Related Experiment Video
Updated: Aug 26, 2026

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
Published on: February 3, 2013
Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER
Fang-Chi Hsu1, Jacqueline B Hetmanski, Lan Li
1Section on Biostatics, Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA. fhsu@wfubmc.edu
Background:
We compare two new software packages for linkage analysis, LODPAL and GENEFINDER. Both allow for covariate adjustment. Replicates 1 to 3 of Genetic Analysis Workshop 13 simulated data sets were used for the analyses. We described the results of searching for evidence of loci contributing to a simulated quantitative trait related to systolic blood pressure (SBP). Individuals with SBP greater than 130 mm Hg were defined as affected individuals, and all others as unaffected. Total cholesterol was treated as a covariate.
Results:
Using LODPAL, the power of detecting one of the three major genes related to SBP is 44.4% when a LOD score of 1 is used as the cut-off point. The power of GENEFINDER is lower than that of LODPAL. It is 22.2%.
Conclusions:
Based on the limited comparison, LODPAL provided the more reasonable power to detect linkage compared to GENEFINDER. After adjusting for the total cholesterol covariate, the current version of both programs appeared to give a high number of false positives.
Related Concept Videos
Critical Region, Critical Values and Significance Level
In hypothesis testing, a sample statistic is converted to a test statistic using z, t, or chi-square distribution. A critical region is an area under the curve in probability distributions demarcated by the critical value. When the test statistic falls in this region, it suggests that the null hypothesis must be rejected. As this region contains all those values of the test...
Significance Testing: Overview
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%...
Comparing the Survival Analysis of Two or More Groups
Evolutionary Relationships through Genome Comparisons
Identifying Statistically Significant Differences: The F-Test
