Document Detail


Basic statistical analysis in genetic case-control studies.
MedLine Citation:
PMID:  21293453     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
This protocol describes how to perform basic statistical analysis in a population-based genetic association case-control study. The steps described involve the (i) appropriate selection of measures of association and relevance of disease models; (ii) appropriate selection of tests of association; (iii) visualization and interpretation of results; (iv) consideration of appropriate methods to control for multiple testing; and (v) replication strategies. Assuming no previous experience with software such as PLINK, R or Haploview, we describe how to use these popular tools for handling single-nucleotide polymorphism data in order to carry out tests of association and visualize and interpret results. This protocol assumes that data quality assessment and control has been performed, as described in a previous protocol, so that samples and markers deemed to have the potential to introduce bias to the study have been identified and removed. Study design, marker selection and quality control of case-control studies have also been discussed in earlier protocols. The protocol should take ~1 h to complete.
Authors:
Geraldine M Clarke; Carl A Anderson; Fredrik H Pettersson; Lon R Cardon; Andrew P Morris; Krina T Zondervan
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2011-02-03
Journal Detail:
Title:  Nature protocols     Volume:  6     ISSN:  1750-2799     ISO Abbreviation:  Nat Protoc     Publication Date:  2011 Feb 
Date Detail:
Created Date:  2011-02-04     Completed Date:  2011-05-13     Revised Date:  2013-06-30    
Medline Journal Info:
Nlm Unique ID:  101284307     Medline TA:  Nat Protoc     Country:  England    
Other Details:
Languages:  eng     Pagination:  121-33     Citation Subset:  IM    
Affiliation:
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. gclarke@well.ox.ac.uk
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MeSH Terms
Descriptor/Qualifier:
Case-Control Studies
Data Interpretation, Statistical
Genetic Association Studies / methods*
Genetic Markers
Genotype
Humans
Polymorphism, Single Nucleotide
Software*
Grant Support
ID/Acronym/Agency:
064890//Wellcome Trust; 081682//Wellcome Trust; 085235//Wellcome Trust; WT91745/Z/10/Z//Wellcome Trust
Chemical
Reg. No./Substance:
0/Genetic Markers
Comments/Corrections

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