Using genotype probabilities in survival analysis: a scrapie case

Free access article

Issue		Genet. Sel. Evol. Volume 37, Number 4, July-August 2005


Page(s)		403 - 415
DOI		10.1051/gse:2005008

Genet. Sel. Evol. 37 (2005) 403-415
DOI: 10.1051/gse:2005008

Using genotype probabilities in survival analysis: a scrapie case

Zulma G. Vitezica^a, Jean-Michel Elsen^a, Rachel Rupp^a and Clara Díaz^b

^a Station d'amélioration génétique des animaux, Institut national de la recherche agronomique, 31326 Castanet Tolosan, France
^b Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7.5, 28040 Madrid, Spain

(Received 5 August 2004; accepted 11 January 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.

Key words: genotype probabilities / survival analysis / PrP genotypes / scrapie

Correspondence and reprints: vitezica@germinal.toulouse.inra.fr

© INRA, EDP Sciences 2005

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