Tag: Association Test

TADA – Transmission And De novo Association test

TADA

:: 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

The Devlin lab

:: 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.

FBAT v2.05_beta – Family-Based Association Test

FBAT v2.05_beta

:: 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.

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

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.

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.

ATOM – Association Test via Optimally-weighted Markers

ATOM

:: DESCRIPTION

ATOM is a software of powerful gene-based Association Test by combining Optimally Weighted Markers within a genomic region. Due to variation in linkage disequilibrium, different markers often associate with the trait of interest at different levels.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ATOM

:: MORE INFORMATION

Citation

Li M, Wang K, Grant SF, Hakonarson H, Li C (2009)
ATOM: A powerful gene-based association test by combining optimally weighted markers.
Bioinformatics 25:497-503 (PMID: 19074959)

 

iECAT 0.8 – Integrating External Controls into Association Test

iECAT 0.8

:: DESCRIPTION

iECAT is an R-package to test for single variant and gene/region-based associations using external control samples.

::DEVELOPER

Lee lab for Statistical Genetics and Data Science

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

iECAT

:: MORE INFORMATION

Citation

Li Y, Lee S.
Novel score test to increase power in association test by integrating external controls.
Genet Epidemiol. 2021 Apr;45(3):293-304. doi: 10.1002/gepi.22370. Epub 2020 Nov 8. PMID: 33161601.

MQLS 1.5 – Case-Control Association Testing with Related Individuals

MQLS 1.5

:: DESCRIPTION

MQLS (More Powerful Quasi-Likelihood Score Test)can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts (“dosages”) generated by MACH and an empirical variance estimator.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

  MQLS

:: MORE INFORMATION

Reference

Thornton T., McPeek M. S. (2007)
Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test.
Am J Hum Genet, 81, 321-337.

GenGen 1.0.1 – Pathway-based Association Tests

GenGen 1.0.1

:: 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

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)