Related Experiment Video
Updated: Aug 18, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Haplotype sharing analysis using mantel statistics
L Beckmann1, D C Thomas, C Fischer
1German Cancer Research Center DKFZ, DE-69120 Heidelberg, Germany.
Objective:
The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take the linkage disequilibrium information between multiple markers into account, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for spacetime clustering, which is developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease.
Methods:
The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. The phenotypic similarity is measured as the mean-corrected cross-product based on the respective phenotypes. We analyzed two tests for statistical significance with respect to type I error: (1) assuming asymptotic normality, and (2) using a Monte Carlo permutation procedure. The results were compared to the chi(2) test for association based on 3-marker haplotypes.
Results:
The results of the type I error rates for the Mantel statistics using the permutational procedure yielded pointwise valid tests. The approach based on the assumption of asymptotic normality was seriously liberal.
Conclusion:
Power comparisons showed that the Mantel statistics were better than or equal to the chi(2) test for all simulated disease models.
Related Concept Videos
The Mantel-Cox Log-Rank Test
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Hardy-Weinberg Principle
Test for Homogeneity
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Wilcoxon Signed-Ranks Test for Matched Pairs

