An SNP linkage scan identifies significant Crohn's disease loci on chromosomes 13q13.3 and, in Jewish families, on 1p35.2 and 3q29

Change in Prevalence of Family History During Long-term Follow-up of Patients With Pediatric-onset Inflammatory Bowel Disease

OBJECTIVES

The aim of the study was to prospectively study changes in prevalence of positive family history (FH+) in pediatric-onset inflammatory bowel disease (IBD) in contrast to previously published cross-sectional data.

METHODS

An observational cohort study was performed using a prospective pediatric-onset IBD database including 485 patients with disease duration ≥10 years as of December 2016. Proband characteristics and FH+ were obtained at diagnosis and subsequently from the database, medical records, and follow-up telephone interviews in 2006 and 2016.

RESULTS

Updated 2016 information was obtained from 322 (66%) patients and included in analysis with median follow-up of 18 years (interquartile range 14, 26). Prevalence of FH+ increased from 13.7% at diagnosis to 26.6% at 20 years for first-degree relatives and from 38.5% to 52.2% for all relatives. At 20-year follow-up, an additional 10.0% of probands had a sibling, 6.1% had a parent, 1.9% had a grandparent, and 4.5% had a cousin diagnosed with IBD. FH+ at diagnosis was associated with greater risk for additional FH+ at 20 years (43% vs 22%, P < 0.001). Non-Jewish Caucasians had significantly lower risk of a FH+ compared to Jewish Caucasians (P = 0.002), but similar risk to African Americans (P = 0.55). FH+ at diagnosis was not associated with disease type (P = 0.33) or age at diagnosis (P = 0.24).

CONCLUSIONS

This prospective study documents changes in family history of IBD in pediatric-onset IBD patients over time. Prevalence of FH+ increased for first-degree and all relatives at 20 years by 12.9% and 13.7%, respectively. FH+ at diagnosis was associated with a 2-fold greater likelihood of subsequent FH+ at 20 years.

Whole-genome single nucleotide polymorphism-based linkage analysis in spondyloarthritis multiplex families reveals a new susceptibility locus in 13q13

OBJECTIVE

Spondyloarthritis (SpA) is a chronic inflammatory disorder with high heritability but with complex genetics. Apart from HLA-B27, most of the underlying genetic components remain to be identified. We conducted a whole-genome high-density non-parametric linkage analysis to identify new genetic factors of susceptibility to SpA.

METHODS

914 subjects including 462 with SpA from 143 multiplex families were genotyped using Affymetrix 250K microarrays. After quality control, 189 368 single nucleotide polymorphisms (SNPs) were kept for further analyses. Both non-parametric and parametric linkage analyses were performed using Merlin software. Association was tested with Unphased.

RESULTS

Non-parametric linkage analysis identified two regions significantly linked to SpA: the major histocompatibility complex (LODmax=24.77) and a new 13q13 locus (LODmax=5.03). Additionally, eight loci achieved suggestive LOD scores, including the previously identified SPA2 locus at 9q33 (LODmax=3.51). Parametric analysis supported a codominant model in 13q13 with a maximum heterogeneity LOD, 'HLOD' score of 3.084 (α=0.28). Identification of meiotic recombination events around the 13q13 linkage peak in affected subjects from the 43 best-linked families allowed us to map the disease interval between 38.753 and 40.040 Mb. Family-based association analysis of the SNPs inside this interval in the best-linked families identified a SNP near FREM2 (rs1945502) which reached a p value close to statistical significance (corrected p=0.08).

CONCLUSION

We report here for the first time a significant linkage between 13q13 and SpA. Identification of susceptibility factor inside this chromosomal region through targeted sequencing in linked families is underway.

The increasing prevalence of inflammatory bowel diseases among Jewish adolescents and the sociodemographic factors associated with diagnosis

BACKGROUND

We investigated the prevalence and sociodemographic factors associated with diagnosis of inflammatory bowel diseases (IBD) among Jewish Israeli adolescents.

METHODS

A total of 953,684 Jewish Israeli adolescents (57.8% men) who underwent a general health examination at mean age 17.3 ± 0.5 years from 1998 to 2010 were included. A definite diagnosis of IBD was based on laboratory, endoscopy, and pathology reports. Covariate data included socioeconomic status (SES) as defined by the Israel Central Bureau Statistics, and origin and number of children in household.

RESULTS

A total of 2021 patients with IBD were identified (0.21%) in 13 annual cohorts. The prevalence of IBD increased from 149.4 cases per 100,000 to 301.0 cases per 100,000 in the first and last cohort (Ptrend = 0.003). Independent factors associated with occurrence of IBD were SES (high: odds ratio [OR] = 1.84, 95% confidence interval [CI]: 1.60-2.1, P < 0.001; medium: OR = 1.47, 95% CI: 1.3-1.69, P < 0.001; low: reference), Western origin (OR = 1.71, 95% CI: 1.53-1.90, P < 0.001; Asia Africa: reference), and male gender (OR = 1.21, 95% CI: 1.10-1.33, P < 0.001; female: reference). Four or more children in the household were associated with reduced OR for IBD [N ≥ 4: OR = 0.70, 95% CI: 0.62-0.72, P < 0.001, N = 1-3: reference]. The OR among adolescents of Western origin-high SES was 2.95 times higher compared with adolescents of Asia-African origin with low SES.

