We followed up 37 SNPs from 31 distinct loci associated at P < 10⁻⁵ on initial analysis of the WTCCC dataset. Support for some of these markers diminished in the final WTCCC analysis after extensive data filtering¹. Two markers were selected for each locus where low LD between associated SNPs in areas of unbroken LD suggested distinct causal variants. SNPs were genotyped in a new panel of 1182 Caucasian CD cases using TaqMan assays (Supplementary Methods and Supplementary Table 1 online). Concordance with Affymetrix data was 99.7%, based on genotyping 96 WTCCC cases on both platforms. To target SNPs for replication testing and limit unnecessary genotyping, preliminary comparison was made between allele frequencies in the new CD panel and 5746 non-autoimmune WTCCC cases (bipolar disorder, coronary artery disease and hypertension). The latter represent a powerful resource of population allele frequencies¹ assuming no overlap with CD aetiology. Twelve SNPs showed a difference in allele frequency between these two groups (Table 1), while for 25 other markers the allele frequencies converged (Supplementary Table 2). To exclude possible bias introduced by this approach, the 12 markers implicated in this preliminary comparison were then genotyped in 2024 independent population controls from the 1958 British Birth Cohort to test formally for association. Results are presented in Table 1, with odds ratios estimated from replication samples only.

Among novel CD loci achieving genome-wide significance in the WTCCC scan¹ the strongest replication adjacent to a known gene was for SNPs rs13361189 and rs4958847 (P_rep=6.6×10⁻⁴ and 3.1×10⁻⁴ respectively) immediately flanking the IRGM gene [MIM 608212] on chromosome 5q33.1. Association in the combined panels of 2930 CD cases and 4962 controls was highly significant (P_comb= 2.1×10⁻¹⁰ and 3.8×10⁻⁹ respectively) (Figure 1). The long coding exon of the human IRGM gene encodes a 20 kD protein of 181 amino acid residues.^6,7 Since none of the associated SNPs are known to be functional, we re-sequenced this coding exon of IRGM and the 4 small putative downstream exons in 48 CD cases homozygous or heterozygous for risk alleles (Supplementary Methods). We detected two novel non-synonymous sequence variants, c.51G>C (p.Glu17Asp) and c.281C>A (p.Thr94Lys) and an exonic synonymous SNP, c.313T>C (rs10065172, p.L105). These SNPs were then genotyped in 769 unselected CD cases from our study and 705 controls. Only the silent 313T>C variant was associated with CD (P=0.008), and was in near perfect LD with SNP rs13361189 (r²=0.91). Sequencing of the IRGM coding region in a further 100 unselected CD cases and 100 controls did not detect additional variants. These results strongly suggest that the causal variant(s) do not change the amino acid sequence of the IRGM protein. They may lie in regulatory sequences, in LD with the associated SNPs, and affect IRGM expression; alternatively, the exonic (c.313T>C) SNP itself might affect transcript splicing or the rate of translation of the protein. Analysis of IRGM expression by PCR screening against uncloned cDNA showed transcription in several tissues, including colon, small bowel, peripheral blood leukocytes and the U937 monocytic cell line (data not shown).

IRGM belongs to the p47 immunity-related GTPase family. LRG-47 (irgm1), its mouse homologue, critically controls intracellular pathogens by autophagy, and LRG-47^−/− mice showed markedly increased susceptibility to Toxoplasma gondii and Listeria monocytogenes.⁸ Consistent with this, IRGM induces autophagy and thereby control of intracellular M. tuberculosis in human macrophages.⁷

Three other associations with genome-wide significance in the WTCCC scan produced strong evidence of replication (P≤0.01), two of which are novel. The strongest was SNP rs9292777 (P_rep=2.9×10⁻⁷; P_comb=3.2×10⁻¹⁸) which maps to a 1.2 Mb gene desert on chromosome 5p13.1 recently associated with CD.⁹ The most significant novel association was SNP rs10883365 (P_rep=0.0037, P_comb=3.7 × 10⁻¹⁰), which maps within the NKX2-3 gene (NK2 transcription factor related, locus 3) on chromosome 10q24.2. Nkx2.3-deficient mice develop splenic and gut-associated lymphoid tissue abnormalities with disordered segregation of T- and B- cells.¹⁰ The second novel locus at rs9858542 (P_rep=0.010, P_comb=4.9×10⁻⁸) on chromosome 3p21 is a 1 Mb region of high LD that contains over 20 genes, including MST1 (macrophage stimulating 1), encoding a protein which induces phagocytosis by resident peritoneal macrophages.

