Computational protocol: Haplotype block structure of the genomic region of the mu opioid receptor gene (OPRM1)

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Protocol publication

[…] Comparative genomic analysis was obtained from the UCSC Genome Browser (http://genome.ucsc.edu/) and is based on the Vertebrate Multiz Alignment & PhastCons Conservation. Regulatory Potential data were based on the ESPERR Regulatory Potential analysis that is computed from alignments of human, chimpanzee, macaque, mouse, rat, dog, and cow. [...] The pattern of pair-wise LD between the three SNPs (#5, 6 and 8) in the original sample was measured by D’ and r2 metrics. Haplotypes were reconstructed using the accelerated expectation-maximization algorithm implemented in Haploview version 4.2. Multi-locus genotype patterns were generated manually. […]

Pipeline specifications

Software tools PHAST, ESPERR, Haploview
Databases UCSC Genome Browser
Diseases Pain Insensitivity, Congenital, Pain
Chemicals Heroin, Nucleotides