High-resolution genetic mapping with pooled sequencing
Name
Edwards-2012-High-resolution genetic mapping with pooled sequencing.pdf
Size
879.5 KB
Format
Adobe PDF
Checksum (MD5)
c170549d1ef52fe7468eb4eda37453a9
Author(s)
Edwards, Matthew Douglas
Gifford, David K.
Date Issued
April 2012
Journal
BMC Bioinformatics
Publisher
BioMed Central
Citation
Edwards, Matthew Douglas and Gifford, David K., "High-resolution genetic mapping with pooled sequencing." BMC Bioinformatics 2012, 13(Suppl 6):S8.
Version
Final published version
Abstract
Background:
Modern genetics has been transformed by high-throughput sequencing. New experimental designs in model organisms involve analyzing many individuals, pooled and sequenced in groups for increased efficiency. However, the uncertainty from pooling and the challenge of noisy sequencing data demand advanced computational methods.
Results:
We present MULTIPOOL, a computational method for genetic mapping in model organism crosses that are analyzed by pooled genotyping. Unlike other methods for the analysis of pooled sequence data, we simultaneously consider information from all linked chromosomal markers when estimating the location of a causal variant. Our use of informative sequencing reads is formulated as a discrete dynamic Bayesian network, which we extend with a continuous approximation that allows for rapid inference without a dependence on the pool size. MULTIPOOL generalizes to include biological replicates and case-only or case-control designs for binary and quantitative traits.
Conclusions:
Our increased information sharing and principled inclusion of relevant error sources improve resolution and accuracy when compared to existing methods, localizing associations to single genes in several cases. MULTIPOOL is freely available at http://cgs.csail.mit.edu/multipool/ webcite.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution
Persistent DSpace Link
DOI of Published Version
http://www.biomedcentral.com/1471-2105/13/S6/S8/
