golden-retrievers/grls-genomics

GRLS Genotyping — Axiom Canine Array

Whole-genome SNP-array genotyping of golden retrievers from the Morris Animal Foundation Golden Retriever Lifetime Study (GRLS), mirrored from the public AWS Open Data registry (s3://mafgrlsgenome). Part of the golden-retrievers collection.

This is the openly-licensed genomics slice only. Phenotypes, clinical, behavioral, and biospecimen data live in the GRLS Data Commons and require an institutional data-use agreement — see "Linking phenotypes" below.

At a glance (verified against source files)

Individuals	3,224 dogs (3,024 GRLS cohort + 200 Golden Oldies controls)
Markers	913,984 QC-passed SNPs (from the ~1.1M-probe Axiom Canine Array Sets A+B)
Assembly	CanFam3 (+ Y from GenBank KP081776.1)
Chromosomes	autosomes chr1–38, chrX, chrY, chrM, unplaced contigs
Format	PLINK 1 binary (.bed/.bim/.fam)
License	CC-BY-SA-4.0
Source	Morris Animal Foundation; APT v1.18, ThermoFisher best-practice QC

Files

• GRLS_Genotyping_Axiom_Canine_Merged_2023_08_02.zip — merged set A+B (AxiomGT1v2.merged.{bed,bim,fam}). Start here.
• GRLS_Genotyping_Axiom_Canine_Array_Sets_A_and_B_2023_08_02.zip — sets A and B separately + map_id_sex.tab (maps genotyping replicate IDs ↔ phenotype sample IDs; includes owner-reported sex).
• README.txt — upstream provenance & QC pipeline.

QC already applied upstream

Sample DQC ≥ 0.82; sample call rate ≥ 95%; probe-set prioritization (PolyHighResolution → NoMinorHom → MonoHighResolution); reference-allele matching to CanFam3; duplicate-marker resolution by genotyping rate; sex updated to computed sex. Phenotype column in .fam is -9 (missing) — phenotypes come from the Data Commons.

Quick start (PLINK)

unzip GRLS_Genotyping_Axiom_Canine_Merged_2023_08_02.zip
cd GRLS_Genotyping_Axiom_Canine_Merged_2023_08_02
# basic QC + PCA for population structure
plink --bfile AxiomGT1v2.merged --dog \
      --geno 0.05 --maf 0.01 --hwe 1e-6 \
      --make-bed --out grls_qc
plink --bfile grls_qc --dog --pca 20 --out grls_pca

Linking phenotypes (the high-value step)

Genotypes here are unlabeled by design. To run disease GWAS (e.g. hemangiosarcoma, lymphoma, mast-cell tumor, hip dysplasia), join on the IDs in map_id_sex.tab to phenotypes from the GRLS Data Commons (free for non-commercial research, institutional DUA required).

Citation

Morris Animal Foundation Golden Retriever Lifetime Study — Whole genome genotyping of Golden Retrievers on Axiom HD Arrays (v1, Aug 2023). Cohort design: Guy et al., Phil. Trans. R. Soc. B 2015 (PMC4581032); profile: PLOS One 2022 (PMC9182714). Mirrored under CC-BY-SA-4.0; please credit Morris Animal Foundation.

Disclaimer

Research data only. Not veterinary advice. Redistribution follows CC-BY-SA-4.0 (share-alike).