Overview of the Type I Diabetes Genetics Consortium

Abstract

The Type I Diabetes Genetics Consortium (T1DGC) is an international, multicenter research program with two primary goals. The first goal is to identify genomic regions and candidate genes whose variants modify an individual’s risk of type I diabetes (T1D) and help explain the clustering of the disease in families. The second goal is to make research data available to the research community and to establish resources that can be used by, and that are fully accessible to, the research community. To facilitate the access to these resources, the T1DGC has developed a Consortium Agreement (http://www.t1dgc.org) that specifies the rights and responsibilities of investigators who participate in Consortium activities. The T1DGC has assembled a resource of affected sib-pair families, parent–child trios, and case–control collections with banks of DNA, serum, plasma, and EBV-transformed cell lines. In addition, both candidate gene and genome-wide (linkage and association) studies have been performed and displayed in T1DBase (http://www.t1dbase.org) for all researchers to use in their own investigations. In this supplement, a subset of the T1DGC collection has been used to investigate earlier published candidate genes for T1D, to confirm the results from a genome-wide association scan for T1D, and to determine associations with candidate genes for other autoimmune diseases or with type II diabetes that may be involved with β-cell function.

Introduction

Type I diabetes (T1D) is characterized by autoimmune destruction of the pancreatic β cells. It has long been known that the likelihood of a person developing T1D is higher the more closely related he or she is to a person with the disease, such that first-degree relatives of cases are at an estimated 15 times greater risk of T1D than a randomly selected member of the general population.^1,2 Earlier, family as well as case–control studies of the genetic basis of T1D have been limited by small sample sizes, resulting in inadequate statistical power to detect genetic risk factors that contribute even modest risk to disease. To address issues of sample size and consistency, the Type I Diabetes Genetics Consortium (T1DGC) has obtained and assembled the largest affected sib-pair (ASP) panel and the largest case–control collections to study T1D to date. This overview provides information on the structure of the T1DGC, access to samples and data, and the current research being performed.

Type I Diabetes Genetics Consortium

The T1DGC, established through the efforts of the National Institute of Diabetes and Digestive and Kidney Diseases and the Juvenile Diabetes Research Foundation, is an international effort to identify genes that determine an individual’s risk of T1D. The T1DGC recognized that earlier progress toward the goal of gene discovery had been limited by a lack of sufficient clinical and genetic resources. A major effort of the T1DGC has been the creation of a resource base of well-characterized families from multiple ethnic groups to facilitate the localization and characterization of T1D susceptibility genes. Building on these T1DGC resources, members and collaborators of the T1DGC can undertake positional cloning to identify candidate genes that determine susceptibility or protection to T1D. All the research activities reported here use subsets of the T1DGC collections. Participation in Consortium activities is available to all investigators who sign a Consortium Agreement (http://www.t1dgc.org). The Agreement provides details of the rights and responsibilities of T1DGC members.

The results from earlier genome-wide linkage scans for T1D suggest that the contributions of known T1D risk loci to familial clustering of T1D (excluding HLA) exhibit a locus-specific genetic risk of λ_s<1.3 (where λ_s=expected zero sharing of alleles identical-by-descent of a marker locus/observed). The λ_s=1.3 for a causal allele frequency of 0.3 under a multiplicative model would correspond to a relative risk >2.3, exceeding that observed for two replicated T1D loci, PTPN22 and INS. To attain appropriate statistical power to detect these T1D susceptibility loci using the ASP family design, the T1DGC established four regional networks: North America, Europe (including Israel), United Kingdom (including Sardinia), and Asia-Pacific. The T1DGC members within the networks recruited over 2500 ASPs, with establishment of EBV-transformed cell lines for a continual supply of DNA, as well as native genomic DNA from most individuals.

In addition to T1DGC-recruited ASP families, the T1DGC has recruited trio families from ethnic groups with lower prevalence of T1D. The T1DGC has also welcomed the inclusion of earlier ascertained case–control collections (from the UK, Denmark, etc.).

Each T1DGC network is composed of members whose activities include recruitment of study participants, autoantibody determination, genotyping and sample handling, informatics and bioinformatics, study coordination, and data analysis. Each network has established a DNA repository (to process samples for DNA and to provide cell immortalization), an HLA laboratory (to determine classical HLA typing), and an autoantibody laboratory (to characterize plasma from cases). The T1DGC Coordinating Center (at Wake Forest University) developed a web-based system of sample transfer and tracking to the T1DGC laboratories and is the central repository of clinical information and genetic data. Samples and data from the T1DGC network laboratories are being transferred to central National Institute of Diabetes and Digestive and Kidney Diseases repositories (data, plasma and serum, and cell lines) from which investigators can make requests. All samples and data assembled by the Consortium are available according to the policies in the T1DGC Access Policy (found on the T1DGC web site, http://www.t1dgc.org).

Research in the T1DGC

Genome-wide linkage scans

A primary experiment of the T1DGC was to conduct a genome-wide linkage scan using ASP families. The linkage scan genotyping was performed at the Center for Inherited Disease Research using the Illumina Human Linkage-12 Genotyping Beadchip that included 6090 single-nucleotide polymorphisms (SNPs) with an average genome-wide spacing of 0.58 cM. The genome-wide linkage scan is comprised of three separate experiments because of the large size of the family collection. The first installment of the linkage scan included ~1200 ASP families.³ The current analysis of the ASP family collection includes many (N=1189) of the T1D ASP families in the earlier report, but with the addition of many (N=1307) newly recruited families.⁴ In this larger data set, in addition to the strong evidence for linkage at HLA, suggestive evidence was observed near CTLA4 on chromosome 2q32.3 (LOD=3.28) and near INS (LOD=3.16) on chromosome 11p15.5. Additional support for linkage was detected at two novel regions on chromosome 19 (LODS=2.84 and 2.54, respectively). There was further evidence of linkage to T1D on chromosome 6q that could not be accounted for by the major linkage signal at the HLA class II loci on chromosome 6p21. These data will be further strengthened by the addition of the final group of ASP families.

