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Functional Annotation of ANimal Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome

Task Force: FarmGTEx
— Farm Animal Genotype-Tissue Expression Task Force

Current Organizers:

FarmGTEx TF priorities

The vast majority of genomic variants control complex phenotypes through modulating intermediate molecular phenotypes (e.g., gene expression and alternative splicing). The systematic characterization of regulatory variants is essential for dissecting the genetic architecture underlying complex traits of economic importance, interpreting adaptive evolution and domestication, and optimising genetic improvement programmes in farm animals. The Farm Animal Genotype-Tissue Expression (FarmGTEx) Task Force aims to provide a comprehensive public resource of regulatory variants (e.g., expression quantitative trait loci, eQTLs) across tissues/cell types in farm animal species. By pulling together public data, the pilot phase of FarmGTEx reports millions of genetic associations with gene expression and alternative splicing across a range of tissues in major farm animals. However, substantial gaps still remain and a global effort is thus urgently needed. The purpose of TF will be defining the current gaps, proposing potential solutions and providing some perspectives based on the pilot phase of FarmGTEx. We believe that the FarmGTEx resource will have unprecedented influences and impacts on the science community.

  1. Identify gap information for next phase of FarmGTEx
    1. Under-represented tissues, cell types, and species such as sheep, goat, horse etc.
    2. Distinct biological contexts (e.g., development, genetic background and physiological responses)
    3. Novel molecular phenotypes from new technologies
    4. Single-cell FarmGTEx (collaborating with single cell TF).
  2. Develop and benchmark standard bioinformatics pipelines (Lingzhao Fang is interested in developing a sub-committee to lead this effort)
    1. Raw data processing protocols
    2. Genotype imputation reference panel and imputation pipelines
    3. Molecular phenotype definitions
    4. QTL mapping and functional annotation
    5. Integrative analysis with results from GWAS and population genomics
    6. Cross-species comparison at system genomics level
    7. Advanced genomic prediction tools and methods (collaborating with FAANGPredictions TF).
    8. Advanced biotechnologies (e.g., gene editing)
  3. Develop a more sustainable infrastructure need for Farm GTEx
    1. Loading page for the structure of FarmGTEx and updating news
    2. Raw data storage (collaborating with HTP&data storage TF)
    3. Web portal for results visualization and query across species
    4. Web server for interactive computational analysis (e.g., genotype imputation and TWAS)
    5. Website for developing and maintaining statistical methods and bioinformatics pipelines
 

Contact

Members

( Group organizer )
  • Fang, Lingzhao 
  • Godia, Marta 
  • Guan, Dailu
  • Kuehn, Christa
  • Pena, Romi
  • Tenesa, Albert 
  • Zhou, Huaijun 
 
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