Whole Genome Sequencing of Norwegian Buhund

Whole genome sequencing, including library preparation, of the two affected Norwegian Buhund siblings was carried out by Edinburgh Genomics laboratories, University of Edinburgh, using Illumina 150 bp paired-end sequencing (approximately 40X coverage). The library preparation method used was TruSeq DNA Nano (Illumina). Sequence reads were aligned to the canine reference genome CanFam3.1 using the Burrows-Wheeler Aligner (BWA-MEM), and SNP and in-del variants were called using the Genome Analysis Toolkit (GATK) Haplotypecaller (v3.6) using GATK best practices [40 (link), 41 (link)]. Consequence predictions were designated for each variant using the Variant Effect Predictor (Ensembl), and variant calls for genomes of 44 unrelated dogs of 29 other breeds, were used to filter variants [42 (link)]. The initial 44 control genomes, and the additional 140 that later became available for assessment of candidate variants, had been accrued over time for other research and as a resource.