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1.  Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia 
PLoS Computational Biology  2012;8(7):e1002587.
With the recent success of genome-wide association studies (GWAS), a wealth of association data has been accomplished for more than 200 complex diseases/traits, proposing a strong demand for data integration and interpretation. A combinatory analysis of multiple GWAS datasets, or an integrative analysis of GWAS data and other high-throughput data, has been particularly promising. In this study, we proposed an integrative analysis framework of multiple GWAS datasets by overlaying association signals onto the protein-protein interaction network, and demonstrated it using schizophrenia datasets. Building on a dense module search algorithm, we first searched for significantly enriched subnetworks for schizophrenia in each single GWAS dataset and then implemented a discovery-evaluation strategy to identify module genes with consistent association signals. We validated the module genes in an independent dataset, and also examined them through meta-analysis of the related SNPs using multiple GWAS datasets. As a result, we identified 205 module genes with a joint effect significantly associated with schizophrenia; these module genes included a number of well-studied candidate genes such as DISC1, GNA12, GNA13, GNAI1, GPR17, and GRIN2B. Further functional analysis suggested these genes are involved in neuronal related processes. Additionally, meta-analysis found that 18 SNPs in 9 module genes had Pmeta<1×10−4, including the gene HLA-DQA1 located in the MHC region on chromosome 6, which was reported in previous studies using the largest cohort of schizophrenia patients to date. These results demonstrated our bi-directional network-based strategy is efficient for identifying disease-associated genes with modest signals in GWAS datasets. This approach can be applied to any other complex diseases/traits where multiple GWAS datasets are available.
Author Summary
The recent success of genome-wide association studies (GWAS) has generated a wealth of genotyping data critical to studies of genetic architectures of many complex diseases. In contrast to traditional single marker analysis, an integrative analysis of multiple genes and the assessment of their joint effects have been particularly promising, especially upon the availability of many GWAS datasets and other high-throughput datasets for numerous complex diseases. In this study, we developed an integrative analysis framework for multiple GWAS datasets and demonstrated it in schizophrenia. We first constructed a GWAS-weighted protein-protein interaction (PPI) network and then applied a dense module search algorithm to identify subnetworks with combinatory disease effects. We applied combinatorial criteria for module selection based on permutation tests to determine whether the modules are significantly different from random gene sets and whether the modules are associated with the disease in investigation. Importantly, considering there are many complex diseases with multiple GWAS datasets available, we proposed a discovery-evaluation strategy to search for modules with consistent combined effects from two or more GWAS datasets. This approach can be applied to any diseases or traits that have two or more GWAS datasets available.
doi:10.1371/journal.pcbi.1002587
PMCID: PMC3390381  PMID: 22792057
2.  GSA-SNP: a general approach for gene set analysis of polymorphisms 
Nucleic Acids Research  2010;38(Web Server issue):W749-W754.
Genome-wide association (GWA) study aims to identify the genetic factors associated with the traits of interest. However, the power of GWA analysis has been seriously limited by the enormous number of markers tested. Recently, the gene set analysis (GSA) methods were introduced to GWA studies to address the association of gene sets that share common biological functions. GSA considerably increased the power of association analysis and successfully identified coordinated association patterns of gene sets. There have been several approaches in this direction with some limitations. Here, we present a general approach for GSA in GWA analysis and a stand-alone software GSA-SNP that implements three widely used GSA methods. GSA-SNP provides a fast computation and an easy-to-use interface. The software and test datasets are freely available at http://gsa.muldas.org. We provide an exemplary analysis on adult heights in a Korean population.
doi:10.1093/nar/gkq428
PMCID: PMC2896081  PMID: 20501604
3.  Ion channels and schizophrenia: a gene set-based analytic approach to GWAS data for biological hypothesis testing 
Human Genetics  2011;131(3):373-391.
Schizophrenia is a complex genetic disorder. Gene set-based analytic (GSA) methods have been widely applied for exploratory analyses of large, high-throughput datasets, but less commonly employed for biological hypothesis testing. Our primary hypothesis is that variation in ion channel genes contribute to the genetic susceptibility to schizophrenia. We applied Exploratory Visual Analysis (EVA), one GSA application, to analyze European-American (EA) and African-American (AA) schizophrenia genome-wide association study datasets for statistical enrichment of ion channel gene sets, comparing GSA results derived under three SNP-to-gene mapping strategies: (1) GENIC; (2) 500-Kb; (3) 2.5-Mb and three complimentary SNP-to-gene statistical reduction methods: (1) minimum p value (pMIN); (2) a novel method, proportion of SNPs per Gene with p-values below a pre-defined α-threshold (PROP); and (3) the truncated product method (TPM). In the EA analyses, ion channel gene set(s) were enriched under all mapping and statistical approaches. In the AA analysis, ion channel gene set(s) were significantly enriched under pMIN for all mapping strategies and under PROP for broader mapping strategies. Less extensive enrichment in the AA sample may reflect true ethnic differences in susceptibility, sampling or case ascertainment differences, or higher dimensionality relative to sample size of the AA data. More consistent findings under broader mapping strategies may reflect enhanced power due to increased SNP inclusion, enhanced capture of effects over extended haplotypes or significant contributions from regulatory regions. While extensive pMIN findings may reflect gene size bias, the extent and significance of PROP and TPM findings suggest that common variation at ion channel genes may capture some of the heritability of schizophrenia.
doi:10.1007/s00439-011-1082-x
PMCID: PMC3278516  PMID: 21866342
4.  GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation 
PLoS Genetics  2014;10(11):e1004787.
