[en] The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes. The data analysis can be adjusted for covariates and gene/environment interactions. Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands. PBAT's screening tools allow the user successfully to handle the multiple comparisons problem at a genome-wide level, even for 100,000 SNPs and more. Moreover, PBAT is computationally fast. A genome scan of 300,000 SNPs in 2,000 trios takes 4 central processing unit (CPU)-days. PBAT is available for Linux, Sun Solaris and Windows XP.
Disciplines :
Physical, chemical, mathematical & earth Sciences: Multidisciplinary, general & others
Author, co-author :
Van Steen, Kristel ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Lange, C.
Language :
English
Title :
PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.
Bibliography
Lange, C., DeMeo, D.L., Silverman, E. et al. (2003), 'Using the non-informative families in family-based association tests: A powerful new testing strategy', Am. J. Hum. Genet. Vol. 73, pp. 801-811.
Lange, C., Lyon, H., DeMeo, D.L. et al. (2003), 'A new powerful non-parametric two-stage approach for testing multiple phenotypes in family-based association studies', Hum. Hered. Vol. 56, pp. 10-17.
Van Steen, K., McQueen, M.B., Herbert, A. et al. (2005), 'Genomic screening in family based association testing for quantitative traits', Nat. Genet. (under review).
Cordell, H.J. and Clayton, D.G. (2002), 'A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: Application to HLA in Type 1 diabetes', Am. J. Hum. Genet. Vol. 70, pp. 124-141.
Thomson, G. (1995), 'Mapping disease genes: Family-based association studies', Am. J. Hum. Genet. Vol. 57, pp. 487-498.
Abecasis, G.R., Cardon, L.R. and Cookson, W.O.C. (2000), 'A general test of association for quantitative traits in nuclear families', Am. J. Hum. Genet, Vol. 66, pp. 279-292.
Horvath, S. and Laird, N. (1998), 'Discordant sibship test for disequilibrium/transmission: No need for parental data', Am. J. Hum. Genet. Vol. 63, pp. 1886-1897.
Horvath, S., Xin, X. and Laird, N.M. (2000), 'The family based association test method: Computing means and variances for general statistics', Technical Report, http://www.biostat.harvard.edu/fbat/ fbattechreport.ps.
Horvath, S., Xu, X. and Laird, N.M. (2001), 'The family based association test method: Strategies for studying general genotype-phenotype associations', Eur. J. Hum. Genet. Vol. 9, pp. 301-306.
Laird, N.M., Horvath, S. and Xu, X. (2000), 'Implementing a unified approach to family-based tests of association', Genet. Epidemiol. Vol. 19(1), pp. S36-S42.
Lake, S., Blacker, D. and Laird, N.M. (2000), 'Family-based tests of association in the presence of linkage', Am. J. Hum. Genet. Vol. 67, pp. 1515-1525.
Clayton, D. (1999), 'A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission', Am. J. Hum. Genet. Vol. 65, pp. 1170-1177.
Martin, E.R., Monks, S.A., Warren, L.L. et al. (2000), 'A test for linkage and association in general pedigrees: the pedigree disequilibrium test (PDT)', Am. J. Hum. Genet. Vol. 67, pp. 146-154.
Lange, C., DeMeo, D.L., Silverman, E.K. et al. (2004), 'PBAT: Tools for family-based association studies', Am. J. Hum. Genet. Vol. 74, pp. 367-369.
Lange, C. and Laird, N.M. (2002), 'Power calculations for a general class of family-based association tests: Dichotomous traits', Am. J. Hum. Genet. Vol. 67, pp. 575-584.
Lange, C., DeMeo, D. and Laird, N.M. (2002), 'Power calculations for a general class of family-based association tests: Quantitative traits', Am. J. Hum. Genet. Vol. 71, pp. 575-584.
Rabinowitz, D. and Laird, N.M. (2000), 'A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information', Hum. Hered. Vol. 50, pp. 227-233.
Spielman, R.S., McGinnis, R.E. and Ewens, W.J. (1993), 'Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM)', Am. J. Hum. Genet. Vol. 65, pp. 578-580.
The International HapMap Consortium (2003), 'The International HapMap Project', Nature Vol. 426, pp. 789-796.
Horvath, S., Xu, X., Lake, S.L. et al. (2004), 'Family-based tests for associating haplotypes with general phenotype data: Application to asthma genetics', Genet. Epidemiol. Vol. 26, pp. 61-69.
DeMeo, D.L., Lange, C., Silverman, E.K. et al. (2002), 'Univariate and multivariate family-based association analysis of the IL-13 ARG130GLN polymorphism in the Childhood Asthma Management Program', Genet. Epidemiol. Vol. 23, pp. 335-348.
Lange, C., Van Steen, K., Andrew, T. et al. (2004), 'A family-based association test for repeatedly measured quantitative traits adjusting for unknown environmental and/or polygenic effects', Stat. Appl. Genet. Mol. Biol. Vol. 1(l), Article 17, http://www.bepress.com/sagmb/vol3/iss1/ art17.
Similar publications
Sorry the service is unavailable at the moment. Please try again later.
This website uses cookies to improve user experience. Read more
Save & Close
Accept all
Decline all
Show detailsHide details
Cookie declaration
About cookies
Strictly necessary
Performance
Strictly necessary cookies allow core website functionality such as user login and account management. The website cannot be used properly without strictly necessary cookies.
This cookie is used by Cookie-Script.com service to remember visitor cookie consent preferences. It is necessary for Cookie-Script.com cookie banner to work properly.
Performance cookies are used to see how visitors use the website, eg. analytics cookies. Those cookies cannot be used to directly identify a certain visitor.
Used to store the attribution information, the referrer initially used to visit the website
Cookies are small text files that are placed on your computer by websites that you visit. Websites use cookies to help users navigate efficiently and perform certain functions. Cookies that are required for the website to operate properly are allowed to be set without your permission. All other cookies need to be approved before they can be set in the browser.
You can change your consent to cookie usage at any time on our Privacy Policy page.