AncesHC 2009 – Association Tests by Inferring Ancestral Haplotypes using a Hidden Markov Model

AncesHC 2009

:: DESCRIPTION

AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 AncesHC

:: MORE INFORMATION

Citation

Shu-Yi Su, David J. Balding and Lachlan J.M. Coin
Disease association tests by inferring ancestral haplotypes using a hidden markov model
Bioinformatics (2008) 24 (7): 972-978.

OVPDT – A Family-based Association Test for Sequencing Data

OVPDT

:: DESCRIPTION

OVPDT (Ordered Subset – Variable Threshold – Pedigree Disequilibrium Test) is a family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OVPDT

:: MORE INFORMATION

Citation

PLoS One. 2014 Sep 22;9(9):e107800. doi: 10.1371/journal.pone.0107800. eCollection 2014.
Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
Chung RH, Tsai WY, Martin ER

OPTPDT – Family-based multi-SNP Association Test

OPTPDT

:: DESCRIPTION

OPTPDT (Optimal P-value Threshold Pedigree Disequilibrium Test)is a family-based multi-SNP association test. A variable p-value threshold algorithm is used in the test to select an optimal subset of SNPs that has the strongest association signals.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OPTPDT

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 15;16:381. doi: 10.1186/s12864-015-1620-3.
A multi-SNP association test for complex diseases incorporating an optimal P-value threshold algorithm in nuclear families.
Wang YT, Sung PY, Lin PL, Yu YW, Chung RH

SIBASS 1.4 – Association Test using Siblings as Controls

SIBASS 1.4

:: DESCRIPTION

SIBASSOC is a program for carrying out association studies using siblings as controls.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SIBASS

:: MORE INFORMATION

Citation:

Curtis, 1997.
Use of siblings as controls in case-control association studies.
Ann Hum Genet, 61.

XQTL 1.0 – Gamily-based Allelic / Haplotype Association Test

XQTL 1.0

:: DESCRIPTION

XQTL is a family-based allelic/haplotype association test for quantitative traits using X-linked SNP/two-locus markers in a nuclear family design. XQTL adopts the framework of the orthogonal model implemented in the QTDT program with modification of the sex-specific score for X-linked genotypes. XQTL also takes into account the dosage effect due to female X chromosome inactivation.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Unix/Windows

:: DOWNLOAD

 XQTL

:: MORE INFORMATION

Citation

Zhang L, Martin ER, Morris RW, Li YJ. (2009)
Association test for X-linked QTL in family-base d designs.
American Journal of Human Genetics

GenGen 20100624 – Pathway-based Association Tests

GenGen 20100624

:: DESCRIPTION

GenGen (Genetic Genomics Analysis of Complex Data) is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GenGen

:: MORE INFORMATION

Reference:

Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genome-wide association studies. American Journal of Human Genetics, 81:1278-1283, 2007
Wang K, (27 authors), et al. Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn disease. American Journal of Human Genetics, 84:399-405, 2009
Wang K, (55 authors), et al. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature, 459:528-533, 2009

FBAT 2.0.4 – Family-Based Association Test

FBAT 2.0.4

:: DESCRIPTION

FBAT is an acronym for Family-Based Association Tests in genetic analyses. Family-based association designs, as opposed to case-control study designs, are particularly attractive, since they test for linkage as well as association, avoid spurious associations caused by admixture of populations, and are convenient for investigators interested in refining linkage findings in family samples.

::DEVELOPER

FBAT-Toolkit Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX /Sun Workstations

:: DOWNLOAD

FBAT

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2001 Apr;9(4):301-6.
The family based association test method: strategies for studying general genotype–phenotype associations.
Horvath S1, Xu X, Laird NM.

TADA 20140624 – Transmission And De novo Association test

TADA 20140624

:: DESCRIPTION

TADA is a novel statistical method that utilizes inherited variation transmitted to affected offspring in conjunction with (de novo) mutations to identify risk genes.

::DEVELOPER

COMPUTATIONAL GENETICS LAB At the UNIVERSITY OF PITTSBURGH MEDICAL CENTER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package

:: DOWNLOAD

 TADA

:: MORE INFORMATION

Citation

PLoS Genet. 2013 Aug;9(8):e1003671. doi: 10.1371/journal.pgen.1003671.
Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.
He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.

CRaVe 0.0.2 – Association Tests between sets of SNPs and a Phenotype

CRaVe 0.0.2

:: DESCRIPTION

CRaVe is a free, open source, software package designed to perform a range of association tests between sets of SNPs and a phenotype.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 CRaVe

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2013 Jun;21(6):680-6. doi: 10.1038/ejhg.2012.220. Epub 2012 Oct 24.
Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation.
Ferguson J, Wheeler W, Fu Y, Prokunina-Olsson L, Zhao H, Sampson J.

qMSAT – Quality-based Multivariate Score Association Test

qMSAT

:: DESCRIPTION

qMSAT is a powerful test that directly incorporates sequencing qualities in association tests with multiple rare variants. It allows for the adjustment of additional covariates and is robust towards the inclusion of noncausal variants and variants having effects with different magnitudes and directions. Furthermore, it can coherently account for missing genotypes and conjoin in a principled way individuals or variants sequenced at varying coverage depths.

::DEVELOPER

Zhi Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 qMSAT

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Apr;40(8):e60. doi: 10.1093/nar/gks024. Epub 2012 Jan 19.
A powerful test for multiple rare variants association studies that incorporates sequencing qualities.
Daye ZJ, Li H, Wei Z.