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  • Review
  • Open Access

Using genotype probabilities in survival analysis: a scrapie case

  • Zulma G. Vitezica1Email author,
  • Jean-Michel Elsen1,
  • Rachel Rupp1 and
  • Clara Díaz2
Genetics Selection Evolution200537:403

https://doi.org/10.1186/1297-9686-37-5-403

Received: 5 August 2004

Accepted: 11 January 2005

Published: 15 July 2005

Abstract

The objective was to evaluate the potential use of genotype probabilities to handle records of non-genotyped animals in the context of survival analysis. To do so, the risks associated with the PrP genotype and other transmission factors in relation to clinical scrapie were estimated. Data from 4049 Romanov sheep affected by natural scrapie were analyzed using survival analysis techniques. The original data set included 1310 animals with missing genotypes; five of those had uncensored records. Different missing genotype-information patterns were simulated for uncensored and censored records. Three strategies differing in the way genotype information was handled were tested. Firstly, records with unknown genotypes were discarded (P1); secondly, those records were grouped in an unknown class (P2). Finally the probabilities of genotypes were assigned (P3). Whatever the strategy, the ranking of relative risks for the most susceptible genotypes (VRQ-VRQ, ARQ-VRQ and ARQ-ARQ) was similar even when the non-genotyped animals were not a negligible part of uncensored records. However, P3 had a more efficient way of handling missing genotype information. As compared to P1, either P2 or P3 avoided discarding the records of non-genotyped animals; however, P3 eliminated the unknown class and the risk associated with this group. Genotype probabilities were shown to be a useful technique to handle records of individuals with unknown genotype.

Keywords

genotype probabilitiessurvival analysisPrP genotypesscrapie

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Authors’ Affiliations

(1)
Station d'amélioration génétique des animaux, Institut national de la recherche agronomique, Castanet Tolosan, France
(2)
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Dpto. Mejora Genética Animal, Madrid, Spain

Copyright

© INRA, EDP Sciences 2005

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