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A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis

Rui Chen, Qiang Wei, Xiaowei Zhan, Xue Zhong, James S. Sutcliffe, Nancy J. Cox, Edwin H. Cook, Chun Li, Wei Chen, Bingshan Li
2015 Computer applications in the biosciences : CABIOS  
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

Yong-Jun Liu, Peng-Yuan Liu, Jirong Long, Yan Lu, Leo Elze, Robert R. Recker, Hong-Wen Deng
2005 Physiological Genomics  
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

Cen Wu, Shaoyu Li, Yuehua Cui
2012 Current Genomics  
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

Yong-Jun Liu, Sonia M.S. Rocha-Sanchez, Peng-Yuan Liu, Ji-Rong Long, Yan Lu, Leo Elze, Robert R. Recker, Hong-Wen Deng
2004 Physiological Genomics  
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

Tongtong Lan, Bo Yang, Xuefen Zhang, Tong Wang, Qing Lu
2019 Current Genomics  
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

S. C. Lim, J. J. Liu, H. Q. Low, N. G. Morgenthaler, Y. Li, L. Y. Yeoh, Y. S. Wu, S. K. Goh, C. Y. Chionh, S. H. Tan, Y. C. Kon, P. C. Soon (+4 others)
2009 Diabetologia  
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

Tie-Lin Yang, Dong-Hai Xiong, Yan Guo, Robert R. Recker, Hong-Wen Deng
2006 Human Genetics  
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

Hugh M. D. Gurling, Hugo Critchley, Susmita R. Datta, Andrew McQuillin, Ekaterina Blaveri, Srinivasa Thirumalai, Jonathan Pimm, Robert Krasucki, Gursharan Kalsi, Digby Quested, Jacob Lawrence, Nicholas Bass (+11 others)
2006 Archives of General Psychiatry  
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

D-H Xiong
2005 Journal of Medical Genetics  
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

Rui Chen, Lea K. Davis, Stephen Guter, Qiang Wei, Suma Jacob, Melissa H. Potter, Nancy J. Cox, Edwin H. Cook, James S. Sutcliffe, Bingshan Li
2017 Molecular Autism  
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)

S. Han, X. Kim-Howard, H. Deshmukh, Y. Kamatani, P. Viswanathan, J. M. Guthridge, K. Thomas, K. M. Kaufman, J. Ojwang, A. Rojas-Villarraga, V. Baca, L. Orozco (+16 others)
2009 Human Molecular Genetics  
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

S J Glatt, S V Faraone, J A Lasky-Su, T Kanazawa, H-G Hwu, M T Tsuang
2008 Molecular Psychiatry  
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

Stephen Bates, Matteo Sesia, Chiara Sabatti, Emmanuel Candès
2020 Proceedings of the National Academy of Sciences of the United States of America  
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  
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

Ian NM Day, Dongfeng Gu, Rosalind H Ganderton, Emmanuel Spanakis, Shu Ye
2001 International Journal of Epidemiology  
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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