A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci

Abstract

Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD-susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2-4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (p<5×10⁻⁶). Novel signals detected among AJs were mapped to chromosomes 5q21.1 (rs7705924, combined p = 2×10⁻⁸; combined odds ratio OR = 1.48), 2p15 (rs6545946, p = 7×10⁻⁹; OR = 1.16), 8q21.11 (rs12677663, p = 2×10⁻⁸; OR = 1.15), 10q26.3 (rs10734105, p = 3×10⁻⁸; OR = 1.27), and 11q12.1 (rs11229030, p = 8×10⁻⁹; OR = 1.15), implicating biologically plausible candidate genes, including RPL7, CPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim.

Figure 1. PCA analysis of the study participants.

(A) PCA showing the first (X-axis) and second (Y-axis) eigenvectors plotting all 3,252 study participants (907 CD cases and 2,345 controls) across ∼22 K unlinked SNPs indicated by light blue open circles. Also included and color-coded in the graph are the four HapMap (www.hapmap.org) reference samples as solid triangles; CEPH-Utah (CEU; green), Yoruban-Nigeria (YRI; red), Han Chinese (CHB; orange) and Japanese (JPT; dark grey); and seven Jewish samples from the Jewish Hapmap project as solid circles, consisting of Ashkenazi Jews (AJ; blue), one European (Italian; purple), three Middle Eastern (Syrian; fuchsia, Iraqi; teal and Iranian; turquoise) and two Sephardic Jewish cohorts (Turkey; brown and Greek; orange). (B) The same analysis excluding the YRI and CHB+JPT reference panels. (C) A histogram of PC1 values for study participants (light blue) near the AJ cluster and intermediate between the AJ and CEU clusters. The histogram of PC1 values for the included samples show three distinct modes (Groups 1–3), with AJ reference (blue) and CEU (green) indicated.

Figure 2. Association mapping of Crohn's disease in Ashkenazi Jews.

(A) QQ-plots of the 100%, 75% and 50% AJ ancestry groups (Groups 1, 2 and 3, respectively). The inflation factors for the p-value distributions are given. For group 3, the p-values were genomic control-adjusted for over-inflation. (B) A Manhattan plot and QQ-plot (inset – in black) of the combined association scores from all three groups. The genome-wide threshold is shown in red and the replication threshold is shown in blue. The QQ-plot also shows association scores from all three groups but with 298 markers around the region of the NOD2 signal on chromosome 16 removed before association mapping (in grey).

Figure 3. Regional plots of five novel associations to Crohn's disease in Ashkenazi Jews.

Regional plots of the SNP p-values obtained in the discovery GWAS for a ±250 kb window around each of the 5 novel SNPs. The X-axis shows the chromosome and physical distance (kb), the left Y-axis shows the negative base ten logarithm of the p-value and the right y-axis shows recombination activity (cM/Mb) as a blue line. The chromosomal band is given above each plot. The replication SNP is indicated as a large red diamond, and linkage disequilibrium of surrounding SNPs with the replication SNP is indicated by a scale of intensity of red color filling as shown in the legend at the upper right hand corner of each plot. The combined discovery and replication p-value for the replication SNP is shown in blue, and is annotated with the SNP identifier and combined p-values. The position and location of any copy number variation in the mapping intervals are shown as a black rectangle. Positions, recombination rates and gene annotations are according the NCBI's build 36 (hg 18).