Haplin - Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Performs genetic association analyses of case-parent triad
(trio) data with multiple markers. It can also incorporate
complete or incomplete control triads, for instance independent
control children. Estimation is based on haplotypes, for
instance SNP haplotypes, even though phase is not known from
the genetic data. 'Haplin' estimates relative risk (RR +
conf.int.) and p-value associated with each haplotype. It uses
maximum likelihood estimation to make optimal use of data from
triads with missing genotypic data, for instance if some SNPs
has not been typed for some individuals. 'Haplin' also allows
estimation of effects of maternal haplotypes and
parent-of-origin effects, particularly appropriate in perinatal
epidemiology. 'Haplin' allows special models, like
X-inactivation, to be fitted on the X-chromosome. A GxE
analysis allows testing interactions between environment and
all estimated genetic effects. The models were originally
described 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".
