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EFBAT: exact family-based association tests.

Kady Schneiter1, James H Degnan, Christopher Corcoran

  • 1Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan, UT 84322-3900, USA. kady.schneiter@usu.edu

BMC Genetics
|December 22, 2007
PubMed
Summary
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The new EFBAT software enables exact family-based association tests for X-chromosome and autosomal genetic markers. This tool enhances the investigation of complex disease genetic risk factors, even with missing family data.

Area of Science:

  • Genetics
  • Statistical genetics

Background:

  • Family-based association tests are crucial for identifying genetic risk factors in complex diseases.
  • These methods offer robustness against population structure, a common confounder in genetic studies.
  • Existing tools primarily focus on autosomal markers.

Purpose of the Study:

  • To introduce EFBAT, a software tool for performing exact family-based association tests.
  • To extend association testing capabilities to the X-chromosome.
  • To accommodate various genetic models and hypotheses.

Main Methods:

  • EFBAT utilizes a network algorithm extended for X-chromosome analysis.
  • It performs exact tests of association under different null hypotheses.
  • The program supports additive, dominant, and recessive genetic models.

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Main Results:

  • EFBAT successfully extends association testing to X-chromosome biallelic markers.
  • The software performs tests under "no association, no linkage" and "no association in the presence of linkage" hypotheses.
  • Tests remain valid irrespective of missing familial data patterns.

Conclusions:

  • The framework for exact family-based association tests has been effectively extended to the X-chromosome.
  • EFBAT is particularly valuable for testing "no association in the presence of linkage" and various genetic models.
  • This advancement aids in the genetic analysis of complex diseases using family data.