Brian P. Kinghorn

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Efficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the pedigree and for all genotyped single nucleotide polymorphisms (SNP) provides a framework to combine all pedigree, genomic, and phenotypic(More)
Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation(More)
Multiple sequence alignment plays an important role in molecular sequence analysis. An alignment is the arrangement of two (pairwise alignment) or more (multiple alignment) sequences of 'residues' (nucleotides or amino acids) that maximizes the similarities between them. Algorithmically, the problem consists of opening and extending gaps in the sequences to(More)
The periodic pattern of DNA in exons is a known phenomenon. It was suggested that one of the initial causes of periodicity could be the universal (RNY) n pattern (R = A or G, Y = C or U, N = any base) of ancient RNA. Two major questions were addressed in this paper. Firstly, the cause of DNA periodicity, which was investigated by comparisons between real(More)
This paper describes a method for screening animal populations on an index of calculated probabilities of genotype status at an unknown single locus. Animals selected by such a method might then be candidates in test matings and genetic marker analyses for major gene detection. The method relies on phenotypic measures for a continuous trait plus(More)
Long range phasing (LRP) is a fast and accurate rule based method which uses information from both related and unrelated individuals by invoking the concepts of surrogate parents and Erdös numbers (Kong et al., 2008). Recursive long range phasing and long haplotype imputation (RLRPLHI; Hickey et al., 2009) is an extended LRP algorithm with increased(More)
Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in(More)
OBJECTIVE To determine prevalence, level of inbreeding, heritability, and mode of inheritance for rupture of the cranial cruciate ligament (RCCL) in Newfoundlands. DESIGN Retrospective and recruitment study. ANIMALS 574 client-owned Newfoundlands. PROCEDURE Medical records from January 1, 1996, to December 31, 2002, were evaluated for prevalence of(More)
Polymorphic bands were detected within the DQB and DRB regions of the ovine major histocompatibility complex by probing TaqI digested DNA from three large sheep half-sib families derived from a highly resistant ram. All animals were phenotypically assessed for Haemonchus contortus resistance by faecal egg counts and associations with RFLP bands and(More)
A genotype probability index (GPI) is proposed to indicate the information content of genotype probabilities derived from a segregation analysis. Typically, some individuals are genotyped at a marker locus or a quantitative trait locus, and segregation analysis is used to make genotype inferences about ungenotyped relatives. Genotype probabilities for a(More)