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A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis
2015
Computer applications in the biosciences : CABIOS
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Results: In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous ...
Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to ...
Acknowledgement The authors thank Goncalo Abecasis in the Department of Biostatistics at the University of Michigan for sharing the Cþþ code for processing pedigrees. ...
doi:10.1093/bioinformatics/btu860
pmid:25568282
pmcid:PMC4410665
fatcat:tlu3h4cwyfe5bddrz36bhlcezu
Linkage and association analyses of the UCP3 gene with obesity phenotypes in Caucasian families
2005
Physiological Genomics
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In this study, using the quantitative transmission disequilibrium test (QTDT), we assessed linkage and association between the UCP3 gene and obesity phenotypes in a large sample of 1,873 subjects from ...
In haplotype analyses, we also observed evidence of linkage (P ϭ 0.002) and association (P ϭ 0.035) with BMI. ...
Haplotypes can also provide more information for the transmission disequilibrium test analyses. However, one trade off is the increase in the degrees of freedom of the test. ...
doi:10.1152/physiolgenomics.00031.2005
pmid:15870396
fatcat:5siqlhhhkvetpicuodrz3tavue
Genetic Association Studies: An Information Content Perspective
2012
Current Genomics
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This paper is intended to give a comprehensive review of the current literature in genetic association analysis casted in the framework of information theory. ...
A handful of novel genetic variants have been identified, which gives much hope and prospects for the future of genetic association studies. ...
One of the commonly used methods in a family-based association study is the Transmission Disequilibrium Test (TDT) [33] . ...
doi:10.2174/138920212803251382
pmid:23633916
pmcid:PMC3468889
fatcat:pkg5hsr7pndfxd7y3zthij7kga
Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families
2004
Physiological Genomics
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Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families. ...
Important to this study is that we employed a robust approach, the family-based transmission disequilibrium test (TDT), which is immune to population stratification, a potential confounding factor to population-based ...
leptin receptor; quantitative transmission disequilibrium test THE DISCOVERY OF LEPTIN and its receptor, LEPR, has defined a novel molecular pathway for energy metabolism and regulation of body weight ...
doi:10.1152/physiolgenomics.00213.2003
pmid:14970363
fatcat:uvayng7zafatrdnmh6ebv4i4ou
Statistical Methods and Software for Substance Use and Dependence Genetic Research
2019
Current Genomics
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During the past few decades, a great deal of progress has been made in identifying genetic variants associated with substance use and dependence (SUD) through linkage, candidate gene association, genome-wide ...
association, and sequencing studies. ...
The well-known method for caseparent trio design is the Transmission Disequilibrium Test (TDT) [56] . ...
doi:10.2174/1389202920666190617094930
pmid:31929725
pmcid:PMC6935956
fatcat:5ws6ubrwazgrreqwuhtdlgyuka
Microarray analysis of multiple candidate genes and associated plasma proteins for nephropathy secondary to type 2 diabetes among Chinese individuals
2009
Diabetologia
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Common NOS1 and Diabetologia (rare NOX1 variants also revealed a suggestive association with diabetic nephropathy. Future studies to validate our observation are needed. Keywords Candidate genes . ...
Results No single nucleotide polymorphism (SNP) remained significant in single locus analysis after correction for multiple testing. Therefore, we explored the best ∼1% SNPs. ...
We would like to thank our colleagues at the Ang Mo Kio and Tao Payoh Polyclinics, and the National Health Group Polyclinic, Singapore for their help in recruiting study volunteers. ...
doi:10.1007/s00125-009-1368-x
pmid:19415232
fatcat:q5aftx6dlzhp5hlkwbrnir6c3e
Association analyses of CYP19 gene polymorphisms with height variation in a large sample of Caucasian nuclear families
2006
Human Genetics
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disequilibrium test) and FBAT (family-based association test) in 1,873 subjects from 405 Caucasian nuclear families. ...
In the present study, we aimed to test the associations between the CYP19 gene polymorphisms with adult height variation, using family-based association methods, such as QTDT (quantitative transmission ...
The quantitative transmission disequilibrium test (QTDT) and the family-based association test (FBAT) (Horvath et al. 2001 ) were used to test the tagging SNPs and haplotypes with estimated frequencies ...
doi:10.1007/s00439-006-0199-9
pmid:16733710
pmcid:PMC1829483
fatcat:ay3vent3ufem7ekyawiglukqpi
Genetic Association and Brain Morphology Studies and the Chromosome 8p22 Pericentriolar Material 1 (PCM1) Gene in Susceptibility to Schizophrenia
2006
Archives of General Psychiatry
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Main Outcome Measures: Tests of transmission disequilibrium between PCM1 locus polymorphisms and schizophrenia using a family sample and tests of allelic association in case-control and trio samples. ...
