File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

Article: UPDG: Utilities package for data analysis of Pooled DNA GWAS

TitleUPDG: Utilities package for data analysis of Pooled DNA GWAS
Authors
Issue Date2012
Citation
BMC Genetics, 2012, v. 13, article no. 1 How to Cite?
AbstractBackground: Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).Results: UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.Conclusions: UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy. © 2012 Ho et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/214733
ISSN
2015 Impact Factor: 2.152
2015 SCImago Journal Rankings: 1.185

 

DC FieldValueLanguage
dc.contributor.authorHo, DWH-
dc.contributor.authorYap, MKH-
dc.contributor.authorYip, SP-
dc.date.accessioned2015-08-21T11:53:32Z-
dc.date.available2015-08-21T11:53:32Z-
dc.date.issued2012-
dc.identifier.citationBMC Genetics, 2012, v. 13, article no. 1-
dc.identifier.issn1471-2156-
dc.identifier.urihttp://hdl.handle.net/10722/214733-
dc.description.abstractBackground: Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).Results: UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.Conclusions: UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy. © 2012 Ho et al; licensee BioMed Central Ltd.-
dc.languageeng-
dc.relation.ispartofBMC Genetics-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleUPDG: Utilities package for data analysis of Pooled DNA GWAS-
dc.typeArticle-
dc.identifier.emailHo, DWH: dwhho@hku.hk-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2156-13-1-
dc.identifier.pmid22252406-
dc.identifier.scopuseid_2-s2.0-84855757443-
dc.identifier.hkuros248463-
dc.identifier.volume13-
dc.identifier.spagearticle no. 1-
dc.identifier.epagearticle no. 1-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats