Independent Replication Of Association Research Articles

Abstract 78: Genetic Associations and Mechanisms in Oncology (GAME-ON): A network approach to post-GWAS research.

Abstract Genome-wide association studies (GWAS) provide the initial evidence that a genetic region harbors a cancer susceptibility locus. However, further research is needed to identify the causal variant(s) and understand the biology of complex diseases. The National Cancer Institute GAME-ON Network consists of five collaborating groups that pursue promising scientific leads from previously generated cancer GWAS and coordinate and accelerate integrative post-GWAS discovery research. The five site-specific groups are ColoRectal Transdisciplinary Study (CORECT), Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE), Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE), Follow-up of Ovarian Cancer Genetic Association and Interaction Studies (FOCI), and Transdisciplinary Research in Cancer of the Lung (TRICL). Each GAME-ON group is structured into three components: 1) Discovery and replication, which works to find new associations through pooled analyses, conducting GWAS in minority populations, independent replication of associations, and fine mapping of association signals; 2) Biological studies, which focus on evaluating risk-modifying variants, determining the biological mechanisms of risk-enhancement, and understanding the functional consequences of variants; and 3) Epidemiology, to evaluate gene-gene and gene-environment interactions, assess penetrance and population attributable risk, and develop risk models and evaluate their clinical validity. Six working groups were formed to facilitate collaborations and share methodological expertise across all groups: 1) Analytic and Risk Modeling, to develop analytic tools, share analytic approaches, develop and validate models to characterize risk factors for cancer, 2) Epidemiology and Clinical, to plan and assist collaborative epidemiologic analysis, such as analyzing pan-cancer genes or pathways common to many cancers and the use of standard control sets across consortia, 3) Functional Assays, to share approaches for the characterization of functional consequences of risk variants, including identification of specific gene targets and their interaction mechanisms, 4) Next-Generation Genomic Technologies, to evaluate current and emerging technologies and platforms for optimal genotyping and sequencing, and assist in the search for less common and rare variants, 5) Epigenetics, to explore modification of genetic expression from epidemiological factors, and 6) the hTERT working group, to evaluate the impact of hTERT variations on risk across multiple cancer sites. Descriptive data for the ongoing projects will be presented. In the past two years, GAME-ON has developed a network infrastructure for post-GWAS research, which will provide an inventory of epidemiologic and clinical data as well as availability of blood and tissue samples. Each group has identified new GWAS variants, completed meta-analyses, and developed strategies for fine-mapping and functional characterization of novel loci. Utilizing the collaborative environment of the network, researchers are currently developing a GAME-ON Oncochip with SNP selection from breast, colon, prostate, ovarian, and lung cancer variants, which will be used to genotype a large and diverse group of cancer cases and controls. Members of GAME-ON have used data from The Cancer Genome Atlas (TCGA) to implement eQTL analyses, conducted methylation and copy number expression analyses, and developed and applied novel methods for gene-environment interaction and pathway analysis. Major achievements and challenges within the past two years will be discussed. Citation Format: Brett M. Kaminski, Christopher I. Amos, Eric DeRycke, Elizabeth M. Gillanders, Stephen B. Gruber, Brian E. Henderson, David J. Hunter, Pascale K. Lepage, Thomas A. Sellers, Daniela Seminara. Genetic Associations and Mechanisms in Oncology (GAME-ON): A network approach to post-GWAS research. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 78.

High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility.

Autism spectrum disorders are a group of highly heritable neurodevelopmental disorders with a complex genetic etiology. The International Molecular Genetic Study of Autism Consortium previously identified linkage loci on chromosomes 7 and 2, termed AUTS1 and AUTS5, respectively. In this study, we performed a high-density association analysis in AUTS1 and AUTS5, testing more than 3000 single nucleotide polymorphisms (SNPs) in all known genes in each region, as well as SNPs in non-genic highly conserved sequences. SNP genotype data were also used to investigate copy number variation within these regions. The study sample consisted of 127 and 126 families, showing linkage to the AUTS1 and AUTS5 regions, respectively, and 188 gender-matched controls. Further investigation of the strongest association results was conducted in an independent European family sample containing 390 affected individuals. Association and copy number variant analysis highlighted several genes that warrant further investigation, including IMMP2L and DOCK4 on chromosome 7. Evidence for the involvement of DOCK4 in autism susceptibility was supported by independent replication of association at rs2217262 and the finding of a deletion segregating in a sib-pair family.

