Name: Golden Retriever Lifetime Study: Whole genome genotyping of Golden Retrievers on Axiom HD Arrays 
Version: v1
Date: Aug. 2,2023
Description:
  Morris Animal Foundation’s Golden Retriever Lifetime Study is a longitudinal, prospective study following 3044 golden retrievers. The Study’s purpose is to identify the nutritional, environmental, lifestyle and genetic risk factors for cancer and other diseases. The Golden Oldie’s study enrolled an additional cohort of golden retrievers that had reached the age of 12 years or older and had not yet been diagnosed with a malignant cancer. This population can be used as a control group for conditions with high mortality in younger age. This dataset contains the data for ~1.1 million genetic markers from 3224 unique individual dogs processed using Axiom Canine Genotyping Array Sets A and B. Of the 3244 individual samples, 3024 were from the Golden Retriever Lifetime Study cohort and 200 from the Golden Oldies cohort. 
Analysis pipeline:
  All the samples were analyzed as one batch. Analysis was done using Applied Biosystems Array Power Tools (APT) version 1.18. The analysis pipeline followed the best practice workflow recommended by Thermofisher with some modification:
    1.	Exclusion of samples with Dish QC (DQC) < 0.82: DQC is a QC metric based on intensities of probe sequences at non-polymorphic genome locations.
    2.	Exclusion of samples with low call rate values < 95%: Call rate was calculated by preliminary genotyping using a recommended subset of probe sets with known high performance.
    3.	No plates were excluded for low average calling rates at Average call rate threshold 98%.
    4.	Probe set prioritization: The probe sets were prioritized based on this order of classes: PolyHighResolution, NoMinorHom, MonoHighResolution.
    5.	Export to PLINK files: using the SNP ids (not the probe set ids)
    6.	QC check: 
        a.  Only markers with a matching reference allele were kept (CanFam3 assembly and an additional Y chromosome assembly from the Genbank with accession: KP081776.1).
        b.  Duplicate markers were identified as those having the same chromosomal position but with different SNP IDs. The Marker with higher genotyping rate was kept while its duplicate was deleted.
        c.  The gender was updated to match the computed gender.

File description:
	GRLS_Genotyping/setA/AxiomGT1.bin.{bed,bim,fam}		Genotyping files of Axiom Array setA
	GRLS_Genotyping/setB/AxiomGT1.bin.{bed,bim,fam}         Genotyping files of Axiom Array setB
	GRLS_Genotyping/map_id_sex.tab  			A text file that maps between replicate IDs in the genotyping files, and their corresponding sample IDs in phenotype data files. 
								The file includes gender information of the dogs as reported by their owners