{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Gershoni M"],"funding":["Israel Milk Marketing Board","Israel Science Foundation"],"pagination":["485"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8948885"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["13(3)"],"pubmed_abstract":["Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain the observed heritability. In the analysis of the genomes of 17 Israeli Holstein bulls, we compared genotyping accuracy between whole-genome sequencing (WGS) and microarray-based techniques. Using the standard GATK pipeline, the short-variant discovery within sequence reads mapped to the reference genome (ARS-UCD1.2) was compared to the genotypes from Illumina BovineSNP50 BeadChip and to an alternative method, which computationally mimics the hybridization procedure by mapping reads to 50 bp spanning the BeadChip source sequences. The number of m"],"journal":["Genes"],"pubmed_title":["Comparing BeadChip and WGS Genotyping: Non-Technical Failed Calling Is Attributable to Additional Variation within the Probe Target Sequence."],"pmcid":["PMC8948885"],"funding_grant_id":["362-0691","946/19"],"pubmed_authors":["Seroussi E","Shirak A","Gershoni M","Raz R"],"additional_accession":[]},"is_claimable":false,"name":"Comparing BeadChip and WGS Genotyping: Non-Technical Failed Calling Is Attributable to Additional Variation within the Probe Target Sequence.","description":"Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain the observed heritability. In the analysis of the genomes of 17 Israeli Holstein bulls, we compared genotyping accuracy between whole-genome sequencing (WGS) and microarray-based techniques. Using the standard GATK pipeline, the short-variant discovery within sequence reads mapped to the reference genome (ARS-UCD1.2) was compared to the genotypes from Illumina BovineSNP50 BeadChip and to an alternative method, which computationally mimics the hybridization procedure by mapping reads to 50 bp spanning the BeadChip source sequences. The number of m","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Mar","modification":"2025-06-01T01:08:19.374Z","creation":"2025-06-01T01:08:19.374Z"},"accession":"S-EPMC8948885","cross_references":{"pubmed":["35328039"],"doi":["10.3390/genes13030485"]}}