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.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of SPIE - The International Society for Optical Engineering |
| Editors | Gerald E. Cohn, Steven A. Soper, C.H.W. Chen |
| Pages | 341-348 |
| Number of pages | 8 |
| State | Published - Jan 1 1996 |
| Event | Ultrasensitive Biochemical Diagnostics - San Jose, CA, USA Duration: Jan 31 1996 → Feb 2 1996 |
Publication series
| Name | Proceedings of SPIE - The International Society for Optical Engineering |
|---|---|
| Volume | 2680 |
| ISSN (Print) | 0277-786X |
Other
| Other | Ultrasensitive Biochemical Diagnostics |
|---|---|
| City | San Jose, CA, USA |
| Period | 1/31/96 → 2/2/96 |
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ASJC Scopus subject areas
- Electronic, Optical and Magnetic Materials
- Condensed Matter Physics
- Computer Science Applications
- Applied Mathematics
- Electrical and Electronic Engineering
Cite this
High-throughput genotyping : practical considerations concerning the day-to-day application. / McIndoe, Richard A.; Bumgarner, R. E.; Welti, Russ; Hood, Leroy M.D.
Proceedings of SPIE - The International Society for Optical Engineering. ed. / Gerald E. Cohn; Steven A. Soper; C.H.W. Chen. 1996. p. 341-348 (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 2680).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - High-throughput genotyping
T2 - practical considerations concerning the day-to-day application
AU - McIndoe, Richard A.
AU - Bumgarner, R. E.
AU - Welti, Russ
AU - Hood, Leroy M.D.
PY - 1996/1/1
Y1 - 1996/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=0029722276&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0029722276&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:0029722276
SN - 0819420549
SN - 9780819420541
T3 - Proceedings of SPIE - The International Society for Optical Engineering
SP - 341
EP - 348
BT - Proceedings of SPIE - The International Society for Optical Engineering
A2 - Cohn, Gerald E.
A2 - Soper, Steven A.
A2 - Chen, C.H.W.
ER -