Issue Special Issue 1/2014
Genetic Analysis Workshop 18: Human sequence data in extended pedigrees
Content (112 Articles)
Genetic Analysis Workshop 18: Methods and strategies for analyzing human sequence and phenotype data in members of extended pedigrees
Heike Bickeböller, