FBAT

Introduction

FBAT implements a broad class of Family Based Association Tests, adjusted for population admixture. FBAT features include:

Download Software

Current version FBAT 2.0.4 is available for the following platforms:


Older version FBAT 2.0.3 is available for the following platforms:


Older version FBAT 1.7.3 is also available for the following platforms:

Documentation

Documentation for FBAT is included in the above packages. In addition, the following documents for FBAT are also available online. Please read the user's manual if you are not sure how to uncompress the archives.

References

*Main methods papers relating to FBAT


De G, Yip WK, Ionita-Laza I, Laird N (2013) Rare variant analysis for family-based design. PLoS One. 8(1):e48495.

Ding X, Lange C, Xu X, Laird N. (2009) New powerful approaches for family-based association tests with longitudinal measurements. Ann Hum Genet. 73(1):74-83.

Horvath S, Xu X and Laird N (2001) The family based association test method: strategies for studying general genotype-phenotype associations. Euro J Hum Gen. 9:301-306.

Horvath, S, Xu, X, Lake, S, Silverman, E, Weiss, S, and Laird, N (2004) Tests for Associating Haplotypes with General Phenotype Data: Application to Asthma GeneticsGenetic Epi. 26:61-69.

Laird NM, Horvath S and Xu X (2000) Implementing a unified approach to family based tests of association. Genetic Epi. 19(Suppl 1): S36-S42.

Laird NM, Kraft P, van Steen, K and Lange, C.(2005) Testing for association in genetic studies in E. Silverman et al., Eds, Hodder Arnold: Boston, MA, 27-46.

Lake S, Blacker, and Laird N (2001) Family based tests in the presence of association. Amer J Hum Gen. 67:1515-1525.

Lange C, Silverman EK, Xu X, Weiss ST, Laird NM (2003) A multivariate family-based association test using generalized estimating equations: FBAT-GEE. Biostatistics. 4:195-306.

Lunetta KL, Farone SV, Biederman J, and Laird NM (2000) Family based tests of association and linkage using unaffected sibs, covariates and interactions. Amer J Hum Gen. 66:605-614.

Rabinowitz D and Laird NM (2000) A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information.  Human Heredity. 504:227-233.

Rakovski C, Xu X, Lazarus R and Laird NM (2007)  A new multi-marker test for family based association studies. Genet Epidemiol. 31(1): p. 9-17. 

Xu X, Rakovski C, Xu X, and Laird NM. (2006). An Efficient Family-Based Association Test using Multiple Markers. Genet Epidemiol. (7):620-6.

Yip WK, De G, Raby BA, Laird N. (2011) Identifying causal rare variants of disease through family-based analysis of Genetics Analysis Workshop 17 data set. BMC Proc. 5 Suppl 9:S21.

Zhou JJ, Yip WK, Cho MH, Qiao D, McDonald MN, Laird NM (2013) GAW18 - A Comparative Analysis of Family and Population Based Association Tests Using Whole Genome Sequence Data. To appear in Genetic Epidemiology.

*Other methods papers related to FBAT and PBAT


Horvath S, Laird NM, Knapp M (2000)  The transmission/disequilibrium test and parental genotype reconstruction for X-chromosomal markers.  Amer J Human Gen. 66:1161C1167.

Horvath S, Wei E, Xu X, Palmer L, and Baur M. (2001) Family-based association test method I: Age of onset traits and covariates. Genetic Epi Suppl (GAW 2000). 9:36-42. 

Lake S and Laird N (2004) Tests of gene-environment interaction for case-parent triads with general environmental exposures. Ann Hum Genet. 68:55-64.

Lange C, Blacker D and Laird NM (2003) Family-based association tests for survival and time-to-onset analysis. Statist Med. 22:179-189.

Lange C, DeMeo D and Laird NM (2002) Power calculations for a general class of family-based association tests: Quantitative traits.  Am J Hum Genet. 71:575-584. 

Lange C and Laird NM (2002) Power calculations for a general class of family-based association tests: Dichotomous traits. Am J Hum Genet. 67:575-584.

Lange C and Laird NM (2002) On a general class of conditional tests for family based association studies in genetics: The asymptotic distribution, the conditional power, and optimality considerations. Gen Epi. 23:1-16

Lange C, DeMeo D, Silverman E, Weiss S and Laird NM (2004) PBAT: tools for family-based association studies. Am J Hum Genet. 74:367-9.

Lange C, DeMeo D, Silverman E, Weiss S and Laird NM (2003) Using the noninformative families in family-based association tests: a powerful new testing strategy. Am J Hum Genet. 73:801-11.

Lange C, Lyon H, DeMeo D, Raby BA, Silverman E and Weiss S (2003) A new powerful non-parametric two-stage approach for testing multiple phenotypes in family-based association studies.  Human Heredity, 56:10-17.

Van Steen K, McQueen MB, Herbert A, Raby B, Lyon H, DeMeo DL, Murphy A, Su J, Datta S, Rosenow C, Christman M, Silverman EK, Laird NM, Weiss ST, Lange C. (2005) Genomic screening and replication using the same data set in family-based association testing. Nat Genet. 37:683-91.

Yang Q, Xu X and Laird NM (2003) Power Evaluation for Family-Based Tests of Association with Incomplete Parental Genotypes. Genetics, 164:399-406.

*Reference for the SDT


Horvath S and Laird NM (1998) A Discordant sibship test for disequilibrium and linkage: No need for parental data. Amer J Hum Gen. 63:1886-97.


*Applications


DeMeo DM, Lange C, Silverman EK,  Senter JM, Drazen JM,  Barth MJ,  Laird N, and Weiss ST. (2002) Univariate and multivariate family based analysis of the ARG130GLN polymorphism of the il13 gene in the childhood asthma management program. Genetic Epi. 23:335-348.

Lyon H,  Lange C, Silverman EK,  Senter JM, Drazen JM,  Barth MJ,  Laird N, and Weiss ST. (2004) Univariate and multivariate family based analysis of the il10 gene in the childhood asthma management program. Genetic Epi. 26:155-165.

Saunders AJ, Bertram L, Mullin K, Sampson AJ, Latifzai K, Basu S, Jones J, Kinney D, MacKenzie-Ingano L, Yu S, Albert MS, Moscarillo TJ, Go RC, Bassett SS, Daly MJ, Laird NM, Wang X, Velicelebi G, Wagner SL, Becker DK, Tanzi RE, Blacker D. (2003) Genetic association of Alzheimer disease with multiple polymorphisms in alpha-2-macroblobulin. Hum Mol Genet. 12:2765-76.

Silverman EK, Kwiatkowski DJ, Sylvia JS, Lazarus R, Drazen JM, Lange C, Laird NM, Weiss ST.(2003) Family-based association analysis of beta2-adrenergic receptor polymorphisms in the childhood asthma management program. J Allergy Clin Immunol. 112:870-6.

Smoller JW, Rosenbaum JF, Biederman J, Kennedy J, Dai D, Racette SR, Laird NM, Kagan J, Snidman N, Hirshfeld-Becker D, Tsuang MT, Sklar PB, Slaugenhaupt SA. (2003) Association of a genetic marker at the corticotropin-releasing hormone locus with behavioral inhibition. Biol Psychiatry. 54: 1376-81.

Smoller JW, Yamaki LH, Faterness JA, Biederman J, Racette S, Laird NM et al., (2005) The corticotrophin-releasing hormone gene and behavioral inhibition in children at risk for panic disorder. Biol Psychiatry 57:1485-92.