CONCLUSIONS

The prevalence of IBD doubled during the 13 years of the study period. Among this large cohort of Jewish adolescents, for each origin, higher SES was associated with increased occurrence of IBD.

Role of genetics in the diagnosis and prognosis of Crohn's disease

Considering epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have been so far related to the diagnosis of Crohn's disease. Those genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the most strong and replicated associations with Crohn's disease have been done with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in prognosis of Crohn's disease and many attempts have been made to classify genetic profiles in Crohn's disease. CARD15 seems not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding on Crohn's disease genetics is important but when combining genetic data with functional data the outcome could be of major importance to clinicians.

Role of genetics in the diagnosis and prognosis of Crohn's disease

Considering the epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have so far been related to the diagnosis of Crohn's disease. These genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the strongest and most replicated associations with Crohn's disease have been demonstrated with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in the prognosis of Crohn's disease and many attempts have been made for classification of genetic profiles in Crohn's disease. CARD15 seems to be not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding of Crohn's disease genetics is of value, but when combining genetic data with functional data the outcome could be of major importance to clinicians.

Epidemiology of Crohn's disease in Québec, Canada

BACKGROUND

Crohn's disease (CD) is an idiopathic inflammatory bowel disease (IBD). We aimed to determine the prevalence and incidence of CD in Québec and characterize the demographic and health-related factors associated with this disease.

METHODS

We identified CD cases in the provincial administrative databases for the years 1993-2002. The CD prevalence and incidence rates were estimated respectively for the periods 1993-2002 and 1998-2000. We validated the identified cases using clinically confirmed IBD cases. Predictor variables of CD were analyzed using the Poisson regression model to explain the variation in CD incidence rates across Québec.

RESULTS

In all, 21,172 patients fulfilled the CD case definition for the period. The age and sex standardized average prevalence rate for 1993-2002 was 189.7 cases / 100,000 population and the age and sex standardized incidence rate of CD for the 1998-2000 period was 20.2 cases / 100,000 person-years. The female/male cases ratio among incident cases was 0.74 for the 0-14-year-old group, 1.30 for the 15-64-year-old group, and 1.77 for the cases older than 65 years old. After adjustment, independent predictors of CD incidence were: incidence of 5 reportable enteric diseases, proportion of individuals of Jewish ethnicity, and proportion of immigrant people.

CONCLUSIONS

The identified predictors of CD explained 20% of the regional variance in the incidence rate of CD in the Québec population. Other factors such as genetic susceptibility to CD or the effect of an environmental cause should be taken into consideration in the models to explain the residual variance.

Contributions of IBD5, IL23R, ATG16L1, and NOD2 to Crohn's disease risk in a population-based case-control study: evidence of gene-gene interactions

BACKGROUND

IBD5, IL23R, and ATG16L1 genetic variations are established Crohn's disease (CD) risks alleles. We evaluated these in a population-based case-control study within a cohort to determine their penetrance, population attributable risk, independence, and relationship to other established CD risk factors, including NOD2.

METHODS

DNA from 213 CD, 118 [corrected] ulcerative colitis, and 315 [corrected] healthy control subjects from the population based University of Manitoba IBD Research Registry were genotyped for IBD5 and IL23R single-nucleotide polymorphisms (SNPs),and for the Thr 300Ala ATG16L1 SNP. Univariate and multivariate analyses were performed for these and nongenetic risk factors.We introduce multidimensionality reduction (MDR) to explore gene– gene interactions.

RESULTS

ATG16L1, IBD5, and IL23R SNPs were significantly associated with CD. Multivariate analysis showed independent CD association for carriers of ATG16L1 (odds ratio [OR] = 1.8, 95% confidence interval [CI] 1.09-3.24), IBD5-IGR2230 (OR = 2.16, 95% CI 1.30-3.59), and IL23R-rs10889677 (OR = 2.13, 95% CI 1.39-3.28) while retaining association for NOD2 mutation carriers (OR = 4.45, 95% CI 2.68-7.38), IBD family history (OR = 2.75, 95% CI 1.42-5.31), tobacco (OR = 2.06, 95% CI 1.35-3.14), and Jewish ethnicity (OR = 20.1, 95% CI 2.16-186.8). IL23R minor variants for Arg381Gln and Intron 6 rs7517848 showed independent, CD protection and 3' untranslated variant rs108896778 showed risk. MDR analysis suggested an interaction between IBD5, ATG16L1, and IL23R risk alleles. Penetrance values for ATG16L1 and IBD5 were 0.27% for heterozygotes, and 0.35% and 0.44%, respectively, for homozygotes. IL23R rs108896778 penetrance was 0.37%.

CONCLUSIONS

A population-based analysis of CD risk factors is useful for characterizing the epidemiology of multiple CD genetic and nongenetic risk factors. Gene-gene interactions are likely, but require further evaluation in large population-based cohorts.