From Buccal to Bonferroni in Genetically Informative Prevention Research II: Execution of Genotyping and Preliminary Analysis of Genetic Data

This second presentation on incorporating genetics into prevention research concentrates on methodologies for genotyping, data collection, collation, and cleaning. In contrast to assumptions that a genotype call yields an absolute answer, genotyping a sample can be fraught with technical difficulties and error at several stages.

The differences between, and reasons for use of Single Nucleotide Polymorphisms (SNPs), Short Tandem Repeats (STRs), and Variable Length Tandem Repeats (VNTRs) will be explained and visualized to aid in interpretation of genotype data. The use of proxy markers to capture genetic information from sites not directly tested is described. The most widely used genotyping methods and platforms, and their relative advantages and disadvantages are discussed. The method of multiplexing markers is described as a means to detect methodological errors and save cost when genotyping. The outputs from each of the above methods are also varied (e.g. assignment of dye colors to alleles in PCR-based assays, and the A/B system of genotype assignment used by some investigators) and require careful attention. Some of the questions that arise when first analyzing genotype data are: a) why is an allele at a specific site sometimes given different labels (DNA strand reported), b) what is the difference between a genotype based on DNA vs. amino acid sequence (codon look-up tables); c) how does one reconcile the numbering systems used with various genetic databases that have evolved over time? Results from each type of genotyping used in the PROSPER project are shown to allow a greater understanding of the processes and outcomes.

Adoption of specific approaches through each stage of the genotyping process will result in high quality genetic data for analysis of behavioral outcomes from prevention projects.