Computational protocol: CHRNA7 Polymorphisms and Dementia Risk: Interactions with Apolipoprotein ε4 and Cigarette Smoking

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Protocol publication

[…] Common (frequency ≥5%) SNPs in CHRNA7 were selected from Han Chinese in Beijing (CHB) genotype data from the International HapMap Project (http://hapmap.ncbi.nlm.nih.gov/). Haplotype blocks were determined by the Haploview program (http://www.broadinstitute.org/haploview/haploview) using a modified Gabriel algorithm. htSNPs were selected from each haplotype block using the tagSNP program with R2 > 0.7 in each haplotype block. Genotypes of CHRNA7 SNPs were determined by TaqMan® Genomic Assays using the ABI 7900HT fast real-time PCR system (Applied Biosystems Inc., Foster City, CA, USA). APOE genotypes were determined by the assay developed by Chapman et al.. The APOE diplotypes (ε2/ε2, ε2/ε3, ε3/ε3, ε2/ε4, ε3/ε4, and ε4/ε4) were determined by APOE112 (rs429358) and APOE158 (rs7412). APOE ε4 carriers were defined by participants carrying ε2/ε4, ε3/ε4, or ε4/ε4 diplotypes. Participants carrying other diplotypes (ε2/ε2, ε2/ε3, and ε3/ε3) were defined as APOE ε4 non-carriers. The genotyping call rate was greater than 95% for each SNP. The internal genotyping quality control obtained from 5% of samples in duplicates had a concordance rate of 100%. […]

Pipeline specifications

Software tools Haploview, SNPinfo
Databases International HapMap Project
Application GWAS
Diseases Alzheimer Disease, Dementia, Dementia, Vascular, Atherosclerosis
Chemicals Acetylcholine, Nicotine