6533b82efe1ef96bd12926fc

RESEARCH PRODUCT

Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS

Jan Christian KässensJorge González-domínguezManfred SchimmlerLars WienbrandtBertil Schmidt

subject

0301 basic medicine03 medical and health sciences030104 developmental biologySoftware suiteComputer architecturePairwise interactionComputer scienceBrute-force searchGenome-wide association studyParallel computingComputer caseField-programmable gate arrayImplementation

description

Interaction between genes has become a major topic in quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Due to the number of tests required for an exhaustive search in genome-wide association studies (GWAS), a large amount of computational power is required. In this paper, we present a hybrid architecture consisting of tightly interconnected CPUs, GPUs and FPGAs and a fine-tuned software suite to outperform other implementations in pairwise interaction analysis while consuming less than 300Watts and fitting into a standard desktop computer case.

yearjournalcountryeditionlanguage
2016-07-012016 IEEE 27th International Conference on Application-specific Systems, Architectures and Processors (ASAP)
https://doi.org/10.1109/asap.2016.7760788