2. Functional genomic annotation of new CRC risk locus overlapping KLF5 super-enhancer.

Top: Regional association plot showing the unconditional −log₁₀(P-value) for the association with CRC risk in the combined meta-analysis of up to 125,478 individuals, as a function of genomic position (Build 37) for each variant in the region. The lead variants are indicated by a diamond symbol and its positions are indicated by dashed vertical lines. The color-labeling and shape of all other variants indicate the lead variant with which they are in strongest LD. Bottom: UCSC genome browser annotations for region overlapping the super-enhancer flanked by KLF5 and KLF12, and spanning variants in LD with rs78341008, and with two conditionally independent association signals indexed by rs45597035 and rs1924816. The region is annotated with the following tracks (from top to bottom): UCSC gene annotations; epigenomic profiles showing MACS2 peak calls as transparent overlays for different samples taken from non-diseased colonic crypt cells or colon tissue (purple) and from different primary CRC cell lines or tumor samples (teal); position of the lead variants and variants in LD with the lead; variants in the 99% credible set; the union of super-enhancers called using the ROSE package; gray bars highlight the targeted enhancers (e1,e3, and e4) previously shown by Zhang et al. to have combinatorial effects on KLF5 expression. ATAC-seq data newly generated for this study show high resolution annotation of putative binding regions within the active super-enhancer further fine-mapping putative causal variants at each of the three signals.

Figure 3. Recommended age to start CRC screening based on a polygenic risk score (PRS).

The PRS was constructed using the 95 known and newly discovered variants. The horizontal lines represent the recommended age for the first endoscopy for an average-risk person in the current screening guideline for CRC. The risk threshold to determine the age for the first screening was set as the average of 10-year CRC risks for a 50-year-old man (1.25%) and woman (0.68%), i.e. (1.25%+0.68%)/2 = 0.97%, who have not previously received an endoscopy. Details are given in the Online Methods.