Results from Genome-Wide Association Studies (GWAS) have shown that complex diseases are often affected by many genetic variants with small or moderate effects. Identifications of these risk variants remain a very challenging problem. There is a need to develop more powerful statistical methods to leverage available information to improve upon traditional approaches that focus on a single GWAS dataset without incorporating additional data. In this paper, we propose a novel statistical approach, GPA (Genetic analysis incorporating Pleiotropy and Annotation), to increase statistical power to identify risk variants through joint analysis of multiple GWAS data sets and annotation information because: (1) accumulating evidence suggests that different complex diseases share common risk bases, i.e., pleiotropy; and (2) functionally annotated variants have been consistently demonstrated to be enriched among GWAS hits. GPA can integrate multiple GWAS datasets and functional annotations to seek association signals, and it can also perform hypothesis testing to test the presence of pleiotropy and enrichment of functional annotation. Statistical inference of the model parameters and SNP ranking is achieved through an EM algorithm that can handle genome-wide markers efficiently. When we applied GPA to jointly analyze five psychiatric disorders with annotation information, not only did GPA identify many weak signals missed by the traditional single phenotype analysis, but it also revealed relationships in the genetic architecture of these disorders. Using our hypothesis testing framework, statistically significant pleiotropic effects were detected among these psychiatric disorders, and the markers annotated in the central nervous system genes and eQTLs from the Genotype-Tissue Expression (GTEx) database were significantly enriched. We also applied GPA to a bladder cancer GWAS data set with the ENCODE DNase-seq data from 125 cell lines. GPA was able to detect cell lines that are biologically more relevant to bladder cancer. The R implementation of GPA is currently available at http://dongjunchung.github.io/GPA/.
Author Summary
In the past 10 years, many genome wide association studies (GWAS) have been conducted to identify the genetic bases of complex human traits. As of January, 2014, more than 12,000 single-nucleotide polymorphisms (SNPs) have been reported to be significantly associated with at least one complex trait/disease. On one hand, about 85% of identified risk variants are located in non-coding regions, which motivates a systematic understanding of the function of non-coding variants in regulatory elements in the human genome. On the other hand, complex diseases are often affected by many genetic variants with small or moderate effects. To address these issues, we propose a statistical approach, GPA, to integrating information from multiple GWAS datasets and functional annotation. Notably, our approach only requires marker-wise p-values as input, making it especially useful when only summary statistics, instead of the full genotype and phenotype data, are available. We applied GPA to analyze GWAS datasets of five psychiatric disorders and bladder cancer, where the central nervous system genes, eQTLs from the Genotype-Tissue Expression (GTEx), and the ENCODE DNase-seq data from 125 cell lines were used as functional annotation. The analysis results suggest that GPA is an effective method for integrative data analysis in the post-GWAS era.
doi:10.1371/journal.pgen.1004787
PMCID: PMC4230845  PMID: 25393678
5.  Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data 
BMC Systems Biology  2012;6(Suppl 3):S15.
Background
Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The computational burden of searching for interactions is compounded by the extremely low threshold for identifying significant p-values due to multiple hypothesis testing corrections. Utilizing prior biological knowledge to restrict the set of candidate SNP pairs to be tested can alleviate this problem, but systematic studies that investigate the relative merits of integrating different biological frameworks and GWAS data have not been conducted.
Results
We developed four biologically based frameworks to identify pairwise interactions among candidate SNP pairs as follows: (1) for each human protein-coding gene, a set of SNPs associated with that gene was constructed providing a gene-based interaction model, (2) for each known biological pathway, a set of SNPs associated with the genes in the pathway was constructed providing a pathway-based interaction model, (3) a set of SNPs associated with genes in a disease-related subnetwork provides a network-based interaction model, and (4) a framework is based on the function of SNPs. The last approach uses expression SNPs (eSNPs or eQTLs), which are SNPs or loci that have defined effects on the abundance of transcripts of other genes. We constructed pairs of eSNPs and SNPs located in the target genes whose expression is regulated by eSNPs. For all four frameworks the SNP sets were exhaustively tested for pairwise interactions within the sets using a traditional logistic regression model after excluding genes that were previously identified to associate with the trait. Using previously published GWAS data for type 2 diabetes (T2D) and the biologically based pair-wise interaction modeling, we identify twelve genes not seen in the previous single locus analysis.
Conclusion
We present four approaches to detect interactions associated with complex diseases. The results show our approaches outperform the traditional single locus approaches in detecting genes that previously did not reach significance; the results also provide novel drug targets and biomarkers relevant to the underlying mechanisms of disease.
doi:10.1186/1752-0509-6-S3-S15
PMCID: PMC3524014  PMID: 23281810
6.  Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS 
Genomics & Informatics  2012;10(2):123-127.
Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.
doi:10.5808/GI.2012.10.2.123
PMCID: PMC3480679  PMID: 23105940
gene set analysis; genome-wide association study; GSA-SNP; i-GSEA4GWAS; imputation
7.  SNP-based pathway enrichment analysis for genome-wide association studies 
BMC Bioinformatics  2011;12:99.
Background
Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS) to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs), have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs.
Results
We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1) for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one) SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2) ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one from European-American (EA) and the other from African-American (AA). In the EA data set, we found 22 pathways with nominal P-value less than or equal to 0.001 and corresponding false discovery rate (FDR) less than 5%. In the AA data set, we found 11 pathways by controlling the same nominal P-value and FDR threshold. Interestingly, 8 of these pathways overlap with those found in the EA sample. We have implemented our method in a JAVA software package, called SNP Set Enrichment Analysis (SSEA), which contains a user-friendly interface and is freely available at http://cbcl.ics.uci.edu/SSEA.
