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Proceedings Paper

High-throughput genotyping: practical considerations concerning the day-to-day application
Author(s): Richard A. McIndoe; R. E. Bumgarner; Russ Welti; Leroy Hood M.D.
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Paper Abstract

Advances in high throughput genotyping protocols over the past few years have been remarkable. Most protocols developed to increase the throughput of genotyping rely on fluorescent based technologies for data acquisition and capture. In general, the number of genotypes per day quoted for these protocols are the result of extrapolations based on ideal situations. Here we present our experience with respect to the day to day problems of high throughput genotyping. Our laboratory is currently working on several genetic mapping projects in both mouse and man. For example, we are looking at the genetic basis for susceptibility to rheumatoid arthritis in a local native American tribe as well as a mouse animal model for the same disease. The machines used to collect gel image data are two Li- Cor infrared DNA sequencers adapted for genotyping. During the evolution of these projects, we have addressed issues concerning the tracking and flow of information from the initial extraction of DNA to the calling of the genotypes. In particular, we have focused on designing methods that are efficient, cost effective and can be easily taught to the technical staff. Computer programs have been written that record gel specific information (e.g. ID information), archive data and capture genotypes in a simple point and click environment. Instrumentation was purchased to ease the repetitive nature of sample allocation, reagent disbursement and gel loading. Using this system, we can produce genotype data on 96 individuals for 20 loci (1920 genotypes) in one day. Solutions to the overall flow of information at each of these junctions are discussed.

Paper Details

Date Published: 1 April 1996
PDF: 8 pages
Proc. SPIE 2680, Ultrasensitive Biochemical Diagnostics, (1 April 1996);
Show Author Affiliations
Richard A. McIndoe, Univ. of Washington (United States)
R. E. Bumgarner, Univ. of Washington (United States)
Russ Welti, Univ. of Washington (United States)
Leroy Hood M.D., Univ. of Washington (United States)

Published in SPIE Proceedings Vol. 2680:
Ultrasensitive Biochemical Diagnostics
Gerald E. Cohn; Steven A. Soper; C. H. Winston Chen, Editor(s)

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