Software

EFBAT: exact family-based association tests

Kady Schneiter¹ , James H Degnan² , Christopher Corcoran¹ , Xin Xu³ and Nan Laird⁴

¹  Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan, UT 84322-3900, USA

²  Human Genetics Department, 2017 Palmer Commons, Ann Arbor, Michigan, USA

³  Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave., Boston, MA 02115, USA

⁴  Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave., Boston, MA 02115, USA

author email corresponding author email

BMC Genetics 2007, 8:86doi:10.1186/1471-2156-8-86

Published:	20 December 2007

Abstract

Background

Family-based association tests are important tools for investigating genetic risk factors of complex diseases. These tests are especially valuable for being robust to population structure. We introduce a tool, EFBAT, which performs exact family-based tests of association for X-chromosome and autosomal biallelic markers.

Results

The program EFBAT extends a network algorithm previously applied to autosomal markers to include the X-chromosome and to perform tests of association under the null hypotheses "no association, no linkage" and "no association in the presence of linkage" under additive, dominant and recessive genetic models. These tests are valid regardless of patterns of missing familial data.

Conclusion

The general framework for performing exact family-based association tests has been usefully extended to the X-chromosome, particularly for the hypothesis of "no association in the presence of linkage" and for different genetic models.