Table 3 Haplotyping software for hypothesis testing and analysis.
Program name | Haplotyping algorithm | Key analysis feature(s) | Discrete outcomea | Continuous outcomeb |
|---|---|---|---|---|
Hypothesis | Â | Â | Â | Â |
CHAPLIN | ECM | Includes likelihood ratio statistic and score statistic for haplotype-phenotype analysis, uses permutation test to determine significance | Yes, case-control | No |
| Â | Â | Includes AIC for model selection, does not accommodate covariates | Â | Â |
EH | EM | Test for LD for unrelated and in case-control | Yes, case-control | No |
| Â | Â | Test for frequency difference between case-control under: H1 association, H2 association for all loci | Â | Â |
EHPLUS | EM | Improves on EH | Yes, case-control | No |
| Â | Â | Model-free analysis and permutation test | Â | Â |
FASTEHPLUS | EM | Implements EH and EHPLUS test | Yes, case-control | No |
| Â | Â | Significant speed improvements | Â | Â |
GENECOUNTING | EM | Compares overall and specific haplotype frequency between cases and controls | Yes, case-control | No |
HAPH | IP | Phylogeny based haplotyping method | Yes, case-control | Yes |
| Â | Â | Uses information from phylogeny for analysis, includes parametric and non-parametric tests for qualitative and quantitative phenotypes | Â | Â |
HAPLO.STATS | EM | Score statistic for haplotype-phenotype analysis | Yes, binary, ordinal, & Poisson | Yes |
| Â | Â | GLM for regression of trait on haplotype, adjustment for covariates and interaction | Â | Â |
HPLUS | EE +PL+ EM | Compares haplotypes frequency between cases and controls, option to adjust for covariates, and interaction assessment | Yes, case-control | No |
| Â | Â | Reports OR, confidence interval and identifies haplotype blocks | Â | Â |
LDSUPPORT | EM | Uses likelihood method to calculate risk of developing disease phenotype from diplotype configuration | Yes, case-control | No |
PHASE v2.0 | MCMC | Allows comparison of haplotype frequency between populations | Yes, case-control | No |
THESIAS | S-EM | Compares haplotypes frequency between cases and controls, survival analysis, option to adjust for covariates and interaction assessment | Yes, case-control, survival analysis | Yes |
| Â | Â | Uses Chi-square statistics/t-test for analysis | Â | Â |
SAS Genetics | EM | Allows comparison of haplotype frequency between populations | Yes, case-control | Yes |
| Â | Â | Haplotype trend regression (HTR) and several population genetic tests | Â | Â |
| Â | Â | TDT test for family data | Â | Â |
SNPEM | EM | Compares overall and specific haplotype frequency between cases and controls | Yes, case-control | No |
| Â | Â | Includes batch feature for sliding windows analysis | Â | Â |
WHAP | EM | Uses SNPHAP for regression based haplotype association test on SNPs, provides beta estimates of effects | Yes, case-control | Yes |
| Â | Â | Includes haplotype weighted likelihood analysis, permutation tests and sliding windows analysis | Â | Â |
Zaykin et al. | EM | Likelihood ratio statistic for haplotype-phenotype analysis | Yes, case-control | Yes |
| Â | Â | Allows sliding windows analysis | Â | Â |
3locus.PAS | EM | Test for global disequilibrium, including pairwise and three | No | No |
| Â | Â | way disequilibrium for an unrelated sample | Â | Â |
Other analysis programs | Â | Â | Â | Â |
Arlequin v2.0/3.0 | EM/ELB | Several population genetic tests | Â | Â |
Zou and Zhao | EM | Adjust haplotype frequency estimates for genotyping error | Â | Â |