GRLS GWAS Tutorial
Golden retrievers are one of the most popular breeds in the world. However, like many pure-bred dogs, golden retrievers are prone to breed specific and non-breed specific health problems. Previous GWAS studies have uncovered the underlying genetics of several disorders but some studies would benefit from replication. There are also many other research questions waiting to be explored!
The Golden Retriever Lifetime Study (GRLS) has a vast amount of phenotypic data collected from veterinarian records and owner questionnaires over the years for 3000+ dogs. In addition, the study has genotyped ~ 1.1 million genetic markers using ThermoFisher's Axiom™ Canine Genotyping Array Sets A and B. This repository provides a tutorial for handling the GRLS phenotypic and genotypic data to produce successful GWAS studies. We are building a growing list of resources to support these studies.
Morris Animal Foundation’s Golden Retriever Lifetime Study (GRLS) is a longitudinal, prospective study following 3044 golden retrievers over their lifetimes. The Study’s primary purpose is to identify the nutritional, environmental, lifestyle and genetic risk factors for cancer and other diseases. The study has collected over 10 years' worth of phenotypic data from both veterinarian and owner’ questionnaires, as well as biological samples.
A subproject of the Golden Retriever Lifetime Study was The Golden Oldies study. In this project, an additional cohort of golden retrievers that had reached the age of 12 years or older and had not yet been diagnosed with cancer were recruited to provide DNA samples. We anticipated this population could serve as a control group. Only DNA samples were collected from this group of dogs. Because the purpose of this study was to create an additional sample inventory, there is no phenotypic data from questionnaires available.
~1.1 million genetic markers from the entire GRLS cohort and 200 of the Golden Oldie’s participants were genotyped using ThermoFisher's Axiom™ Canine Genotyping Array Sets A and B.
How to access the GRLS data?
2.1. Genotyping data
The GRLS genotyping dataset is publicly available in a PLINK file format. More information about this dataset and how to access it can be found here.
2.2. Phenotype data
Morris Animal Foundation Data Commons provides open access to a growing collection of data provided by participants in the Golden Retriever Lifetime Study. To download the data, you will need to register for an account.