Computational protocol: Ablation of Mrds1/Ofcc1 Induces Hyper γ Glutamyl Transpeptidasemia without Abnormal Head Development and Schizophrenia Relevant Behaviors in Mice

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Protocol publication

[…] The genomic structure of human MRDS1/OFCC1 is based on Human Feb. 2009 (GRCh37/hg19) of the UCSC database (http://genome.ucsc.edu/) (). The single nucleotide polymorphism (SNP) search was performed using Entrez SNP from the NCBI database (http://www.ncbi.nlm.nih.gov/SNP/). We selected 32 SNPs within the MRDS1/OFCC1 gene, including SNPs that showed strong evidence of association with schizophrenia in a prior study . Twenty-five SNPs that could be unequivocally genotyped and showed sufficient heterozygosity (minor allele frequency >0.1) in our preliminary examinations were used for further analyses ( and ). MRDS1/OFCC1 SNPs span a genomic stretch of 483,168 bp and the average marker-to-marker interval was ∼20 kb. These SNPs were selected to cover the MRDS1/OFCC1 region as evenly as possible.DNA was extracted from whole blood according to a standard protocol. We used Assays-by-Design SNP genotyping products to score SNPs (Applied Biosystems, Carlsbad, CA, USA) (http://www.appliedbiosystems.com/), based on the TaqMan assay methods. Genotypes were determined using an ABI7900 sequence detection system instrument (Applied Biosystems) and the SDS v2.0 software package (Applied Biosystems).The normalized LD coefficient D′ and squared correlation coefficient r2 , parameters indicating a degree of LD between markers, were calculated, and haplotype structures were constructed, using HAPLOVIEW version 4.2 (http://www.broad.mit.edu/mpg/haploview/) . Transmission distortions in the family panel were evaluated using the pedigree disequilibrium test (PDT) program, v5.1 (http://www.chg.duke.edu/research/software.html) –. The PDT program computes two statistical measures, PDT-sum and PDT-ave. Briefly, PDT-sum gives more weight to larger families, whereas PDT-ave places equal weight on all families. The suitability of both statistical methods depends on family structure and genetic models . […]

Pipeline specifications

Software tools snp-search, PASsiT, Haploview
Application GWAS
Organisms Mus musculus, Oryzias latipes, Homo sapiens
Diseases Eye Abnormalities, Liver Diseases, Intellectual Disability