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Pipeline publication

[…] o opiates, vulnerability to develop opioid addiction, and perception of pain). In addition, a combination of linked variants could contribute to the phenotypic difference in a different way than a single polymorphism., Toward this goal, we performed an analysis of genetic variations and haplogroups in the OPRM1 100 kb 5′ flanking region, exon 1, and the 50 kb intron 1, and searched for regions in high LD with the 118G and/or the intron 1 variants. Genotype data were obtained from the International HapMap Project and from tag SNPs in a sample of European Americans., 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. , HapMap genotype and phased haplotype data were obtained from the genome browser of The International HapMap Project Phase 2 (http://www.hapmap.org/). The sample populations used were CEU (Utah residents with Northern and Western European ancestry from the CEPH collection), YRI (Yoruba in Ibadan, Nigeria) and the combined JPN/CHB (Japanese in Tokyo and Han Chinese in Beijing). Only the founders in these sample populations were included. The phased haplotype data was generated using a maximum likelihood algorithm. The chromosomal region was set to position 154,300–15 […]

Pipeline specifications

Software tools TBA, PHAST, ESPERR
Databases International HapMap Project