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ASSOCIATION AND TDT PROGRAMS

ETDT (Extended Transmission/Disequilibrium Test)
*Description Extended transmission/disequilibrium test. TDT test on markers with more than two alleles using a logistic regression analysis.
Authors PC Sham, Dave Curtis
References Sham PC, Curtis D. (1995). Ann Hum Genet, 59, 323-336.
Website http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

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ET-TDT (Evolutionary Tree - Transmission Disequilibrium Test)
*Description Evolutionary Tree - Transmission Disequilibrium Test. Transmission/Disequilibrium Test Meets Measured haplotype analysis: family-based association analysis guided by evolution of haplotypes.
Authors Kathryn Roeder (Carnegie Mellon University)
References Seltman H, Roeder K, Devlin B. (2001). Transmission/Disequilibrium Test Meets Measured haplotype analysis: family-based association analysis guided by evolution of haplotypes. Am J Hum Genet, 68:1250-1263.
Website http://www.stat.cmu.edu/~roeder/=ettdt/

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FBAT (Family Based Association Test)
*Description Haplotype FBAT is a user-friendly, well-documented software that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, "SDT" and "Rabinowitz TDT" for nuclear families (not supported anymore).
Authors Xin Xu, Steve Horvath, Nan Laird (Harvard Univ)
References
  • Laird NM. (2004). Family based tests for associating haplotypes with general phenotype data: application to asthma genetics. Genet. Epidemiol, 26(1):61-69.
  • Laird NM, Horvath S, Xu X. (2000). Implementing a unified approach to family based tests of association, Genetic Epi., supp. 1, 19:36-42.
  • Rabinowitz, Laird NM. (2000). A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum. Heredity, 50:211-223.
  • Horvath S, Xu X, Laird NM. (2001). The family based association test method: strategies for studying general genotype-phenotype associations, European J. Hum. Genet. 9:301-306.
Website http://www.biostat.harvard.edu/~fbat/fbat.htm

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GASSOC (Genetic ASSOCiation)   
*Description Statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms.
Authors D. J. Schaid, C. M. Rowland (Mayo Clinic/Foundation)
References
  • Am Soc Hum Genet annual meeting, 1996.
  • Rowland CM, Schaid DJ. (1996). Am J. Hum Genet, suppl, 59, A234.
  • Schaid DJ. (1996). Genetic Epidemiology, 13, 423-449.
Website http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

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LAMP
*Description LAMP uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees. It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.
Author Li M, Boehnke M, and Abecasis GR
References Li M, Boehnke M, and Abecasis GR (2005). Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal. Am J Hum Genet 76:934-949.
Website http://www.sph.umich.edu/csg/abecasis/LAMP/

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PDT (Pedigree Disequilibrium Test)
*Description Pedigree disequilibrium test. The PDT analysis program allows the user to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets.
Author Eden Martin (Duke Univ)
References Martin ER, Monks SA, Warren LL, Kaplan NL. (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test (PDT). Am J Hum Genet 67:146-154
Website http://www.chg.duke.edu/software/pdt.html

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QTDT (Quantitative (Trait) Transmission/Disequilibrium Test)  
*Description Quantitative (Trait) Transmission/Disequilibrium Test. Performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation.
Authors Goncalo Abecasis
References Abecasis GR, Cardon L, Cookson WOC. (2000). A general test of association for quantitative traits in nuclear families. Am J Hum Genet, 66, 279-292.
Website http://www.sph.umich.edu/csg/abecasis/QTDT/

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RC-TDT (Reconstruction-Combined Transmission Disequilibrium Test)
*Description Reconstruction-Combined Transmission Disequilibrium Test. A family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. The distribution contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values.
Authors Michael Knapp (Univ Bonn)
References
  • Knapp M. (1999). The transmission/disequilibrium test and parental-genotype reconstruction: the reconstruction-combined transmission/disequilibrium test. Am J Human Genet, 64:861-870.
  • Knapp M. (1999b). Using exact P values to compare the power between the reconstruction-combined transmission/disequilibrium test and the sib transmission/disequilibrium test. Am J Human Genet, 65:1208-1210.
  • Horvath S, Laird NM, Knapp M. (2000). The transmission/disequilibrium test and parental-genotype reconstruction for X-chromosomal markers, Am J Human Genet, 66:1161-1167.
Website http://www.uni-bonn.de/~umt70e/soft.htm

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SNP ASSISTANT
*Description SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects.
Authors Biodata Ltd., Estonia
References Online manual
Website http://www.biodata.ee/SNPassistant.htm

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TDT-AE (Transmission Disequilibrium Test Allowing for Errors)
*Description Transmission Disequilibrium Test Allowing for Errors. This program computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors.
Authors Chad Haynes,  Derek Gordon, Xin Liu
References
  • Gordon D, Heath SC, Liu X, Ott J. (2001). A Transmission/Disequilibrium Test That Allows for Genotyping Errors in the Analysis of Single-Nucleotide Polymorphism Data. Am J Hum Genet, 69:371-380.
  • Gordon D, Haynes C, Johnnidis C, Patel SB, Bowcock AM, Ott J. (2004). A transmission disequilibrium test for general pedigrees that is robust to the presence of random genotyping errors and any number of untyped parents. Eur J Hum Genet.
  • User's Guide
Website ftp://linkage.rockefeller.edu/software/tdtae2

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TDTHAP (Transmission Disequilibrium Test with extended HAPlotypes)
*Description A package for TDT with extended haplotypes in the "R" language. "R" is the public domain dialect of "S". It should be possible to port this library to the commercial "Splus" product. The main problem would be translation of the help files.
Authors David Clayton (Cambridge Institute)
References Clayton D, Jones H. (1999). Transmission/Disequilibrium Tests for Extended Marker Haplotypes. Am J Hum Genet, 65:1161-1169
Website http://www-gene.cimr.cam.ac.uk/clayton/software/

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TDT/S-TDT
*Description Transmission Disequilibrium Test and Sib Transmission Disequilibrium Test. The program provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate.
Authors Info not available
References
  • Spielman RS, McGinnis RE, Ewens WJ. (1993). Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet, 52:506-516.
  • Spielman RS, Ewens WJ. (1998). A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet, 62:450-458
Website http://genomics.med.upenn.edu/spielman/TDT.htm

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TRANSMIT
*Description TRANSMIT tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are:
  1. It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and
  2. Parental genotypes may be unknown.
Authors David Clayton (Cambridge Institute)
References Online document
Website http://www-gene.cimr.cam.ac.uk/clayton/software/

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* Description retrieved from http://linkage.rockefeller.edu/soft/