The modest evidence of replication for SNP rs2542151 (P = 0.048) at the PTPN2 locus (protein tyrosine phosphatase, non-receptor type 2) on chromosome 18p11 (P_comb = 3.2 × 10⁻⁸) is of interest since PTPN2 encodes a T cell protein tyrosine phosphatase, a key negative regulator of inflammation and is also associated with Type 1 Diabetes.¹¹ Allele frequencies for rs10761659 on chromosome 10q21, strongly associated in the WTCCC scan, were similar in replication CD cases and population controls (SOM table 2), but association in this intergenic region was recently detected in a North American whole-genome CD scan.¹²

Allele frequencies for most of the markers from the 25 other loci studied that did not achieve genome-wide significance in the WTCCC scan but had an initial P<10⁻⁵ converged with control frequencies in the CD replication panel (Supplementary Table 2). Five of these loci, however, provided evidence of replication, thus indicating that a systematic follow-up of all CD hits in the 10⁻⁵-10⁻⁷ range is likely to yield a number of additional CD susceptibility loci. Four of these loci are novel putative CD risk loci; intriguingly they include two gene deserts, both on chromosome 1q. SNP rs10801047 (P_rep=4.8×10⁻⁵, P_comb=2.8×10⁻⁸) is located in a gene desert of 1.7Mb on chromosome 1q31.2, and rs12035082 (P_rep=0.017, P_comb=2.1×10⁻⁷) maps to chromosome 1q24 (the association signal does not extend to nearest gene, TNFSF18). Although previous studies did not implicate IL12B (interleukin 12B),^4,13 modest WTCCC association at rs6887695 from this locus replicated here (P_rep=8.4×10⁻⁵, P_comb=9.2×10⁻⁶) and warrants follow up, particularly given its association with psoriasis¹⁴ and the common association of IL23R with psoriasis and CD.^4,14 SNP rs10077785 (P_rep=0.008) tags the known IBD5 locus¹⁵ on chromosome 5q31 in which, despite extensive resequencing, disease-causing coding variants have yet to be confirmed. Finally, rs2836754 (P_rep=0.012, P_comb=5.5×10⁻⁷) maps to an intron in FLJ45139, a gene of unknown function on chromosome 21 that is expressed in bone marrow and colon.

We performed ‘within-cases’ interaction analysis between known CD susceptibility variants and replicating SNPs. For CARD15, rs2066844, rs2066845 and rs2066847 were tested independently or in combination classifying individuals as homozygous wild type, heterozygous or compound heterozygote/rare-allele homozygote. No significant interactions were seen. Testing CD associated variants rs11805303 in IL23R and rs10210302 in ATG16L1 also showed no interactions. Thus risk loci in CD appear to act independently.

We examined six sub-phenotypes of CD and two modifiers for differential effects within cases at markers studied. Cases were classified as affected or unaffected for disease site (‘pure ileal’, ‘pure colorectal’, ‘perianal involvement’) and behaviour (‘inflammatory’, ‘stenosing’ and ‘penetrating’); and by age of onset and smoking status (Supplementary Table 3). Inflammatory behaviour appeared less strongly associated with rs10210302 (in ATG16L1, P=0.0003, Bonferroni P=0.010) than stenosing or penetrating behaviour. No further significant differential associations were seen, although ‘pure ileal’ tends to associate more strongly with most replicating SNPs than ‘pure colorectal’.

Supplementary Material