Ren Wenlong, Liang Zhikai
Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, 226019, China.
Department of Plant Sciences, North Dakota State University, Fargo, 58108, USA.
Mol Genet Genomics. 2024 Dec 29;300(1):10. doi: 10.1007/s00438-024-02214-6.
Detecting genome-wide SNP-SNP interactions (epistasis) efficiently is essential to harnessing the vast data now available from modern biobanks. With millions of SNPs and genetic information from hundreds of thousands of individuals, researchers are positioned to uncover new insights into complex disease pathways. However, this data scale brings significant computational and statistical challenges. To address these, recent approaches leverage GPU-based parallel computing for high-throughput, cost-effective analysis and refine algorithms to improve time and memory efficiency. In this survey, we systematically review GPU-accelerated methods for exhaustive epistasis detection, detailing the statistical models used and the computational strategies employed to enhance performance. Our findings indicate substantial speedups with GPU implementations over traditional CPU approaches. We conclude that while GPU-based solutions hold promise for advancing genomic research, continued innovation in both algorithm design and hardware optimization is necessary to meet future data challenges in the field.
高效检测全基因组范围内的单核苷酸多态性-单核苷酸多态性相互作用(上位性)对于利用现代生物样本库现有的海量数据至关重要。有了数百万个单核苷酸多态性以及来自数十万个体的遗传信息,研究人员有能力揭示复杂疾病途径的新见解。然而,这种数据规模带来了重大的计算和统计挑战。为了解决这些问题,最近的方法利用基于图形处理器(GPU)的并行计算进行高通量、经济高效的分析,并改进算法以提高时间和内存效率。在本次综述中,我们系统地回顾了用于详尽上位性检测的GPU加速方法,详细介绍了所使用的统计模型以及为提高性能而采用的计算策略。我们的研究结果表明,与传统的中央处理器(CPU)方法相比,GPU实现显著加速。我们得出结论,虽然基于GPU的解决方案有望推动基因组研究,但在算法设计和硬件优化方面持续创新对于应对该领域未来的数据挑战是必要的。