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Originally published as Genetics Published Articles Ahead of Print on February 4, 2007.
Genetics, Vol. 176, 2521-2527, August 2007, Copyright © 2007
doi:10.1534/genetics.106.063982
Genetic Mapping in the Presence of Genotyping Errors
Dustin A. Cartwright*,
,1,
Michela Troggio,
Riccardo Velasco and
Alexander Gutin*
* Myriad Genetics, Salt Lake City, Utah 84108 and Genetics and Molecular Biology Department, IASMA Research Center, San Michele a/Adige (TN) 38010, Italy
1 Corresponding author: Myriad Genetics, 320 Wakara Way, Salt Lake City, UT 84108.
E-mail: dcartwri{at}myriad.com
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.
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