GWAS Procedures for Gene Mapping in Diverse Populations With Complex Structures Article Swipe
Zhen Zuo
,
Mingliang Li
,
Defu Liu
,
Qi Li
,
Bin Huang
,
G. Ye
,
Jiabo Wang
,
You Tang
,
Zhiwu Zhang
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21769/bioprotoc.5284
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21769/bioprotoc.5284
With reduced genotyping costs, genome-wide association studies (GWAS) face more challenges in diverse populations with complex structures to map genes of interest. The complex structure demands sophisticated statistical models, and increased marker density and population size require efficient computing tools. Many statistical models and computing tools have been developed with varied properties in statistical power, computing efficiency, and user-friendly accessibility. Some statistical models were developed with dedicated computing tools, such as efficient mixed model analysis (EMMA), multiple loci mixed model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK). However, there are computing tools (e.g., GAPIT) that implement multiple statistical models, retain a constant user interface, and maintain enhancement on input data and result interpretation. In this study, we developed a protocol utilizing a minimal set of software tools (BEAGLE, BLINK, and GAPIT) to perform a variety of analyses including file format conversion, missing genotype imputation, GWAS, and interpretation of input data and outcome results. We demonstrated the protocol by reanalyzing data from the Rice 3000 Genomes Project and highlighting advancements in GWAS model development.
Related Topics
Concepts
Genome-wide association study
Computational biology
Data science
Biology
Evolutionary biology
Geography
Computer science
Gene
Genetics
Single-nucleotide polymorphism
Genotype
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.21769/bioprotoc.5284
- OA Status
- diamond
- Cited By
- 2
- References
- 1
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
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- DOI
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https://doi.org/10.21769/bioprotoc.5284Digital Object Identifier
- Title
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GWAS Procedures for Gene Mapping in Diverse Populations With Complex StructuresWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-01-01Full publication date if available
- Authors
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Zhen Zuo, Mingliang Li, Defu Liu, Qi Li, Bin Huang, G. Ye, Jiabo Wang, You Tang, Zhiwu ZhangList of authors in order
- Landing page
-
https://doi.org/10.21769/bioprotoc.5284Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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diamondOpen access status per OpenAlex
- OA URL
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https://doi.org/10.21769/bioprotoc.5284Direct OA link when available
- Concepts
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Genome-wide association study, Computational biology, Data science, Biology, Evolutionary biology, Geography, Computer science, Gene, Genetics, Single-nucleotide polymorphism, GenotypeTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2025: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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