Genetic Mapping in the Presence of Genotyping Errors

Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Ea...

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Bibliographic Details
Published in:Genetics (Austin) 2007-08, Vol.176 (4), p.2521-2527
Main Authors: Cartwright, Dustin A, Troggio, Michela, Velasco, Riccardo, Gutin, Alexander
Format: Article
Language:English
Subjects:
Advantages
Algorithms
Chromosome Mapping - statistics & numerical data
Data Interpretation, Statistical
Errors
Genetic Markers
Genetics
Genotype
Genotype & phenotype
Investigations
Likelihood Functions
Methods
Models, Genetic
Monte Carlo Method
Software
Studies
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Summary:Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.106.063982