Axiom canine hd array

Blood samples were collected from semi-feral dogs captured around the Chernobyl Nuclear Power Plant (NPP) and 16.5 km away in Chernobyl City (CC). Blood samples were taken during sterilization and vaccination procedures conducted by the Clean Futures Fund Dogs of Chernobyl program in 2018 and 2019. In total, 116 unique dogs were included in the study, 60 from Nuclear Power Plant and 56 from Chernobyl City (Fig. 1). Blood samples were preserved in PAXGene Blood DNA tubes (Qiagen) and transported at 0 °C back to the United States for DNA extraction. We isolated genomic DNA from 500 μL of whole blood using the Maxwell RSC Whole Blood DNA kit (Promega) according to the manufacturer’s protocol. Following conventional QC for integrity and concentration, each DNA sample was genotyped using the Axiom Canine HD array (Thermo Fisher Scientific), yielding data for over 710,000 single nucleotide polymorphism (SNP) loci aligned to the CanFam3 genome build. All animal protocols, handling, husbandry, and care were approved by the Columbia University Institutional Animal Care and Use Committees (IACUC).

Chromosomal sequences from CanFam3.1 and Dog10K_Boxer_Tasha_1.0 were aligned to each other using blat [34 (link)]. The aligned fragments were processed using UCSC tools to create the necessary chain file for use with the liftOver tool. The liftOver was performed using the default settings with the “-multiple” option included. Genomic positions from both the Affymetrix (Santa Clara, CA, USA) Axiom Canine HD Array and Illumina (San Diego, CA, USA) CanineHD BeadChip were converted from CanFam3.1 to Dog10K_Boxer_Tasha_1.0. Genomic positions were obtained for the Axiom Canine HD Array from: https://sec-assets.thermofisher.com/TFS-Assets/LSG/Support-Files/Axiom_K9_HD.na35.r5.a7.annot.csv.zip (accessed on 21 November 2020); and for the CanineHD BeadChip: ftp://webdata2:[email protected]/downloads/ProductFiles/CanineHD/CanineHD_B.csv (accessed on 21 November 2020). The bed files resulting from the lift over were converted to Plink map files. All markers were included in each map file and markers were ordered sequentially according to the order they were downloaded from their corresponding URLs. Markers for which no position was obtained were placed on chromosome “0” at position “0”.