paperKB
coga / coga-kb
Help
Sign in

Chunk #15 — Methods — Genotyping

Source
The association between DRD2/ANKK1 and genetically informed measures of alcohol use and problems.
Embedded
yes

Text

A total of 602 individuals were genotyped using Sequenom’s homogeneous Mass Extend (hME) and iPLEX Gold technology (Sequenom, San Diego, CA, USA). Thirty-one tagging single-nucleotide polymorphisms (SNPs) in DRD2/ANKK1 were selected based on the HapMap Project (http://www.hapmap.org) and NCBI (http://www.ncbi.nlm.nih.gov) databases. The selected variants were bi-allelic and had a minor allele frequency (MAF) >10% in the Caucasian population. The ability to amplify the flanking regions of each SNP was determined by using the applications SNPper (http://www.snpper.chip.org) and RealSNP (http://www.realsnp.com), which define the most reliable regions for designing primers and the quality of the amplicons, respectively. All tagging SNPs failing during the procedure were replaced by newly generated tagging SNPs proposed by Haploview (Barrett, Fry, Maller, & Daly, 2005). The PCR and extension primers were designed using Sequenom’s Mass ARRAY Assay Design software (version 2.0). SNPs were genotyped in 384-well plates according to manufacturer’s instructions. For quality controls, each plate contained at least eight water controls and 22 duplicate samples. PCR reactions were performed in a total reaction volume of 5μl using 20ng of genomic DNA obtained by blood draw (Kettunen