Conclusions
The SNP-based pathway enrichment method described here offers a new alternative approach for analysing GWAS data. By applying it to schizophrenia GWAS studies, we show that our method is able to identify statistically significant pathways, and importantly, pathways that can be replicated in large genetically distinct samples.
doi:10.1186/1471-2105-12-99
PMCID: PMC3102637  PMID: 21496265
8.  Use of the gamma method for self-contained gene-set analysis of SNP data 
Gene-set analysis (GSA) evaluates the overall evidence of association between a phenotype and all genotyped single nucleotide polymorphisms (SNPs) in a set of genes, as opposed to testing for association between a phenotype and each SNP individually. We propose using the Gamma Method (GM) to combine gene-level P-values for assessing the significance of GS association. We performed simulations to compare the GM with several other self-contained GSA strategies, including both one-step and two-step GSA approaches, in a variety of scenarios. We denote a ‘one-step' GSA approach to be one in which all SNPs in a GS are used to derive a test of GS association without consideration of gene-level effects, and a ‘two-step' approach to be one in which all genotyped SNPs in a gene are first used to evaluate association of the phenotype with all measured variation in the gene and then the gene-level tests of association are aggregated to assess the GS association with the phenotype. The simulations suggest that, overall, two-step methods provide higher power than one-step approaches and that combining gene-level P-values using the GM with a soft truncation threshold between 0.05 and 0.20 is a powerful approach for conducting GSA, relative to the competing approaches assessed. We also applied all of the considered GSA methods to data from a pharmacogenomic study of cisplatin, and obtained evidence suggesting that the glutathione metabolism GS is associated with cisplatin drug response.
doi:10.1038/ejhg.2011.236
PMCID: PMC3330217  PMID: 22166939
Fisher's method; gamma method; principal components; gene-level association; pathway; random effects model
9.  Gene set analysis of SNP data: benefits, challenges, and future directions 
The last decade of human genetic research witnessed the completion of hundreds of genome-wide association studies (GWASs). However, the genetic variants discovered through these efforts account for only a small proportion of the heritability of complex traits. One explanation for the missing heritability is that the common analysis approach, assessing the effect of each single-nucleotide polymorphism (SNP) individually, is not well suited to the detection of small effects of multiple SNPs. Gene set analysis (GSA) is one of several approaches that may contribute to the discovery of additional genetic risk factors for complex traits. Complex phenotypes are thought to be controlled by networks of interacting biochemical and physiological pathways influenced by the products of sets of genes. By assessing the overall evidence of association of a phenotype with all measured variation in a set of genes, GSA may identify functionally relevant sets of genes corresponding to relevant biomolecular pathways, which will enable more focused studies of genetic risk factors. This approach may thus contribute to the discovery of genetic variants responsible for some of the missing heritability. With the increased use of these approaches for the secondary analysis of data from GWAS, it is important to understand the different GSA methods and their strengths and weaknesses, and consider challenges inherent in these types of analyses. This paper provides an overview of GSA, highlighting the key challenges, potential solutions, and directions for ongoing research.
doi:10.1038/ejhg.2011.57
PMCID: PMC3172936  PMID: 21487444
pathway analysis; multilocus; complex traits; genetic association studies
10.  dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks 
Bioinformatics  2010;27(1):95-102.
Motivation: An important question that has emerged from the recent success of genome-wide association studies (GWAS) is how to detect genetic signals beyond single markers/genes in order to explore their combined effects on mediating complex diseases and traits. Integrative testing of GWAS association data with that from prior-knowledge databases and proteome studies has recently gained attention. These methodologies may hold promise for comprehensively examining the interactions between genes underlying the pathogenesis of complex diseases.
Methods: Here, we present a dense module searching (DMS) method to identify candidate subnetworks or genes for complex diseases by integrating the association signal from GWAS datasets into the human protein–protein interaction (PPI) network. The DMS method extensively searches for subnetworks enriched with low P-value genes in GWAS datasets. Compared with pathway-based approaches, this method introduces flexibility in defining a gene set and can effectively utilize local PPI information.
Results: We implemented the DMS method in an R package, which can also evaluate and graphically represent the results. We demonstrated DMS in two GWAS datasets for complex diseases, i.e. breast cancer and pancreatic cancer. For each disease, the DMS method successfully identified a set of significant modules and candidate genes, including some well-studied genes not detected in the single-marker analysis of GWA studies. Functional enrichment analysis and comparison with previously published methods showed that the genes we identified by DMS have higher association signal.
Availability: dmGWAS package and documents are available at http://bioinfo.mc.vanderbilt.edu/dmGWAS.html.
Contact: zhongming.zhao@vanderbilt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btq615
PMCID: PMC3008643  PMID: 21045073
11.  Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics 
PLoS Genetics  2014;10(5):e1004383.
Genetic association studies, in particular the genome-wide association study (GWAS) design, have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits, in particular cardiovascular diseases and lipid biomarkers. The next challenge consists of understanding the molecular basis of these associations. The integration of multiple association datasets, including gene expression datasets, can contribute to this goal. We have developed a novel statistical methodology to assess whether two association signals are consistent with a shared causal variant. An application is the integration of disease scans with expression quantitative trait locus (eQTL) studies, but any pair of GWAS datasets can be integrated in this framework. We demonstrate the value of the approach by re-analysing a gene expression dataset in 966 liver samples with a published meta-analysis of lipid traits including >100,000 individuals of European ancestry. Combining all lipid biomarkers, our re-analysis supported 26 out of 38 reported colocalisation results with eQTLs and identified 14 new colocalisation results, hence highlighting the value of a formal statistical test. In three cases of reported eQTL-lipid pairs (SYPL2, IFT172, TBKBP1) for which our analysis suggests that the eQTL pattern is not consistent with the lipid association, we identify alternative colocalisation results with SORT1, GCKR, and KPNB1, indicating that these genes are more likely to be causal in these genomic intervals. A key feature of the method is the ability to derive the output statistics from single SNP summary statistics, hence making it possible to perform systematic meta-analysis type comparisons across multiple GWAS datasets (implemented online at http://coloc.cs.ucl.ac.uk/coloc/). Our methodology provides information about candidate causal genes in associated intervals and has direct implications for the understanding of complex diseases as well as the design of drugs to target disease pathways.