Evaluation of the human major histocompatibility complex

Genes in the HLA region on chromosome 6p21 (the major histocompatibility complex, MHC) are recognized to contain the major genetic risk factors for T1D susceptibility, as the region accounts for ~50% of the familial clustering. It remains unclear, however, whether the T1D susceptibility risk in the MHC is restricted to the HLA genes, or other (non-HLA) loci that have yet to be identified or characterized. The T1DGC has conducted an MHC Fine Mapping experiment (MHC Fine Mapping Workshop). This Workshop used a subset of the T1DGC samples, including 2321 ASP families (9976 subjects) with classical HLA genotyping, ~3000 SNPs and 63 microsatellite markers to better understand T1D risk in the 4Mb MHC region. The data were provided to over 18 research teams, results presented during a 2-day meeting, and publications collected in a Supplement.⁵ These data are also available through the T1DGC (http:// www.t1dgc.org) and summary results may be viewed in T1DBase (http://www.t1dbase.org).

Examination of published candidate genes for T1D

Although the MHC accounts for ~50% of the familial clustering of T1D, other genes also contribute to susceptibility. Many publications that used case–control and linkage designs have proposed genes as candidates for T1D. To facilitate evaluation of these candidate genes with larger family based sample sizes, the T1DGC conducted the ‘Rapid Response’ experiment. For the T1DGC Rapid Response Workshop, investigators who had published the initial reports were invited to participate. Further, the same DNA samples (as for the MHC Fine Mapping Workshop) from the 2321 ASP families were evaluated for evidence of association of SNPs in selected candidate loci with T1D. These data^6,7 appear in this Supplement to Genes and Immunity. The genes that were evaluated and presented here are IL4R,⁸ SUMO4,⁹ CTLA4,¹⁰ IL2RA,¹¹ PTPN22,¹² IRS1 and PAX4,¹³ TCF7,¹⁴ VDR,¹⁵ IL12B,¹⁶ and OAS1,¹⁷ either by complete tagging of the gene or by characterizing the most associated SNP.⁷ A standard analysis of all 19 genes that were available has also been conducted and presented in this Supplement.¹⁸

Examination of the Wellcome Trust Case Control Consortium SNPs for T1D

The Wellcome Trust Case Control Consortium genome-wide association scan (GWAS) was conducted to identify SNPs associated with seven diseases.¹⁹ SNPs in 2000 cases for each disease were compared with 3000 common controls. For T1D, four new loci were identified and later confirmed and others provided some evidence for association that, while suggestive, did not reach statistical significance.²⁰ As a separate component of the evaluation of published candidate gene association, the T1DGC conducted a follow-up study of 1715 SNPs from the Wellcome Trust Case Control Consortium GWAS in 1410 families to provide addition characterization of the associations with T1D.²¹

Examination of autoimmune disease genes and those affecting β-cell function in type II diabetes

The use of GWAS technology has permitted many disease-focused experiments to be conducted. An increasing number of autoimmune diseases have been explored using GWAS approaches, including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, systemic lupus erythematosis, as well as T1D. The clustering of autoimmune diseases in families has been observed earlier, and examples of differential contribution of a candidate gene (PTPN22) have been shown in some diseases, but not others.²² Individual GWAS results have highlighted the commonality (and differences) between diseases, and associated SNPs in genes in one autoimmune disease are now candidates for other autoimmune diseases. In addition, recent GWAS results in type II diabetes have shown that many of the candidate genes for type II diabetes may have effects through dysfunction of the β cell.²³ The T1DGC initiated a candidate gene study of 456 SNPs from known type II diabetes loci associated with β-cell function (CDKAL1, IGF2BP2, CDKN2B, SLC30A8, HHEX, and FTO) and from 31 earlier identified autoimmune disease regions (including IL23R, NOD2, PADI4). SNPs were genotyped in 1410 T1D families and result reported in this volume.²⁴

GWAS in T1D

Recently, GWASs in T1D have identified at least 18 genomic regions with significant evidence of association to T1D. Unlike the genome-wide linkage scan strategy that can detect genomic regions with major effect on risk, the GWAS approach detects common variants with relatively small, possibly typical, effects in the population. The T1DGC has used existing collections of cases and controls to perform the largest GWAS for T1D to date (4000 cases and 2500 controls genotyped using the Illumina, Inc., 550K SNP assay). A final meta-analysis of data was conducted using over 7500 cases and over 9000 controls with over 800K SNPs (by imputation). These data indicate that many confirmed, replicated, and statistically significant novel loci and pathways will be emerging that require additional examination.²⁵

Summary

The goals of the T1DGC are to identify the genes that contribute to the risk of T1D in families and in the general population. Earlier limitations to understanding the genetic basis of T1D have been due to the limited number of samples available for analysis, the lack of large-scale molecular genetic approaches and data available to pinpoint susceptibility loci within the human genome, and restricted access of analytic results from inadequate bioinformatics infrastructure available to understand the genetic data. At present, progress in several of these areas provides new opportunities. The T1DGC has assembled renewable genetic materials for use in family based linkage and association studies (http://www.t1dgc.org) and has supported a web-based portal for display and examination of these results (www.T1DBase.org). The T1DGC is continuing to collect samples from ethnic groups with decreased susceptibility to T1D to understand the occurrence of T1D in these populations, and help in the identification of causal genes.