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QTDT specifications

Information


Unique identifier OMICS_33202
Name QTDT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some matched data and pedigree files.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 2.6.1
Stability Stable
Source code URL http://csg.sph.umich.edu/abecasis/qtdt/download/qtdt-2.6.1.tar.gz
Maintained Yes

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Versioning


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Additional information


http://csg.sph.umich.edu/abecasis/qtdt/docs/index.html

Publication for QTDT

QTDT citations

 (87)
call_split

Familial resemblances in human whole blood transcriptome

2018
BMC Genomics
PMCID: 5921553
PMID: 29703154
DOI: 10.1186/s12864-018-4698-6
call_split See protocol

[…] expression analyses), using a standard least squares model in JMP software v12. We used residuals from this model to compute heritability estimates using the variance component method implemented in QTDT v2.6.1. [] We used full general models in which the variance in gene expression levels of each probe and DNA methylation levels of each CpG site were partitioned into polygenic effects (Vg), comm […]

library_books

GWAS of epigenetic aging rates in blood reveals a critical role for TERT

2018
Nat Commun
PMCID: 5786029
PMID: 29374233
DOI: 10.1038/s41467-017-02697-5

[…] the Haplotype Reference Consortium (N = 64,976). FHS used linear mixed models to account for pedigree structure via a kinship matrix, as implemented in R “lmekin” package. The BSGS cohort used Merlin/QTDT for family-based association analysis. For other association analyses, we regressed the age acceleration trait values on estimated genotype dosage (counts of test alleles) or expected genotype do […]

library_books

cophesim: a comprehensive phenotype simulator for testing novel association methods

2017
F1000Res
PMCID: 5605948
PMID: 28979766
DOI: 10.5256/f1000research.12938.r24718

[…] Output files are in the formats as the direct inputs for the following tools: EMMAX , Blossoc , Plink (.ped file), QTDT , TASSEL , GenABEL (see ). […]

call_split

The DCDC2 deletion is not a risk factor for dyslexia

2017
PMCID: 5538127
PMID: 28742079
DOI: 10.1038/tp.2017.151
call_split See protocol

[…] ribed protocol and checked for Mendelian errors and deviation from Hardy-Weinberg equilibrium using PEDSTATS. Family-based cohorts were tested using the Quantitative Transmission Disequilibrium Test (QTDT) under the total association model after estimating the identical-by-descent (IBD) sharing with MERLIN. No population stratification was observed for the UK cohorts following analysis of genome-w […]

call_split

Rs12970134 near MC4R is associated with appetite and beverage intake in overweight and obese children: A family based association study in Chinese population

2017
PLoS One
PMCID: 5433775
PMID: 28520814
DOI: 10.1371/journal.pone.0177983
call_split See protocol

[…] . For the analyses of quantitative variables in trios, PBAT software package [] was used. As compared to other computer programs that are available for family-based association tests, including FBAT, QTDT [] and PDT [], PBAT was considered to have the advantage of handling various trait types, could include covariates and gene/covariate-interactions, and P values could be computed on the basis of […]

library_books

Transmission and decorrelation methods for detecting rare variants using sequencing data from related individuals

2016
BMC Proc
PMCID: 5133523
PMID: 27980637
DOI: 10.1186/s12919-016-0031-z

[…] between-family information, which could explain why the FBAT tests generally had lower power than MONSTER. Recently, a new method was developed that addresses both of these issues by integrating the QTDT (quantitative transmission disequilibrium test) framework [] into the kernel based model, KMFAM []. Another possible explanation of the differences seen between FBAT and MONSTER is that FBAT only […]

Citations

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QTDT institution(s)
The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
QTDT funding source(s)
Supported by the Wellcome Trust, a Wellcome Trust Prize Studentship and a Wellcome Trust Senior Clinical Research Fellow.

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