PSAT – Population Stratification Association Test

PSAT

:: DESCRIPTION

PSAT (Population Stratification Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease with stratification. Population stratification can be a serious obstacle in the analysis of genome-wide association studies. We have developed a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes account not only of the population structure but also of the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false positive rates than existing methods. In addition, it can be easily applied to whole genome association studies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows with Cygwin /Linux

:: DOWNLOAD

  PSAT

:: MORE INFORMATION

Citation

A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)

RAT – A software for Rapid Association Tests

RAT

:: DESCRIPTION

RAT (Rapid Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease. The main advantage of RAT is its ability to calculate accurately and quickly high significance disease association. For large data set and low p-values, RAT is 2-4 orders of magnitude faster than the standard permutation test.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows with Cygwin /Linux

:: DOWNLOAD

  RAT

:: MORE INFORMATION

Citation

Gad Kimmel and Ron Shamir.
A Fast Method for Computing High Significance Disease Association in Large Population-Based Studies.
Am. J. Hum. Genet. 2006

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

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.

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.