Analysis ofFGGYas a risk factor for sporadic amyotrophic lateral sclerosis

A genome-wide association study (GWAS) using pooled DNA samples from 386 sporadic ALS patients and 542 controls from the USA, identified genetic variation in FGGY (FLJ10986) as a risk factor, as well as 66 additional candidate SNPs. Considering the large number of hypotheses that are tested in GWAS, independent replication of associations is crucial for identifying true-positive genetic risk factors for disease. The primary aim of this study was to study the association between FGGY and sporadic ALS in large, homogeneous populations from northern Europe. Genotyping experiments were performed using Illumina Beadchips, Sequenom iPLEX assays and Taqman technology on large case-control series from The Netherlands, Belgium, Sweden and Ireland (total: 1883 sporadic ALS patients and 2063 controls). No significant association between sporadic ALS and the six previously reported associated SNPs in FGGY was observed: rs6700125 (p =0.56), rs6690993 (p =0.30), rs10493256 (p =0.68), rs6587852 (p =0.64), rs1470407 (p =0.28) and rs333662 (p =0.44). Screening of the additional candidate loci did not yield significant associations either, with the lowest p-value in joint analysis for rs7772593 (p =0.14). We concluded that common genetic variation in FGGY is not associated with susceptibility to sporadic ALS in genetically homogeneous populations from northern Europe.

The SERPINE2 Gene Is Associated with Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a complex human disease likely influenced by multiple genes, cigarette smoking, and gene-by-smoking interactions, but only severe alpha 1-antitrypsin deficiency is a proven genetic risk factor for COPD. Prior linkage analyses in the Boston Early-Onset COPD Study have demonstrated significant linkage to a key intermediate phenotype of COPD on chromosome 2q. We integrated results from murine lung development and human COPD gene-expression microarray studies with human COPD linkage results on chromosome 2q to prioritize candidate-gene selection, thus identifying SERPINE2 as a positional candidate susceptibility gene for COPD. Immunohistochemistry demonstrated expression of serpine2 protein in mouse and human adult lung tissue. In family-based association testing of 127 severe, early-onset COPD pedigrees from the Boston Early-Onset COPD Study, we observed significant association with COPD phenotypes and 18 single-nucleotide polymorphisms (SNPs) in the SERPINE2 gene. Association of five of these SNPs with COPD was replicated in a case-control analysis, with cases from the National Emphysema Treatment Trial and controls from the Normative Aging Study. Family-based and case-control haplotype analyses supported similar regions of association within the SERPINE2 gene. When significantly associated SNPs in these haplotypic regions were included as covariates in linkage models, LOD score attenuation was observed most markedly in a smokers-only linkage model (LOD 4.41, attenuated to 1.74). After the integration of murine and human microarray data to inform candidate-gene selection, we observed significant family-based association and independent replication of association in a case-control study, suggesting that SERPINE2 is a COPD-susceptibility gene and is likely influenced by gene-by-smoking interaction.

Genetic Factors and Insulin Secretion

IGFs are important regulators of pancreatic beta-cell development, growth, and maintenance. Mutations in the IGF genes have been found to be associated with type 2 diabetes, myocardial infarction, birth weight, and obesity. These associations could result from changes in insulin secretion. We have analyzed glucose-stimulated insulin secretion using hyperglycemic clamps in carriers of a CA repeat in the IGF-I promoter and an ApaI polymorphism in the IGF-II gene. Normal and impaired glucose-tolerant subjects (n = 237) were independently recruited from three different populations in the Netherlands and Germany to allow independent replication of associations. Both first- and second-phase insulin secretion were not significantly different between the various IGF-I or IGF-II genotypes. Remarkably, noncarriers of the IGF-I CA repeat allele had both a reduced insulin sensitivity index (ISI) and disposition index (DI), suggesting an altered balance between insulin secretion and insulin action. Other diabetes-related parameters were not significantly different for both the IGF-I and IGF-II gene variant. We conclude that gene variants in the IGF-I and IGF-II genes are not associated with detectable variations in glucose-stimulated insulin secretion in these three independent populations. Further studies are needed to examine the exact contributions of the IGF-I CA repeat alleles to variations in ISI and DI.