Author Summary
Genome-wide association studies (GWAS) have found a large number of genetic regions (“loci”) affecting clinical end-points and phenotypes, many outside coding intervals. One approach to understanding the biological basis of these associations has been to explore whether GWAS signals from intermediate cellular phenotypes, in particular gene expression, are located in the same loci (“colocalise”) and are potentially mediating the disease signals. However, it is not clear how to assess whether the same variants are responsible for the two GWAS signals or whether it is distinct causal variants close to each other. In this paper, we describe a statistical method that can use simply single variant summary statistics to test for colocalisation of GWAS signals. We describe one application of our method to a meta-analysis of blood lipids and liver expression, although any two datasets resulting from association studies can be used. Our method is able to detect the subset of GWAS signals explained by regulatory effects and identify candidate genes affected by the same GWAS variants. As summary GWAS data are increasingly available, applications of colocalisation methods to integrate the findings will be essential for functional follow-up, and will also be particularly useful to identify tissue specific signals in eQTL datasets.
doi:10.1371/journal.pgen.1004383
PMCID: PMC4022491  PMID: 24830394
12.  Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis 
BMC Medical Genetics  2009;10:86.
Background
Amyotrophic lateral sclerosis (ALS) is a fatal, degenerative neuromuscular disease characterized by a progressive loss of voluntary motor activity. About 95% of ALS patients are in "sporadic form"-meaning their disease is not associated with a family history of the disease. To date, the genetic factors of the sporadic form of ALS are poorly understood.
Methods
We proposed a two-stage approach based on seventeen biological plausible models to search for two-locus combinations that have significant joint effects to the disease in a genome-wide association study (GWAS). We used a two-stage strategy to reduce the computational burden associated with performing an exhaustive two-locus search across the genome. In the first stage, all SNPs were screened using a single-marker test. In the second stage, all pairs made from the 1000 SNPs with the lowest p-values from the first stage were evaluated under each of the 17 two-locus models.
Results
we performed the two-stage approach on a GWAS data set of sporadic ALS from the SNP Database at the NINDS Human Genetics Resource Center DNA and Cell Line Repository http://ccr.coriell.org/ninds/. Our two-locus analysis showed that two two-locus combinations--rs4363506 (SNP1) and rs3733242 (SNP2), and rs4363506 and rs16984239 (SNP3) -- were significantly associated with sporadic ALS. After adjusting for multiple tests and multiple models, the combination of SNP1 and SNP2 had a p-value of 0.032 under the Dom∩Dom epistatic model; SNP1 and SNP3 had a p-value of 0.042 under the Dom × Dom multiplicative model.
Conclusion
The proposed two-stage analytical method can be used to search for joint effects of genes in GWAS. The two-stage strategy decreased the computational time and the multiple testing burdens associated with GWAS. We have also observed that the loci identified by our two-stage strategy can not be detected by single-locus tests.
doi:10.1186/1471-2350-10-86
PMCID: PMC2752455  PMID: 19740415
13.  Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies 
PLoS Genetics  2008;4(7):e1000130.
Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in stochastic search methods. We used a Bayesian-inspired penalised maximum likelihood approach in which every SNP can be considered for additive, dominant, and recessive contributions to disease risk. Posterior mode estimates were obtained for regression coefficients that were each assigned a prior with a sharp mode at zero. A non-zero coefficient estimate was interpreted as corresponding to a significant SNP. We investigated two prior distributions and show that the normal-exponential-gamma prior leads to improved SNP selection in comparison with single-SNP tests. We also derived an explicit approximation for type-I error that avoids the need to use permutation procedures. As well as genome-wide analyses, our method is well-suited to fine mapping with very dense SNP sets obtained from re-sequencing and/or imputation. It can accommodate quantitative as well as case-control phenotypes, covariate adjustment, and can be extended to search for interactions. Here, we demonstrate the power and empirical type-I error of our approach using simulated case-control data sets of up to 500 K SNPs, a real genome-wide data set of 300 K SNPs, and a sequence-based dataset, each of which can be analysed in a few hours on a desktop workstation.
Author Summary
Tests of association with disease status are normally conducted one SNP at a time, ignoring the effects of all other genotyped SNPs. We developed a computationally efficient method to simultaneously analyse all SNPs, either in a genome-wide association (GWA) study, or a fine-mapping study based on re-sequencing and/or imputation. The method selects a subset of SNPs that best predicts disease status, while controlling the type-I error of the selected SNPs. This brings many advantages over standard single-SNP approaches, because the signal from a particular SNP can be more clearly assessed when other SNPs associated with disease status are already included in the model. Thus, in comparison with single-SNP analyses, power is increased and the false positive rate is reduced because of reduced residual variation. Localisation is also greatly improved. We demonstrate these advantages over the widely used single-SNP Armitage Trend Test using GWA simulation studies, a real GWA dataset, and a sequence-based fine-mapping simulation study.
doi:10.1371/journal.pgen.1000130
PMCID: PMC2464715  PMID: 18654633
14.  Evaluating Gene Set Enrichment Analysis Via a Hybrid Data Model 
Cancer Informatics  2014;13(Suppl 1):1-16.
Gene set enrichment analysis (GSA) methods have been widely adopted by biological labs to analyze data and generate hypotheses for validation. Most of the existing comparison studies focus on whether the existing GSA methods can produce accurate P-values; however, practitioners are often more concerned with the correct gene-set ranking generated by the methods. The ranking performance is closely related to two critical goals associated with GSA methods: the ability to reveal biological themes and ensuring reproducibility, especially for small-sample studies. We have conducted a comprehensive simulation study focusing on the ranking performance of seven representative GSA methods. We overcome the limitation on the availability of real data sets by creating hybrid data models from existing large data sets. To build the data model, we pick a master gene from the data set to form the ground truth and artificially generate the phenotype labels. Multiple hybrid data models can be constructed from one data set and multiple data sets of smaller sizes can be generated by resampling the original data set. This approach enables us to generate a large batch of data sets to check the ranking performance of GSA methods. Our simulation study reveals that for the proposed data model, the Q2 type GSA methods have in general better performance than other GSA methods and the global test has the most robust results. The properties of a data set play a critical role in the performance. For the data sets with highly connected genes, all GSA methods suffer significantly in performance.
doi:10.4137/CIN.S13305
PMCID: PMC3929260  PMID: 24558298
gene set enrichment analysis; feature ranking; data model; simulation study
15.  Finding type 2 diabetes causal single nucleotide polymorphism combinations and functional modules from genome-wide association data 
Background
Due to the low statistical power of individual markers from a genome-wide association study (GWAS), detecting causal single nucleotide polymorphisms (SNPs) for complex diseases is a challenge. SNP combinations are suggested to compensate for the low statistical power of individual markers, but SNP combinations from GWAS generate high computational complexity.
