gTDT 0.01 – A group-wise TDT for Haplotype-based Association Testing of Rare Variants with complex Disease

gTDT 0.01

:: DESCRIPTION

gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.

::DEVELOPER

gTDT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

gTDT

:: MORE INFORMATION

Citation

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.
Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe J, Cox N, Cook EH, Li C, Chen W, Li B.
Bioinformatics. 2015 Jan 6. pii: btu860.

Genie 2.7.2.1 – Analyze Association and Transmission Disequilibrium (TDT)

Genie 2.7.2.1

:: DESCRIPTION

GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests

::DEVELOPER

Genetic Epidemiology University of Utah

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

Genie

:: MORE INFORMATION

Citation

Allen-Brady K, Wong J, Camp NJ (2006).
PedGenie: An Analysis Approach for Genetic Association Testing in Extended Pedigrees and Genealogies of Arbitrary Size.
BMC Bioinformatics 2006 7:209

Curtin K, Wong J, Allen-Brady K, Camp NJ (2007).
PedGenie: Meta Genetic Association Testing in Mixed Family and Case-Control Designs.
BMC Bioinformatics 2007 8:448

Curtin K, Wong J, Allen-Brady K, Camp NJ (2007).
Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1
BMC Proc. 2007;1 Suppl 1:S12. Epub 2007 Dec 18

TDT Power Calculator 1.2.1 – Power Calculation for the TDT

TDT Power Calculator 1.2.1

:: DESCRIPTION

TDT Power Calculator is a software for Power Calculation for the TDT (Transmission disequilibrium test).

::DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

TDT Power Calculator

:: MORE INFORMATION

Citation

Chen WM and Deng HW (2001).
A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes.
Genet Epidemiol 21:53-67

rTDT 1.0 – software for TDT with missing data

rTDT 1.0

:: DESCRIPTION

rTDT (robust TDT) handles incomplete genotypes on both parents and children and that does not rest on any assumption about the missing data mechanism. rTDT returns minimum and maximum values of TDT ( the transmission disequilibrium test) that are consistent with all the possible completions of the missing data. We also show that, in some situations, rTDT can achieve both greater power and greater significance than the popular TDT analysis of incomplete data. rTDT is applied to a database of markers of susceptibility to Crohn’s disease and it shows that only 2 of the 11 markers originally associated with the phenotype do not depend on assumptions about the missing data mechanism.

::DEVELOPER

Bios, University of GranadaGranada , Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
C Compiler
Matlab

:: DOWNLOAD

rTDT

:: MORE INFORMATION

Citation:

Sebastiani, P; Abad, M.M.; Alpargu, G; Ramoni, M.F.
“Robust Transmission/Disequilibrium Test for Incomplete Family Genotypes“,
Genetics 168, 2329-2337, 2004