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Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures

Jorge Gonzalez-Dominguez, Sabela Ramos, Juan Tourino, Bertil Schmidt
2016 IEEE Transactions on Parallel and Distributed Systems  
In this paper we investigate approaches to map pairwise epistasic detection on heterogeneous clusters using both types of accelerators.  ...  Development of new methods to detect pairwise epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important task in bioinformatics as they can help to explain genetic influences  ...  The main contribution of this work consists in the development of two hybrid approaches to detect pairwise epistatic interactions on heterogeneous systems with GPUs and Xeon Phi coprocessors.  ... 
doi:10.1109/tpds.2015.2460247 fatcat:x4xjzvjmarcwncmjpmq26mlwb4

EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards

G. Hemani, A. Theocharidis, W. Wei, C. Haley
2011 Bioinformatics  
Results: By partitioning the 2D search grid across the multicore architecture of a modern consumer graphics processing unit (GPU), we report a 92× increase in the speed of an exhaustive pairwise epistasis  ...  to search for epistasis [for n SNPs the computational time resource is O(n(n-1)/2)].  ...  ACKNOWLEDGEMENT We thank Dr Sara Knott for her comments on the manuscript. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr172 pmid:21471009 fatcat:jlfjf5njoncepfldpsgdfvhloe

Machine learning approaches for the discovery of gene-gene interactions in disease data

R. Upstill-Goddard, D. Eccles, J. Fliege, A. Collins
2012 Briefings in Bioinformatics  
with the analytical and computational issues arising from the enormous number of potential interactions.  ...  We review here recent and current approaches focusing, wherever possible, on applications to real data (particularly in the context of genome-wide association studies) and looking ahead to the further  ...  [11] employed an SVM approach which was combined with search algorithms to produce four different models to detect epistasis, in the absence of genetic heterogeneity.  ... 
doi:10.1093/bib/bbs024 pmid:22611119 fatcat:j4mwnep7jzcy3pgcw5ykyh7kmy

Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model

Jorge González-Domínguez, Jan Christian Kässens, Lars Wienbrandt, Bertil Schmidt
2015 The international journal of high performance computing applications  
In this work we present multiEpistSearch, a tool to detect epistasis that works on GPU clusters.  ...  Detecting epistasis, such as 2-SNP interactions, in Genome-Wide Association Studies (GWAS) is an important but time consuming operation.  ...  Targeting this problem with High Performance Computing (HPC) architectures can help to speedup the process. Parallel codes exist to detect epistasis [1, 2] .  ... 
doi:10.1177/1094342015585846 fatcat:id5feksdhzdq7mo2h6d7pucp3q

Retargeting Tensor Accelerators for Epistasis Detection

Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jimenez, Leonel Augusto Sousa
2021 IEEE Transactions on Parallel and Distributed Systems  
Some contemporary computer architectures support fused XOR and population count as the highest throughput operations as part of tensor operations.  ...  This paper presents a new approach for efficiently repurposing this capability to accelerate 2-way (pairs) and 3-way (triplets) epistasis detection searches.  ...  This raises the importance of synergically combining software development and hardware architectures to address this problem. Epistasis detection suits parallel architectures.  ... 
doi:10.1109/tpds.2021.3060322 fatcat:6hdqf4abfzgspn3bypahzzim5i

Parallelism-based approaches in computational biology: a view from diverse case studies

Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
2017 Cluster Computing  
Computational biology allows and encourages the application of many different parallelism-based approaches.  ...  The special issue collects considerably extended and improved versions of the best papers, accepted and presented in PBio 2016 (4th International Workshop on Parallelism in Bioinformatics, and part of  ...  filter, namely SingleMI, with massively parallel computation on modern GPUs to further accelerate epistasis discovery.  ... 
doi:10.1007/s10586-017-1037-7 fatcat:ptpiyxc6uzft3hzno7zyo5gtai

1,000x Faster Than PLINK: Genome-Wide Epistasis Detection with Logistic Regression Using Combined FPGA and GPU Accelerators [chapter]

Lars Wienbrandt, Jan Christian Kässens, Matthias Hübenthal, David Ellinghaus
2018 Lecture Notes in Computer Science  
Performing billions of tests with PLINK takes days if not weeks, for which reason prefiltering techniques and fast epistasis screenings are applied to reduce the computational burden.  ...  computing platform.  ...  Implementation Heterogeneous FPGA-GPU Computing Architecture Our implementation targets a heterogeneous FPGA-GPU computing architecture.  ... 
doi:10.1007/978-3-319-93701-4_28 fatcat:ob4qner7ibf4rovngbkqo7bmhq

Kernel Methods and Applications in Bioinformatics [chapter]

Yan Fu
2014 Springer Handbook of Bio-/Neuroinformatics  
Bioinformatics, or computational biology, is an interdisciplinary field of study for interpreting biological data using computer science.  ...  Several efforts are being made by the computer scientists and statisticians to design and implement algorithms and techniques for efficient storage, management, processing and analysis of biological databases  ...  modern Table 1 : 1 Machine learning methods comparison table Epistasis detection in breast cancer -Suitable for non-additive gene-gene interactions detection -High computational complexity -High order  ... 
doi:10.1007/978-3-642-30574-0_18 fatcat:ghta2jsk7jcyheujnktp5xetxe

