Title: 2018 ACVIM Forum Research Abstract Program: Seattle, Washington, June 14 - 15, 2018 Document date: 2018_10_25
ID: 60ceejq1_390
Snippet: The targeted region on Ch11, 1Mb up-and downstream of the most significant SNPs, was captured using the custom-designed sequence capture array (SelectSure XT custom 0.5-2.9 Mb, Agilent). Subsequently, captured libraries were indexed and subjected to DNA sequencing on Illumina platform, followed by alignment/mapping to the canine genome (CanFam3.1). Haplotypecaller was used to call variants, followed by hard-filtering extracted SNPs and Indels as .....
Document: The targeted region on Ch11, 1Mb up-and downstream of the most significant SNPs, was captured using the custom-designed sequence capture array (SelectSure XT custom 0.5-2.9 Mb, Agilent). Subsequently, captured libraries were indexed and subjected to DNA sequencing on Illumina platform, followed by alignment/mapping to the canine genome (CanFam3.1). Haplotypecaller was used to call variants, followed by hard-filtering extracted SNPs and Indels as recommended in GATK's best practices. SNPs were annotated using the SNPEff and Variant Effect Predicting (VEP) tools. The variants were divided into different groups based on genomic coordinates. The SNPs present only in cases (diagnosed with IBD), controls as well as overlapping SNPs with different alternative alleles in case vs control groups were further investigated.
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