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Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks
Ritsuko Onuki1, Rui Yamaguchi2, Tetsuo Shibuya2
1Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan.
Plos One
|April 27, 2017
Summary
Ancient positive selection influences common diseases. Our novel method identifies genomic regions linked to ancient selection, revealing immune and disease pathway enrichments.
Area of Science:
- Genomics
- Evolutionary Biology
- Human Genetics
Background:
- Genome-wide scans identify genomic regions under positive selection, crucial for understanding disease risk alleles.
- Most studies focus on recent positive selection, potentially overlooking ancient adaptive events.
- Ancient positive selection may play a significant role in adaptation to pathogens and the development of immune-mediated diseases.
Purpose of the Study:
- To develop and apply a novel linkage disequilibrium-based pipeline for detecting ancient positive selection across populations.
- To investigate the association of ancient positive selection with immune system pathways and common diseases.
Main Methods:
- Development of a novel linkage disequilibrium-based pipeline.
- Application of the pipeline to single nucleotide polymorphism (SNP) data from the International HapMap project.
- Enrichment analysis of genes within detected regions for biological pathways.
- Mapping of associated SNPs to biological pathways to understand phenotype-molecular function associations.
Main Results:
- The pipeline successfully detected regions associated with ancient positive selection.
- Genes in these regions are significantly enriched in pathways related to the immune system and infectious diseases.
- Detected regions contain SNPs previously associated with cancers, metabolic diseases, obesity, type 2 diabetes, and allergic sensitization.
Conclusions:
- Ancient positive selection is a significant factor in human adaptation and disease.
- The developed pipeline is effective in identifying regions under ancient positive selection.
- Further research is needed to assess candidate regions and their functions in disease variation.
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