Dealing with missing phase and missing data in phylogeny-based analysis. - Inserm - Institut national de la santé et de la recherche médicale Access content directly
Journal Articles BMC Proceedings Year : 2007

Dealing with missing phase and missing data in phylogeny-based analysis.


ABSTRACT : We recently described a new method to identify disease susceptibility loci, based on the analysis of the evolutionary relationships between haplotypes of cases and controls. However, haplotypes are often unknown and the problem of phase inference is even more crucial when there are missing data. In this work, we suggest using a multiple imputation algorithm to deal with missing phase and missing data, prior to a phylogeny-based analysis. We used the simulated data of Genetic Analysis Workshop 15 (Problem 3, answer known) to assess the power of the phylogeny-based analysis to detect disease susceptibility loci after reconstruction of haplotypes by a multiple-imputation method. We compare, for various rates of missing data, the performance of the multiple imputation method with the performance achieved when considering only the most probable haplotypic configurations or the true phase. When only the phase is unknown, all methods perform approximately the same to identify disease susceptibility sites. In the presence of missing data however, the detection of disease susceptibility sites is significantly better when reconstructing haplotypes by multiple imputation than when considering only the best haplotype configurations.


Fichier principal
Vignette du fichier
1753-6561-1-S1-S22.pdf (217.37 Ko) Télécharger le fichier

Dates and versions

inserm-00284150 , version 1 (02-06-2008)


  • HAL Id : inserm-00284150 , version 1
  • PUBMED : 18466519


Claire Bardel, Pascal Croiseau, Emmanuelle Génin. Dealing with missing phase and missing data in phylogeny-based analysis.. BMC Proceedings, 2007, 1 Suppl 1 (1), pp.S22. ⟨inserm-00284150⟩
237 View
300 Download



Gmail Mastodon Facebook X LinkedIn More