1/13/2024 0 Comments Phoenix viewer go to coordinatesReference and target datasets were compared using the Conform-gt software, keeping only variants shared between the target and the reference dataset. Outliers, duplicated and misclassified samples were removed from the dataset. We computed the relatedness PIHAT metric using PLINK v1.9 for each pair of samples aiming to identify duplicated samples (PIHAT=1.0). The resulting dataset was subjected to principal component analysis (PCA) in PLINK v1.9 to identify outliers and dogs whose PCA clustering would differ from the owner-identified breed information. The SNP array dataset of all 241 dogs on our study (target dataset) was filtered excluding sex chromosomes and duplicate variants, including variants with: minor allele frequency (MAF) ≥ 0.005, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. The reference dataset was filtered excluding sex chromosomes, removing insertion/deletions, non-PASS variants, and variants with more than two alleles. SNP array data imputation was conducted using a phased genotype reference dataset of 365 dogs from multiple breeds genotyped by whole-genome sequencing. Genotype calling of SNPs as well as data visualization were performed with GenomeStudio v2.0 and exported to PLINK format using the CanFam3.1.75 genome assembly to retrieve chromosomal coordinates. SNP array genotyping was performed on samples using the Illumina CanineHD Whole-Genome Genotyping BeadChip arrays including 173,662 SNPs located on autosomes and sex chromosomes. Signal amplification of the incorporated label further improves the overall signal-to-noise ratio of the assay. C and G nucleotides are biotin-labeled A and T nucleotides are dinitrophenyl-labeled. DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).Įxtension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). Status (hc = healthy control, gdv: gastric dilatation-volvulus: Acute_GDV GEO help: Mouse over screen elements for information.
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