Cargando…
Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER
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...
Autores principales: | , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2003
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866482/ https://www.ncbi.nlm.nih.gov/pubmed/14975114 http://dx.doi.org/10.1186/1471-2156-4-S1-S46 |
_version_ | 1782133280332578816 |
---|---|
author | Hsu, Fang-Chi Hetmanski, Jacqueline B Li, Lan Markakis, Diane Jacobs, Kevin Shugart, Yin Yao |
author_facet | Hsu, Fang-Chi Hetmanski, Jacqueline B Li, Lan Markakis, Diane Jacobs, Kevin Shugart, Yin Yao |
author_sort | Hsu, Fang-Chi |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-1866482 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2003 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18664822007-05-11 Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER Hsu, Fang-Chi Hetmanski, Jacqueline B Li, Lan Markakis, Diane Jacobs, Kevin Shugart, Yin Yao BMC Genet Proceedings 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. BioMed Central 2003-12-31 /pmc/articles/PMC1866482/ /pubmed/14975114 http://dx.doi.org/10.1186/1471-2156-4-S1-S46 Text en Copyright © 2003 Hsu et al; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Proceedings Hsu, Fang-Chi Hetmanski, Jacqueline B Li, Lan Markakis, Diane Jacobs, Kevin Shugart, Yin Yao Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title | Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title_full | Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title_fullStr | Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title_full_unstemmed | Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title_short | Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER |
title_sort | comparison of significance level at the true location using two linkage approaches: lodpal and genefinder |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866482/ https://www.ncbi.nlm.nih.gov/pubmed/14975114 http://dx.doi.org/10.1186/1471-2156-4-S1-S46 |
work_keys_str_mv | AT hsufangchi comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder AT hetmanskijacquelineb comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder AT lilan comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder AT markakisdiane comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder AT jacobskevin comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder AT shugartyinyao comparisonofsignificancelevelatthetruelocationusingtwolinkageapproacheslodpalandgenefinder |