Variation in brain morphology associated with pericentriolar material 1 (PCM1) alleles was examined using voxel-based morphometry and statistical parametric mapping with magnetic resonance imaging. ...
the US Trio Sample* Transmission Dinucleotide Repeat Lengths and Allele Counts Abbreviations: bp, base pairs; TDT, transmission disequilibrium test. * 2 9 for allele-wise TDT = 18.88, P = .03. 2 25 for ...
doi:10.1001/archpsyc.63.8.844
pmid:16894060
pmcid:PMC2634866
fatcat:yev2lf4ftbdmpegmxi4puitxtu
Vitamin D receptor gene polymorphisms are linked to and associated with adult height
2005
Journal of Medical Genetics
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QTDT (quantitative transmission disequilibrium test). ...
Analyses based on BsmI/TaqI haplotypes also revealed evidence for linkage (p = 0.05) and association (p = 0.001) with height. ...
However, given potential population stratification, population associations could lead to spurious results. 22 In comparison, family based approaches, such as the transmission disequilibrium test (TDT ...
doi:10.1136/jmg.2004.024083
pmid:15744036
pmcid:PMC1736013
fatcat:cyed3evpcrffpa5qfdq32ofgia
Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism
2017
Molecular Autism
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Finally, we carried out rare variant group-wise transmission disequilibrium tests (gTDT) and observed significant association of rare variants in genes encoding a subset of the serotonin pathway with ASD ...
Through analysis of rare recessively acting variants (RAVs), we also found that rare compound heterozygotes (CHs) in the High-5HT group were enriched for loci in an ASD-associated gene set. ...
We would like to thank the individuals with ASD and their family members for their participation. ...
doi:10.1186/s13229-017-0130-3
pmid:28344757
pmcid:PMC5361831
fatcat:wtmvklle3belpm7fbaetmjto5e
Evaluation of imputation-based association in and around the integrin- -M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE)
2009
Human Molecular Genetics
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We would like to thank the PROFILE Study Group (Drs Michelle Petri, John Reveille, Rosalind Ramsey-Goldman, Jeffrey Edberg and Graciela Alarcón) for contributing samples. ...
ACKNOWLEDGEMENTS These authors are grateful to the patients and their families for their cooperation and blood samples. ...
association test in a frequentist framework. ...
doi:10.1093/hmg/ddp007
pmid:19129174
pmcid:PMC2649018
fatcat:tiee6ziuuneijpjxbfqxo4pr3u
Family-based association testing strongly implicates DRD2 as a risk gene for schizophrenia in Han Chinese from Taiwan
2008
Molecular Psychiatry
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Our objective was to test 21 haplotype-tagging and all three known nonsynonymous singlenucleotide polymorphisms (SNPs) in DRD2 for association with schizophrenia in a familybased study of 2408 Han Chinese ...
and no adequately powered family-based association study has been performed to date. ...
Acknowledgments This work was supported in part by a Young Investigator Award from NARSAD ...
doi:10.1038/mp.2008.30
pmid:18332877
pmcid:PMC2755547
fatcat:eu43vodxq5hf3lg2rj3qn2q2x4
Causal inference in genetic trio studies
2020
Proceedings of the National Academy of Sciences of the United States of America
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We compare our method to the widely used transmission disequilibrium test and demonstrate enhanced power and localization. ...
We make this observation actionable by developing a conditional independence test that identifies regions of the genome containing distinct causal variants. ...
known as family-based association tests. ...
doi:10.1073/pnas.2007743117
pmid:32948695
pmcid:PMC7533659
fatcat:vmlgey7wsrfr3pf7je3apv4nre
44th European Mathematical Genetics Meeting (EMGM) 2016. Newcastle upon Tyne, UK, May 11-12, 2016: Abstracts
2015
Human Heredity
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We adapt this model to the genetic association setting in order to identify features predictive of shared associations at a SNP, accounting for the marginal trait associations; each subject corresponds ...
The AMMI model combines analysis of variance (ANOVA) for the main effects of genotype and environment and uses principal component analysis (PCA) only for interaction GxE. ...
The allele counts of each SNP were weighted by their respective natural logarithm of the Odds Ratio values found from a recent Genome Wide Association Study by the Schizophrenia Working Group of the Psychiatric ...
doi:10.1159/000445228
pmid:27111916
fatcat:553k64equ5f7lkbhpwun7nbgkm
Epidemiology and the genetic basis of disease
2001
International Journal of Epidemiology
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Acknowledgements Ian NM Day is a Lister Institute Professor (1996)(1997)(1998)(1999)(2000). Dongfeng Gu was a Royal Society Visiting Professor 1999-2000. ...
The 'control' is not a real individual, but consists of the two parental alleles that have not been transmitted to the affected child Transmission disequilibrium test Examining transmission of marker allele ...
Classical examples predating DNA-based genotyping, include association studies of HLA and ABO blood group. ...
doi:10.1093/ije/30.4.661
pmid:11511580
fatcat:bifazi3fxzb3bhhlmr64yh75j4
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