方法对比

	基于网络的变异检测	全基因组关联研究 (GWAS)
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2017–2018	2005–2007
提出者	Erik Garrison, Paten lab (UCSC); Hannes Eggertsson, deCODE Genetics	Klein et al. (age-related macular degeneration GWAS, 2005); landmark scale: Wellcome Trust Case Control Consortium (2007)
类型	Computational genomics pipeline	Observational genomic association study
开创性文献	Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., Paten, B., & Durbin, R. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 36(9), 875–879.	Wellcome Trust Case Control Consortium. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447(7145), 661–678.
别名	graph-genome variant calling, variation graph genotyping, vg-based variant calling, pangenome variant calling	GWAS, genome-wide association analysis, whole-genome association study, WGAS
相关	6	6
摘要	Network-based (graph-genome) variant calling replaces the conventional single linear reference genome with a variation graph — a network in which nodes represent sequence segments and edges represent known alternative paths through the genome. Reads are mapped onto this graph, enabling detection of SNPs, indels, and structural variants with substantially lower reference bias than linear-reference pipelines. Key tools include the Variation Graph Toolkit (vg) and Graphtyper.	A genome-wide association study (GWAS) systematically tests hundreds of thousands to millions of single-nucleotide polymorphisms (SNPs) across the human genome for statistical association with a trait or disease. By comparing allele frequencies between cases and controls — or by regressing SNP genotypes on a quantitative phenotype — GWAS identifies genomic loci that harbor common genetic variants contributing to complex traits. Since its large-scale debut in 2007, GWAS has catalogued thousands of robust disease–variant associations across virtually every common human condition.