Dataset Information

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.

SUBMITTER: Clarke GM

PROVIDER: S-EPMC3154648 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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Publications

Basic statistical analysis in genetic case-control studies.

Clarke Geraldine M GM Anderson Carl A CA Pettersson Fredrik H FH Cardon Lon R LR Morris Andrew P AP Zondervan Krina T KT

Nature protocols 20110203 2

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 softwar ...[more]

PMID: 21293453

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Dataset Information

Basic statistical analysis in genetic case-control studies.

Publications

Basic statistical analysis in genetic case-control studies.

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