Thus, the challenge consisting in finding the most appropriate π value can be relaxed when using the haplotype-based approach.
Haplotype analyses were carried out using the haplotype-based association testing (HBAT) empirical variance (-e) option in the FBAT program.
This shows that our investigation using the haplotype-based method provides additional evolutionary insights for the PASNP data, where it not only provided additional evidence for regions identified by Fst, but also discovered novel regions under positive selection.
The original set of markers consisted of 681,257 SNPs generated by the approach described by Elshire et al. [ 27] and Glaubitz et al. [ 28] with missing data imputed using the haplotype-based imputation method described by Romay et al. [ 26].
As several SNPs in MACROD2-AS1 show p-values < 0.05, we performed haplotype analysis for the 16 SNPs in the gene to investigate whether there are haplotype effects in the gene on autism, using the haplotype-based transmission disequilibrium test (hap-TDT) implemented in PLINK.
Sequence data was used to produce a phylogenetic network using statistical parsimony to connect the haplotypes based on 95% confidence interval (TCS 1.21) [ 28].
Using only the unique haplotypes, the tree clearly grouped the haplotypes based on the allele present at SNP WUR10000125, with the B haplotypes grouped at the bottom of the tree in Figure 3.
Haplotype frequencies and individual haplotypes were generated by using SAS PROC HAPLOTYPE based on the observed genotypes.
The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information.
First, we used the dating method BATWING [Wilson and Balding, 1998] to estimate the TMRCA (time to most recent common ancestor) of each set of chromosomes in the three haplogroups, using 16-locus haplotypes based on single-copy microsatellites, excluding DYS385.
