# Advanced GWAS tutorial in Golden Retriever dogs **Date**: Jan 22-23, 2024 (9AM-5PM Pacific Time) **Design**: Hybrid (You may attend in person at UC-Davis or join us via zoom) **Expected capacity**: Up to 30 attendees (<ins>*Priority for attending in person*</ins>). **Instructors**: [Tamer Mansour](https://scholar.google.ca/citations?user=xo-4__IAAAAJ&hl=en), Mohamed Abuelanin, and Brenna Swafford **Material link**: https://morrisanimalfoundation.github.io/grGWAS/ ## Background: The [Golden Retriever Lifetime Study](https://www.morrisanimalfoundation.org/golden-retriever-lifetime-study) is one of the largest, most comprehensive prospective canine health studies in the United States. The Study’s purpose is to identify the nutritional, environmental, lifestyle and genetic risk factors for cancer and other diseases in Golden Retriever dogs. You can learn more data collected by the study [here](https://datacommons.morrisanimalfoundation.org/node/221). ## Why is this workshop different? Effective participation in the workshop allows you to submit a follow up proposal to finish your GWAS analysis. In the follow up project, you will gain access to the most complete version of the phenotypic data. Also, you can get computational resources, bioinformatic support, and extra funding for a small sequencing project if needed. ## Registration: Each attendant should create log-in credentials at the [MAF data portal](https://datacommons.morrisanimalfoundation.org/), choose a phenotype of interest and write a proposal for why the chosen phenotype is likely heritable. You will also need to define the inclusion and exclusion criteria of the subjects of the study. Please fill in your information [here](https://forms.gle/KBmXTPC6D9SWksZ77) (up to 1500 characters). ## Schedule ### Day 1 | Time | Topic | | ---- | ---- | | 09:00-10:30 AM | Setup | | 10:30-10:45 AM | Coffee Break | | 10:45-12:00 AM | GRLS Phenotype Dataset | | 12:00-01:00 PM | Lunch Break | | 01:00-02:30 PM | GRLS Genotype Dataset | | 02:30-02:45 PM | Coffee Break | | 02:45-04:45 PM | Data QC & filtration | | 04:45-05:00 PM | Wrap up | ### Day 2 | Time | Topic | | -------- | -------- | | 09:00-10:30 AM | Study design 1 | | 10:30-10:45 AM | Coffee Break | | 10:45-12:00 AM | Study design 2 | | 12:00-01:00 PM | Lunch Break | | 01:00-02:30 PM | Heritability analysis | | 02:30-02:45 PM | Coffee Break | | 02:45-04:45 PM | GWAS analysis | | 04:45-05:00 PM | Wrap up | ## Computer requirements We will use a UC Davis supercomputer to run the tutorial. However, attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install [MobaXterm](https://mobaxterm.mobatek.net/) before the workshop.
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Genomic imputation

Define genomic imputation Genomic imputation is a statistical method used in genetics research to infer missing genotype data. In genotyping experiments, it is not always possible or cost-effective to genotype every single genetic variant in a sample of individuals. By using a reference panel of genotyped individuals, imputation allows researchers to infer the genotypes of the ungenotyped variants in their sample. This can greatly increase the number of variants that can be studied and improve the power of the analysis. Imputation methods use the linkage disequilibrium (LD) between variants to predict the genotype of ungenotyped variants based on the genotypes of nearby genotyped variants. Imputation can be performed using either phased haplotypes (complete sets of genetic variations that are inherited together on one chromosome) or unphased genotypes. It is important to note that imputation is a statistical process and the imputed genotypes are not the true genotypes, they are estimates. Therefore, imputed genotypes need to be validated before they can be used for downstream analysis. How linkage disequilibrium is related to genomic imputation Linkage disequilibrium (LD) is a measure of the association between the alleles of two or more genetic variants, and it is an important concept in genomic imputation. LD refers to the non-random association of alleles at different genetic loci, which means that certain alleles tend to occur together more frequently than expected by chance. This is because of the proximity of the variants on the chromosome and the fact that they are inherited together.

1/15/2023
Opening position: A remote bioinformatic postdoc for the Golden Retriever Lifetime Study

[toc] (Posted Nov. 23rd, 2022) The Lab for Data Intensive Biology at UC Davis is seeking to hire a postdoc for the Golden Retriever Lifetime Study. This project is funded by the Morris Animal Foundation to maximize the scientific utilization of datasets collected in this project over many years. The Golden Retriever Lifetime Study (GRLS) investigates the potential environmental, lifestyle, genetic and nutritional risk factors of major diseases including cancer in dogs. There is a vast amount of data collected so far and even more is still pending. The postdoc is expected to lead projects and collaborate with a group of expert clinicians and geneticists on bioinformatic studies to discover the sequence variants identifying the dogs of this breed and responsible for their common diseases. This work is expected to result in several publications. In addition, the postdoc is expected to collaborate with the GRLS portal team on enhancements to the findability and accessibility of data, develop training tutorials and bioinformatics workflows, and arrange community engagement events. This job can be part of a transition-to-industry career track as well as a continuing-in-academia plan - we support both. We will happily train you in workflow development, automation, and community engagement!

11/30/2022
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