There is increasing evidence that genome-wide association (GWA) studies represent a powerful approach to the identification of genes involved in common human diseases. We describe a joint GWA study (using the Affymetrix GeneChip 500K Mapping Array Set) undertaken in the British population, which has examined approximately 2,000 individuals for each of 7 major diseases and a shared set of approximately 3,000 controls. Case-control comparisons identified 24 independent association signals at

Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5m genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N≤71,225 European ancestry, N=12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N=29,136). We identified association between systolic or diastolic blood pressure and common variants in 8 regions near the CYP17A1 (P=7×10−24), CYP1A2 (P=1×10−23), FGF5 (P=1×10−21), SH2B3 (P=3×10−18), MTHFR (P=2×10−13), c10orf107 (P=1×10−9), ZNF652 (P=5×10−9) and PLCD3 (P=1×10−8) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.

A genome-wide association scan in Crohn disease by the Wellcome Trust Case Control Consortium1 detected strong association at 6 novel loci. We tested 37 SNPs from these and other loci for association in an independent case control sample. Replication was obtained for the IRGM gene on chromosome 5q33.1 which induces autophagy (replication P = 6.6 × 10 −4 , combined P = 2.1 × 10 −10 ), and for 9 other loci including NKX2-3 and gene deserts on chromosomes 1q and 5p13. Crohn disease (CD) is a common form of chronic inflammatory bowel disease. Established CD susceptibility genes NOD2 (CARD15), IL23R and ATG16L1 2-5 showed strong evidence of association in the Wellcome Trust Case Control Consortium (WTCCC) genome-wide scan of 1748 CD cases and 2938 controls genotyped using the Affymetrix 500K chip. Six other loci also showed highly significant association. Although satisfying stringent statistical thresholds for significance (P < 5 × 10 −7 ), replication in independent panels represents a key validation step.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. 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. 12Allele 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 ev...

We have genotyped 14,436 nonsynonymous SNPs (nsSNPs) and 897 major histocompatibility complex (MHC) tag SNPs from 1,000 independent cases of ankylosing spondylitis (AS), autoimmune thyroid disease (AITD), multiple sclerosis (MS) and breast cancer (BC). Comparing these data against a common control dataset derived from 1,500 randomly selected healthy British individuals, we report initial association and independent replication in a North American sample of two new loci related to ankylosing spondylitis, ARTS1 and IL23R, and confirmation of the previously reported association of AITD with TSHR and FCRL3. These findings, enabled in part by increased statistical power resulting from the expansion of the control reference group to include individuals from the other disease groups, highlight notable new possibilities for autoimmune regulation and suggest that IL23R may be a common susceptibility factor for the major 'seronegative' diseases.

Background Anti-TNF drugs are effective treatments for the management of Crohn's disease but treatment failure is common. We aimed to identify clinical and pharmacokinetic factors that predict primary non-response at week 14 after starting treatment, non-remission at week 54, and adverse events leading to drug withdrawal.Methods The personalised anti-TNF therapy in Crohn's disease study (PANTS) is a prospective observational UK-wide study. We enrolled anti-TNF-naive patients (aged ≥6 years) with active luminal Crohn's disease at the time of first exposure to infliximab or adalimumab between March 7, 2013, and July 15, 2016. Patients were evaluated for 12 months or until drug withdrawal. Demographic data, smoking status, age at diagnosis, disease duration, location, and behaviour, previous medical and drug history, and previous Crohn's disease-related surgeries were recorded at baseline. At every visit, disease activity score, weight, therapy, and adverse events were recorded; drug and total anti-drug antibody concentrations were also measured. Treatment failure endpoints were primary non-response at week 14 ,non-remission at week 54, and adverse events leading to drug withdrawal. We used regression analyses to identify which factors were associated with treatment failure. Findings We enrolled 955 patients treated with infliximab (753 with originator; 202 with biosimilar) and 655 treated with adalimumab. Primary non-response occurred in 295 (23•8%, 95% CI 21•4-26•2) of 1241 patients who were assessable at week 14. Non-remission at week 54 occurred in 764 (63•1%, 60•3-65•8) of 1211 patients who were assessable, and adverse events curtailed treatment in 126 (7•8%, 6•6-9•2) of 1610 patients. In multivariable analysis, the only factor independently associated with primary non-response was low drug concentration at week 14 (infliximab: odds ratio 0•35 [95% CI 0•20-0•62], p=0•00038; adalimumab: 0•13 [0•06-0•28], p<0•0001); the optimal week 14 drug concentrations associated with remission at both week 14 and week 54 were 7 mg/L for infliximab and 12 mg/L for adalimumab. Continuing standard dosing regimens after primary non-response was rarely helpful; only 14 (12•4% [95% CI 6•9-19•9]) of 113 patients entered remission by week 54. Similarly, week 14 drug concentration was also independently associated with non-remission at week 54 (0•29 [0•16-0•52] for infliximab; 0•03 [0•01-0•12] for adalimumab; p<0•0001 for both). The proportion of patients who developed anti-drug antibodies (immunogenicity) was 62•8% (95% CI 59•0-66•3) for infliximab and 28•5% (24•0-32•7) for adalimumab. For both drugs, suboptimal week 14 drug concentrations predicted immunogenicity, and the development of anti-drug antibodies predicted subsequent low drug concentrations. Combination immuno-modulator (thiopurine or methotrexate) therapy mitigated the risk of developing anti-drug antibodies (hazard ratio 0•39 [95% CI 0•32-0•46] for infliximab; 0•44 [0•31-0•64] for adalimumab; p<0•0001 for both). For infliximab, multivariable analysis of immunododulator ...