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To increase the chances of identifying SLE susceptibility loci in this region, two different statistical analyses were performed on genotyped data; Pedigree Disequilibrium Test (PDT) [21] and Haplotype Pattern Mining (HPM) [22].
It has several important features including pre-publication encryption, data pedigree, data integrity, immutability, and versioning.
We estimated relatedness by using genotype data, pedigree data, and the combination of both genotype and pedigree data under various models.
First, the haplotype of each chromosome was reconstructed for each animal in the F2 population using the 60 K SNP data, pedigree information and a Hidden Markov model [ 22].
This approach combines pedigree, genomic and performance details from animals with differing amounts of information; animals may have any combination of the types of data, pedigree, genomic and performance.
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Hence, for real data, pedigree-based evaluation may actually give larger scaling errors than IBD-GS using selective genotyping.
Using existing mutation screening and microsatellite linkage data, pedigrees were selected to have low probability of being due to mutations in the genes BRCA1 and BRCA2.
We designed GeneLink to facilitate the merging of our genotype data with pedigree and phenotype information (from either the Pedigrees table or the Trait Score table).
Genomic BLUP (GBLUP) used a relationship matrix, G, estimated from marker data and pedigree BLUP (BLUP) estimated the relationship matrix, A, from pedigree records.
Publicly available data including pedigree, genotypic and phenotypic information on heterogeneous stock mice were used [ 21]; http://gscan.well.ox.ac.uk/.ac.uk/
Data and pedigree information used in this study were collected during 1994 2011 by the Agriculture Organization of Guilan Province in Iran.
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