Methods
We aim to detect type 2 diabetes (T2D) causal SNP combinations from a GWAS dataset with optimal filtration and to discover the biological meaning of the detected SNP combinations. Optimal filtration can enhance the statistical power of SNP combinations by comparing the error rates of SNP combinations from various Bonferroni thresholds and p-value range-based thresholds combined with linkage disequilibrium (LD) pruning. T2D causal SNP combinations are selected using random forests with variable selection from an optimal SNP dataset. T2D causal SNP combinations and genome-wide SNPs are mapped into functional modules using expanded gene set enrichment analysis (GSEA) considering pathway, transcription factor (TF)-target, miRNA-target, gene ontology, and protein complex functional modules. The prediction error rates are measured for SNP sets from functional module-based filtration that selects SNPs within functional modules from genome-wide SNPs based expanded GSEA.
Results
A T2D causal SNP combination containing 101 SNPs from the Wellcome Trust Case Control Consortium (WTCCC) GWAS dataset are selected using optimal filtration criteria, with an error rate of 10.25%. Matching 101 SNPs with known T2D genes and functional modules reveals the relationships between T2D and SNP combinations. The prediction error rates of SNP sets from functional module-based filtration record no significance compared to the prediction error rates of randomly selected SNP sets and T2D causal SNP combinations from optimal filtration.
Conclusions
We propose a detection method for complex disease causal SNP combinations from an optimal SNP dataset by using random forests with variable selection. Mapping the biological meanings of detected SNP combinations can help uncover complex disease mechanisms.
doi:10.1186/1472-6947-13-S1-S3
PMCID: PMC3618247  PMID: 23566118
16.  Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes 
Background
Genome-wide association studies (GWAS) for epithelial ovarian cancer (EOC), the most lethal gynecologic malignancy, have identified novel susceptibility loci. GWAS for survival after EOC have had more limited success. The association of each single nucleotide polymorphism (SNP) individually may not be well-suited to detect small effects of multiple SNPs, such as those operating within the same biological pathway. Gene set analysis (GSA) overcomes this limitation by assessing overall evidence for association of a phenotype with all measured variation in a set of genes.
Methods
To determine gene sets associated with EOC overall survival, we conducted GSA using data from two large GWASes (N cases = 2,813, N deaths = 1,116), with a novel Principal Component – Gamma GSA method. Analysis was completed for all cases and then separately for high grade serous (HGS) histological subtype.
Results
Analysis of the HGS subjects resulted in 43 gene sets with p<0.005 (1.7%); of these, 21 gene sets had p < 0.10 in both GWASes, including intracellular signaling pathway (p = 7.3 × 10−5) and macrolide binding (p = 6.2 ×10−4) gene sets. The top gene sets in analysis of all cases were meiotic mismatch repair (p=6.3 ×10−4) and macrolide binding (p=1.0×10−3). Of 18 gene sets with p<0.005 (0.7%), eight had p < 0.10 in both GWASes.
Conclusion
This research detected novel gene sets associated with EOC survival.
Impact
Novel gene sets associated with EOC survival might lead to new insights and avenues for development of novel therapies for EOC and pharmacogenomic studies.
doi:10.1158/1055-9965.EPI-11-0741
PMCID: PMC3297690  PMID: 22302016
pathway analysis; genetic association; GWAS; SNPs; gynecologic neoplasm
17.  Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes 
PLoS Genetics  2010;6(5):e1000932.
Genome-wide association studies (GWAS) have demonstrated the ability to identify the strongest causal common variants in complex human diseases. However, to date, the massive data generated from GWAS have not been maximally explored to identify true associations that fail to meet the stringent level of association required to achieve genome-wide significance. Genetics of gene expression (GGE) studies have shown promise towards identifying DNA variations associated with disease and providing a path to functionally characterize findings from GWAS. Here, we present the first empiric study to systematically characterize the set of single nucleotide polymorphisms associated with expression (eSNPs) in liver, subcutaneous fat, and omental fat tissues, demonstrating these eSNPs are significantly more enriched for SNPs that associate with type 2 diabetes (T2D) in three large-scale GWAS than a matched set of randomly selected SNPs. This enrichment for T2D association increases as we restrict to eSNPs that correspond to genes comprising gene networks constructed from adipose gene expression data isolated from a mouse population segregating a T2D phenotype. Finally, by restricting to eSNPs corresponding to genes comprising an adipose subnetwork strongly predicted as causal for T2D, we dramatically increased the enrichment for SNPs associated with T2D and were able to identify a functionally related set of diabetes susceptibility genes. We identified and validated malic enzyme 1 (Me1) as a key regulator of this T2D subnetwork in mouse and provided support for the association of this gene to T2D in humans. This integration of eSNPs and networks provides a novel approach to identify disease susceptibility networks rather than the single SNPs or genes traditionally identified through GWAS, thereby extracting additional value from the wealth of data currently being generated by GWAS.
Author Summary
Genome-wide association studies (GWAS) seek to identify loci in which changes in DNA are correlated with disease. However, GWAS do not necessarily lead directly to genes associated with disease, and they do not typically inform the broader context in which disease genes operate, thereby providing limited insights into the mechanisms driving disease. One critical task to providing further insights into GWAS is developing an understanding of the genetics of gene expression (GGE). We present the first empiric study demonstrating that SNPs in human cohorts that associate with gene expression in liver and adipose tissues are enriched for associating with Type 2 Diabetes (T2D) in humans. By filtering “eSNPs” based on causal gene networks defined in an experimental cross population segregating T2D traits, we demonstrate a dramatically increased enrichment of T2D SNPs that enhance our ability to assess T2D risk. We demonstrate the utility of this approach by identifying malic enzyme 1 (ME1) as a novel T2D susceptibility gene in humans and then functionally validating the causal connection between ME1 and T2D in a mouse knockout model for Me1. This approach provides a path to identifying disease susceptibility networks rather than single SNPs or genes traditionally identified through GWAS.
doi:10.1371/journal.pgen.1000932
PMCID: PMC2865508  PMID: 20463879
18.  A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations 
BMC Medical Genomics  2010;3:38.
