Haplin is a free software package designed to analyze case-parent triad (trio) data and/or case-control data. Some of its main features are:

  • Analyses of the case-parent triad design, the case-control design, and “hybrid” designs, i.e. combinations of case-parent triads and control-parent triads.
  • Optimal use of designs with missing genotypic data, for instance if a single SNP has not been typed in some individuals, or when the case father has not been genotyped at all, or when the control parents are not available.
  • Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data.
  • Estimation of relative risk (RR) associated with each haplotype, not only significance testing.
  • Optional estimation of effects of maternal haplotypes, particularly relevant to perinatal epidemiology.
  • Estimation of RRs, haplotypes etc. also on the X chromosome, with models including dose-response and X-inactivation.
  • Estimation of parent-of-origin (PoO) effects.
  • Gene-environment (GxE) interactions can be estimated for all genetic effects
  • For instance, estimation of PoO interactions with environmental exposure (PoOxE effects).
  • Support for GWAS data and parallel processing.
  • Extensive facilities for power calculations.
The models estimated by Haplin are described in detail in Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396.

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Also available from Blackwell