Immunogenetics pp 245-266 | Cite as

Analytical Methods for Disease Association Studies with Immunogenetic Data

  • Jill A. Hollenbach
  • Steven J. Mack
  • Glenys Thomson
  • Pierre-Antoine Gourraud
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 882)

Abstract

Disease association studies involving highly polymorphic immunogenetic data may involve analyses at one or many units of analysis, including amino acid, allele, genotype and haplotype levels, as well as consideration of gene–gene or gene–environment interactions. The selection of the appropriate statistical tests is critical and will be dependent on the nature of the dataset (e.g., case-control vs. family data) as well as the specific research hypotheses being tested. This paper describes the various study and analysis categories used for such analyses, including the advantages and limitations of such techniques.

Key words

HLA KIR Immunogenetic Data analysis Disease association Case-control Family 

Notes

Acknowledgments

This work was supported by National Institutes of Health (NIH) grants U01AI067068 (JAH, SJM) and U19 AI067152 (PAG) awarded by the National Institute of Allergy and Infectious Diseases (NIAID) and 1R01DK061722 (JAH) awarded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Glossary

Bonferroni correction

The most commonly used method of correcting for multiple comparisons. Generally, the test significance level is divided by the number of comparisons made in the study, thereby increasing the overall stringency of the significance testing.

Confidence interval

A likely range of values for an estimate of a particular parameter within a particular level of significance.

Contingency table

Also known as a cross-tabulation. A 2  ×  n table used to analyze heterogeneity between two sets of observations of two or more categorical variables.

Genetic association

The occurrence within a population, greater than that expected by chance, of a genetic trait with a particular phenotype.

Logistic regression

A statistical method to determine which in a set of independent variables has a predictive relationship to a binary-dependent outcome variable.

Multiple comparisons

Also know as multiple testing. Performing a statistical test multiple times in the same analysis, thereby increasing the number of chances that the null hypothesis will be incorrectly rejected, leading to false positive associations.

Odds ratio

The ratio of odds of an outcome occurring in one group to the odds of it occurring in another group.

Population stratification

Also referred to as population substructure. Allele frequency differences between subpopulations within a study population due to ancestry differences or selection biases.

Relative risk

A measure that describes the risk of having the outcome of interest relative to exposure.

Yates correction for continuity

An adjustment to the χ 2 test statistic performed by subtracting 0.5 from the (O-E) value for each cell in a contingency table. The purpose of this correction is to account for sparse cells in the table which may introduce discontinuity with regard to the χ 2 distribution.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Jill A. Hollenbach
    • 1
  • Steven J. Mack
    • 1
  • Glenys Thomson
    • 2
  • Pierre-Antoine Gourraud
    • 3
  1. 1.Center for GeneticsChildren’s Hospital and Research Center OaklandOaklandUSA
  2. 2.Department of Integrative BiologyUniversity of CaliforniaBerkeleyUSA
  3. 3.Department of NeurologyUniversity of CaliforniaSan FranciscoUSA

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