Background
According to the Genetic Analysis Workshops (GAW), hundreds of thousands of SNPs have been tested for association with rheumatoid arthritis. Traditional genome-wide association studies (GWAS) have been developed to identify susceptibility genes using a "most significant SNPs/genes" model. However, many minor- or modest-risk genes are likely to be missed after adjustment of multiple testing. This screening process uses a strict selection of statistical thresholds that aim to identify susceptibility genes based only on statistical model, without considering multi-dimensional biological similarities in sequence arrangement, crystal structure, or functional categories/biological pathways between candidate and known disease genes.
Methods
Multidimensional screening approaches combined with traditional statistical genetics methods can consider multiple biological backgrounds of genetic mutation, structural, and functional annotations. Here we introduce a newly developed multidimensional screening approach for rheumatoid arthritis candidate genes that considers all SNPs with nominal evidence of Bayesian association (BFLn > 0), and structural and functional similarities of corresponding genes or proteins.
Results
Our multidimensional screening approach extracted all risk genes (BFLn > 0) by odd ratios of hypothesis H1 to H0, and determined whether a particular group of genes shared underlying biological similarities with known disease genes. Using this method, we found 6614 risk SNPs in our Bayesian screen result set. Finally, we identified 146 likely causal genes for rheumatoid arthritis, including CD4, FGFR1, and KDR, which have been reported as high risk factors by recent studies. We must denote that 790 (96.1%) of genes identified by GWAS could not easily be classified into related functional categories or biological processes associated with the disease, while our candidate genes shared underlying biological similarities (e.g. were in the same pathway or GO term) and contributed to disease etiology, but where common variations in each of these genes make modest contributions to disease risk. We also found 6141 risk SNPs that were too minor to be detected by conventional approaches, and associations between 58 candidate genes and rheumatoid arthritis were verified by literature retrieved from the NCBI PubMed module.
Conclusions
Our proposed approach to the analysis of GAW16 data for rheumatoid arthritis was based on an underlying biological similarities-based method applied to candidate and known disease genes. Application of our method could identify likely causal candidate disease genes of rheumatoid arthritis, and could yield biological insights that not detected when focusing only on genes that give the strongest evidence by multiple testing. We hope that our proposed method complements the "most significant SNPs/genes" model, and provides additional insights into the pathogenesis of rheumatoid arthritis and other diseases, when searching datasets for hundreds of genetic variances.
doi:10.1186/1755-8794-3-38
PMCID: PMC2939610  PMID: 20727150
19.  Systems-Level Analysis of Genome-Wide Association Data 
G3: Genes|Genomes|Genetics  2013;3(1):119-129.
Genome-wide association studies (GWAS) have emerged as the method of choice for identifying common variants affecting complex disease. In a GWAS, particular attention is placed, for obvious reasons, on single-nucleotide polymorphisms (SNPs) that exceed stringent genome-wide significance thresholds. However, it is expected that many SNPs with only nominal evidence of association (e.g., P < 0.05) truly influence disease. Efforts to extract additional biological information from entire GWAS datasets have primarily focused on pathway-enrichment analyses. However, these methods suffer from a number of limitations and typically fail to lead to testable hypotheses. To evaluate alternative approaches, we performed a systems-level analysis of GWAS data using weighted gene coexpression network analysis. A weighted gene coexpression network was generated for 1918 genes harboring SNPs that displayed nominal evidence of association (P ≤ 0.05) from a GWAS of bone mineral density (BMD) using microarray data on circulating monocytes isolated from individuals with extremely low or high BMD. Thirteen distinct gene modules were identified, each comprising coexpressed and highly interconnected GWAS genes. Through the characterization of module content and topology, we illustrate how network analysis can be used to discover disease-associated subnetworks and characterize novel interactions for genes with a known role in the regulation of BMD. In addition, we provide evidence that network metrics can be used as a prioritizing tool when selecting genes and SNPs for replication studies. Our results highlight the advantages of using systems-level strategies to add value to and inform GWAS.
doi:10.1534/g3.112.004788
PMCID: PMC3538337  PMID: 23316444
genome-wide association study (GWAS); systems biology; coexpression network; osteoporosis
20.  Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee 
PLoS Genetics  2011;7(8):e1002237.
Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P2df = 10−6, GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10−7) but not in light coffee-drinkers. The a priori Replication hypothesis that “Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers” was confirmed: ORReplication = 0.59, PReplication = 10−3; ORPooled = 0.51, PPooled = 7×10−8. Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10−3), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10−13). Imputation revealed a block of SNPs that achieved P2df<5×10−8 in GWAIS, and OR = 0.41, P = 3×10−8 in heavy coffee-drinkers. This study is proof of concept that inclusion of environmental factors can help identify genes that are missed in GWAS. Both adenosine antagonists (caffeine-like) and glutamate antagonists (GRIN2A-related) are being tested in clinical trials for treatment of PD. GRIN2A may be a useful pharmacogenetic marker for subdividing individuals in clinical trials to determine which medications might work best for which patients.
Author Summary
Parkinson's disease (PD), like most common disorders, involves interactions between genetic make-up and environmental exposures that are unique to each individual. Caffeinated-coffee consumption may protect some people from developing PD, although not all benefit equally. In a genome-wide search, we discovered that variations in the glutamate-receptor gene GRIN2A modulate the risk of developing PD in heavy coffee drinkers. The study was hypothesis-free, that is, we cast a net across the entire genome allowing statistical significance to point us to a genetic variant, regardless of whether it fell in a genomic desert or an important gene. Fortuitously, the most significant finding was in a well-known gene, GRIN2A, which regulates brain signals that control movement and behavior. Our finding is important for three reasons: First, it is a proof of concept that studying genes and environment on the whole-genome scale is feasible, and this approach can identify important genes that are missed when environmental exposures are ignored. Second, the knowledge of interaction between GRIN2A, which is involved in neurotransmission in the brain, and caffeine, which is an adenosine-A2A-receptor antagonist, will stimulate new research towards understanding the cause and progression of PD. Third, the results may lead to personalized prevention of and treatment for PD.
doi:10.1371/journal.pgen.1002237
PMCID: PMC3158052  PMID: 21876681
21.  A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose 
PLoS Genetics  2009;5(3):e1000433.