A survey about methods dedicated to epistasis detection

Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
2015 Frontiers in Genetics  
Unfortunately, epistasis detection gives rise to analytic challenges since analyzing every SNP combination is at present impractical at a genome-wide scale.  ...  Interaction between SNPs, namely epistasis, must be considered.  ...  (Lille) on the other hand.  ... 
doi:10.3389/fgene.2015.00285 pmid:26442103 pmcid:PMC4564769 fatcat:5e5bqfpcbjbchf5n7mhurtejny

High-performance epistasis detection in quantitative trait GWAS

Nathan T Weeks, Glenn R Luecke, Brandon M Groth, Marina Kraeva, Li Ma, Luke M Kramer, James E Koltes, James M Reecy
2016 The international journal of high performance computing applications  
epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS).  ...  Abstract epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS).  ...  The research reported in this paper is partially supported by the HPC@ISU equipment at Iowa State University, some Author Biographies Nathan Weeks received B.S. degrees in Computer Science (2002)  ... 
doi:10.1177/1094342016658110 fatcat:q7uxhrq34rb3vnbvrpdri7bc6m

GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies

Jorge González-Domínguez, Bertil Schmidt
2015 Journal of Computational Science  
Detecting epistasis, i.e. interactions among k markers (k ≥ 2), is an important but time consuming operation since statistical computations have to be performed for each k-tuple of measured markers.  ...  For instance, a dataset consisting of 50,000 markers measured from 1,000 individuals can be analyzed in less than 22 hours on a single compute node with 4 NVIDIA GTX Titan boards.  ...  Figure 1 1 shows the structure of the GPU architecture. CUDA-enabled GPUs have evolved into highly parallel many-core processors with tremendous compute power and very high memory bandwidth.  ... 
doi:10.1016/j.jocs.2015.04.001 fatcat:qddjjo3lnng5xm2hpfxfe37byu

Discovering epistasis in large scale genetic association studies by exploiting graphics cards

Gary K. Chen
2013 Frontiers in Genetics  
FIGURE 1 | 1 Comparison of CPU and GPU architecture. FIGURE 2 | 2 Parallel execution work-items on a GPU.  ...  In the next section we describe four methods implemented on GPUs that put these concepts into practice in the context of epistasis detection.  ... 
doi:10.3389/fgene.2013.00266 pmid:24348518 pmcid:PMC3848199 fatcat:ydy66374rjd7nbvqhaferhhyay

Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

Liyuan Zhou, Shouye Liu, Weixun Wu, Daibo Chen, Xiaodeng Zhan, Aike Zhu, Yingxin Zhang, Shihua Cheng, Liyong Cao, Xiangyang Lou, Haiming Xu
2016 Scientific Reports  
Using a saturated mixed linear model including epistasis and environmental interaction, we identified a total of 31 QTSs associated with either the PH or the HD.  ...  By re-sequencing of 138 recombinant inbred lines (RILs), a total of ~0.7 million SNPs were identified for the association studies on the PH and HD.  ...  Acknowledgements We gratefully acknowledge our former colleague Xiangdong Kong for his helpful instruction on processing sequence data.  ... 
doi:10.1038/srep29718 pmid:27406081 pmcid:PMC4942822 fatcat:djn73r72kffkrp6q242vawpcqu

Cis-epistasis at the LPA locus and risk of cardiovascular diseases

Lingyao Zeng, Sylvain Moser, Nazanin Mirza-Schreiber, Claudia Lamina, Stefan Coassin, Christopher P Nelson, Tarmo Annilo, Oscar Franzén, Marcus E Kleber, Salome Mack, Till F M Andlauer, Beibei Jiang (+23 others)
2021 Cardiovascular Research  
These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease.  ...  In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases.  ...  statistical epistasis in quantitative genetics as proposed by Hansen and Wagner 33 on the pairwise epistasis between two loci (SNPs) and implemented a two-stage statistical scanning procedure ( Figure  ... 
doi:10.1093/cvr/cvab136 pmid:33878186 pmcid:PMC8930071 fatcat:4r5vxwnkyjhtjau6qnygftdeme

Experimental Methods for Measuring Gene Interactions

Jeffery P. Demuth, Michael J. Wade
2006 Annual Review of Ecology, Evolution and Systematics  
We review statistical genetic methods based on analyses of variances and means as well as molecular genetic methods for detecting gene interactions.  ...  The evolution of genetic architectures and the divergence of natural populations. See Wolf et al. 2000, pp. 245-63 Brem RB, Kruglyak L. 2005.  ...  Development of more-efficient algorithms and the incorporation of parallel processing have drastically reduced computational limitations (Foster 2001 , Ljungberg et al. 2004 .  ... 
doi:10.1146/annurev.ecolsys.37.091305.110124 fatcat:yigv4ddd3rfjvehhnw73tqccwi
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