title: Basic statistical analysis in genetic case-control studies.
abstract: 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.affiliation: Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. gclarke@well.ox.ac.uk
authors.forename: Geraldine M
authors.initials: GM
authors.lastname: Clarke
authors.forename: Carl A
authors.initials: CA
authors.lastname: Anderson
authors.forename: Fredrik H
authors.initials: FH
authors.lastname: Pettersson
authors.forename: Lon R
authors.initials: LR
authors.lastname: Cardon
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Morris
authors.forename: Krina T
authors.initials: KT
authors.lastname: Zondervan
mesh_terms: D016022:Case-Control Studies; D003627:Data Interpretation, Statistical; D056726:Genetic Association Studies / Q000379:methods*; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D005819:Genetic Markers