We report the first genome-wide association study (GWAS) whose sample size (1,053 Swedish subjects) is sufficiently powered to detect genome-wide significance (p<1.5×10−7) for polymorphisms that modestly alter therapeutic warfarin dose. The anticoagulant drug warfarin is widely prescribed for reducing the risk of stroke, thrombosis, pulmonary embolism, and coronary malfunction. However, Caucasians vary widely (20-fold) in the dose needed for therapeutic anticoagulation, and hence prescribed doses may be too low (risking serious illness) or too high (risking severe bleeding). Prior work established that ∼30% of the dose variance is explained by single nucleotide polymorphisms (SNPs) in the warfarin drug target VKORC1 and another ∼12% by two non-synonymous SNPs (*2, *3) in the cytochrome P450 warfarin-metabolizing gene CYP2C9. We initially tested each of 325,997 GWAS SNPs for association with warfarin dose by univariate regression and found the strongest statistical signals (p<10−78) at SNPs clustering near VKORC1 and the second lowest p-values (p<10−31) emanating from CYP2C9. No other SNPs approached genome-wide significance. To enhance detection of weaker effects, we conducted multiple regression adjusting for known influences on warfarin dose (VKORC1, CYP2C9, age, gender) and identified a single SNP (rs2108622) with genome-wide significance (p = 8.3×10−10) that alters protein coding of the CYP4F2 gene. We confirmed this result in 588 additional Swedish patients (p<0.0029) and, during our investigation, a second group provided independent confirmation from a scan of warfarin-metabolizing genes. We also thoroughly investigated copy number variations, haplotypes, and imputed SNPs, but found no additional highly significant warfarin associations. We present power analysis of our GWAS that is generalizable to other studies, and conclude we had 80% power to detect genome-wide significance for common causative variants or markers explaining at least 1.5% of dose variance. These GWAS results provide further impetus for conducting large-scale trials assessing patient benefit from genotype-based forecasting of warfarin dose.
Author Summary
Recently, geneticists have begun assaying hundreds of thousands of genetic markers covering the entire human genome to systematically search for and identify genes that cause disease. We have extended this “genome-wide association study” (GWAS) method by assaying ∼326,000 markers in 1,053 Swedish patients in order to identify genes that alter response to the anticoagulant drug warfarin. Warfarin is widely prescribed to reduce blood clotting in order to protect high-risk patients from stroke, thrombosis, and heart attack. But patients vary widely (20-fold) in the warfarin dose needed for proper blood thinning, which means that initial doses in some patients are too high (risking severe bleeding) or too low (risking serious illness). Our GWAS detected two genes (VKORC1, CYP2C9) already known to cause ∼40% of the variability in warfarin dose and discovered a new gene (CYP4F2) contributing 1%–2% of the variability. Since our GWAS searched the entire genome, additional genes having a major influence on warfarin dose might not exist or be found in the near-term. Hence, clinical trials assessing patient benefit from individualized dose forecasting based on a patient's genetic makeup at VKORC1, CYP2C9 and possibly CYP4F2 could provide state-of-the-art clinical benchmarks for warfarin use during the foreseeable future.
doi:10.1371/journal.pgen.1000433
PMCID: PMC2652833  PMID: 19300499
22.  Genetic distance as an alternative to physical distance for definition of gene units in association studies 
BMC Genomics  2014;15(1):408.
Background
Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as ± 50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances.
Results
Standardized recombination rates (SRR) from the deCODE recombination map were used as units of genetic distances. We searched for a SRR producing flanking sequences near the ± 50 Kb offset that has been common in previous studies. A SRR ≥ 2 was selected because it led to gene extensions with median length = 45.3 Kb and the simplicity of an integer value. As expected, boundaries of the genes defined with the ± 50 Kb and with the SRR ≥2 rules were rarely concordant. The impact of these differences was illustrated with the interpretation of top association signals from two large studies including many hits and their detailed analysis based in different criteria. The definition based in genetic distance was more concordant with the results of these studies than the based in physical distance. In the analysis of 18 top disease associated loci form the first study, the SRR ≥2 genes led to a fully concordant interpretation in 17 loci; the ± 50 Kb genes only in 6. Interpretation of the 43 putative functional genes of the second study based in the SRR ≥2 definition only missed 4 of the genes, whereas the based in the ± 50 Kb definition missed 10 genes.
Conclusions
A gene definition based on genetic distance led to results more concordant with expert detailed analyses than the commonly used based in physical distance. The genome coordinates for each gene are provided to maintain a simple use of the new definitions.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-408) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-408
PMCID: PMC4048458  PMID: 24884992
23.  Genome-wide association study combined with biological context can reveal more disease-related SNPs altering microRNA target seed sites 
BMC Genomics  2014;15(1):669.
Background
Emerging studies demonstrate that single nucleotide polymorphisms (SNPs) resided in the microRNA recognition element seed sites (MRESSs) in 3′UTR of mRNAs are putative biomarkers for human diseases and cancers. However, exhaustively experimental validation for the causality of MRESS SNPs is impractical. Therefore bioinformatics have been introduced to predict causal MRESS SNPs. Genome-wide association study (GWAS) provides a way to detect susceptibility of millions of SNPs simultaneously by taking linkage disequilibrium (LD) into account, but the multiple-testing corrections implemented to suppress false positive rate always sacrificed the sensitivity. In our study, we proposed a method to identify candidate causal MRESS SNPs from 12 GWAS datasets without performing multiple-testing corrections. Alternatively, we used biological context to ensure credibility of the selected SNPs.
