Genome-wide association (GWA) studies offer a powerful unbiased method for the identification of multiple susceptibility genes for complex diseases. Here we report the results of a GWA study for Crohn's disease (CD) using family trios from the Quebec Founder Population (QFP). Haplotype-based association analyses identified multiple regions associated with the disease that met the criteria for genome-wide significance, with many containing a gene whose function appears relevant to CD. A proportion of these were replicated in two independent German Caucasian samples, including the established CD loci NOD2 and IBD5. The recently described IL23R locus was also identified and replicated. For this region, multiple individuals with all major haplotypes in the QFP were sequenced and extensive fine mapping performed to identify risk and protective alleles. Several additional loci, including a region on 3p21 containing several plausible candidate genes, a region near JAKMIP1 on 4p16.1, and two larger regions on chromosome 17 were replicated. Together with previously published loci, the spectrum of CD genes identified to date involves biochemical networks that affect epithelial defense mechanisms, innate and adaptive immune response, and the repair or remodeling of tissue.haplotype ͉ complex disease ͉ IL23R C rohn's disease (CD) is a chronic inflammatory bowel disease characterized by transmural inflammatory lesions that can affect the entire gastrointestinal tract (1). The lifetime prevalence is 0.5-1% in Caucasian populations (2) and reflects the combined effects of genetic predisposition and environmental factors (3). Genetic linkage and candidate gene approaches (4-14) have contributed to the elucidation of loci influencing genetic susceptibility to CD. More recently, genome-wide association (GWA) studies (15-21) have provided further insight into the molecular pathogenesis of the disease. The top candidate genes or loci that consistently replicate include NOD2, IL23R, ATG16L1, the IBD5 region on chromosome 5q31, and a region on 5p13.1 near the PTGER4 gene. The nature of these genes suggests that the major genetic risk factors for CD are involved in the innate immune response and destruction of intracellular bacteria.It is now clear that GWA studies provide a powerful and robust new tool for the identification of the multiple susceptibility alleles involved in complex diseases. Importantly, these types of studies have the ability to identify genes that impart only moderate increases in risk (21,22). However, most studies performed to date have identified only a few top signals, and the validation of true association among signals with lower statistical significance remains a challenge. In addition, most of the GWA studies to date have been performed by using general populations, for which very large sample sizes are required for success. They have also largely relied on single-marker analysis, with genome-wide haplotype-based association analyses receiving little attention.In early 2004, we conducted a GWA study for CD...

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BackgroundWe have examined the genomic distribution of large rare autosomal deletions in a sample of 440 parent-parent-child trios from the Quebec founder population (QFP) which was recruited for a study of Attention Deficit Hyperactivity Disorder.Methodology/Principal FindingsDNA isolated from blood was genotyped on Illumina Hap300 arrays. PennCNV combined with visual evaluation of images generated by the Beadstudio program was used to determine deletion boundary definition of sufficient precision to discern independent events, with near-perfect concordance between parent and child in about 98% of the 399 events detected in the offspring; the remaining 7 deletions were considered de novo. We defined several genomic regions of very high deletion frequency (‘hotspots’), usually of 0.4–0.6 Mb in length where independent rare deletions were found at frequencies of up to 100 fold higher than the average for the genome as a whole. Five of the 7 de novo deletions were in these hotspots. The same hotspots were also observed in three other studies on members of the QFP, those with schizophrenia, with endometriosis and those from a longevity cohort.Conclusions/SignificanceNine of the 13 hotspots carry one gene (7 of which are very long), while the rest contain no known genes. All nine genes have been implicated in disease. The patterns of exon deletions support the proposed roles for some of these genes in human disease, such as NRXN1 and PARKIN, and suggest limited roles or no role at all, for others, including MACROD2 and CTNNA3. Our results also offer an alternative interpretation for the observations of deletions in tumors which have been proposed as reflecting tumor-suppressive activity of genes in these hotspots.

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