Results
In 11 out of the 12 GWAS datasets, MRESS SNPs were over-represented in SNPs with p-value ≤ 0.05 (odds ratio (OR) ranged from 1.1 to 2.4). Moreover, host genes of susceptible MRESS SNPs in each of the 11 GWAS dataset shared biological context with reported causal genes. There were 286 MRESS SNPs identified by our method, while only 13 SNPs were identified by multiple-testing corrections with a given threshold of 1 × 10−5, which is a common cutoff used in GWAS. 27 out of the 286 candidate SNPs have been reported to be deleterious while only 2 out of 13 multiple-testing corrected SNPs were documented in PubMed. MicroRNA-mRNA interactions affected by the 286 candidate SNPs were likely to present negatively correlated expression. These SNPs introduced greater alternation of binding free energy than other MRESS SNPs, especially when grouping by haplotypes (4210 vs. 4105 cal/mol by mean, 9781 vs. 8521 cal/mol by mean, respectively).
Conclusions
MRESS SNPs are promising disease biomarkers in multiple GWAS datasets. The method of integrating GWAS p-value and biological context is stable and effective for selecting candidate causal MRESS SNPs, it reduces the loss of sensitivity compared to multiple-testing corrections. The 286 candidate causal MRESS SNPs provide researchers a credible source to initialize their design of experimental validations in the future.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-669) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-669
PMCID: PMC4246476  PMID: 25106527
microRNA; Genome-wide association study; Single nucleotide polymorphisms; Human diseases and cancers
24.  Data Mining Approaches for Genome-Wide Association of Mood Disorders 
Psychiatric Genetics  2012;22(2):55-61.
Mood disorders are highly heritable forms of major mental illness. A major breakthrough in elucidating the genetic architecture of mood disorders was anticipated with the advent of genome-wide association studies (GWAS). However, to date few susceptibility loci have been conclusively identified. The genetic etiology of mood disorders appears to be quite complex, and as a result, alternative approaches for analyzing GWAS data are needed. Recently, a polygenic scoring approach that captures the effects of alleles across multiple loci was successfully applied to the analysis of GWAS data in schizophrenia and bipolar disorder (BP). However, this method may be overly simplistic in its approach to the complexity of genetic effects. Data mining methods are available that may be applied to analyze the high dimensional data generated by GWAS of complex psychiatric disorders. We sought to compare the performance of five data mining methods, namely, Bayesian Networks (BN), Support Vector Machine (SVM), Random Forest (RF), Radial Basis Function network (RBF), and Logistic Regression (LR), against the polygenic scoring approach in the analysis of GWAS data on BP. The different classification methods were trained on GWAS datasets from the Bipolar Genome Study (2,191 cases with BP and 1,434 controls) and their ability to accurately classify case/control status was tested on a GWAS dataset from the Wellcome Trust Case Control Consortium. The performance of the classifiers in the test dataset was evaluated by comparing area under the receiver operating characteristic curves (AUC). BN performed the best of all the data mining classifiers, but none of these did significantly better than the polygenic score approach. We further examined a subset of SNPs in genes that are expressed in the brain, under the hypothesis that these might be most relevant to BP susceptibility, but all the classifiers performed worse with this reduced set of SNPs. The discriminative accuracy of all of these methods is unlikely to be of diagnostic or clinical utility at the present time. Further research is needed to develop strategies for selecting sets of SNPs likely to be relevant to disease susceptibility and to determine if other data mining classifiers that utilize other algorithms for inferring relationships among the sets of SNPs may perform better.
doi:10.1097/YPG.0b013e32834dc40d
PMCID: PMC3306768  PMID: 22081063
data mining; Genome-Wide Association; Mood Disorders
25.  Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data 
PLoS Genetics  2011;7(6):e1002101.
Genome-wide association studies (GWAS) have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However, while typical GWAS analysis techniques treat markers individually, complex diseases (cancers, diabetes, and Alzheimers, amongst others) are unlikely to have a single causative gene. Thus, there is a pressing need for multi–SNP analysis methods that can reveal system-level differences in cases and controls. Here, we present a novel multi–SNP GWAS analysis method called Pathways of Distinction Analysis (PoDA). The method uses GWAS data and known pathway–gene and gene–SNP associations to identify pathways that permit, ideally, the distinction of cases from controls. The technique is based upon the hypothesis that, if a pathway is related to disease risk, cases will appear more similar to other cases than to controls (or vice versa) for the SNPs associated with that pathway. By systematically applying the method to all pathways of potential interest, we can identify those for which the hypothesis holds true, i.e., pathways containing SNPs for which the samples exhibit greater within-class similarity than across classes. Importantly, PoDA improves on existing single–SNP and SNP–set enrichment analyses, in that it does not require the SNPs in a pathway to exhibit independent main effects. This permits PoDA to reveal pathways in which epistatic interactions drive risk. In this paper, we detail the PoDA method and apply it to two GWAS: one of breast cancer and the other of liver cancer. The results obtained strongly suggest that there exist pathway-wide genomic differences that contribute to disease susceptibility. PoDA thus provides an analytical tool that is complementary to existing techniques and has the power to enrich our understanding of disease genomics at the systems-level.
Author Summary
We present a novel method for multi–SNP analysis of genome-wide association studies. The method is motivated by the intuition that, if a set of SNPs is associated with disease, cases and controls will exhibit more within-group similarity than across-group similarity for the SNPs in the set of interest. Our method, Pathways of Distinction Analysis (PoDA), uses GWAS data and known pathway–gene and gene–SNP associations to identify pathways that permit the distinction of cases from controls. By systematically applying the method to all pathways of potential interest, we can identify pathways containing SNPs for which the cases and controls are distinguished and infer those pathways' role in disease. We detail the PoDA method and describe its results in breast and liver cancer GWAS data, demonstrating its utility as a method for systems-level analysis of GWAS data.
doi:10.1371/journal.pgen.1002101
PMCID: PMC3111473  PMID: 21695280

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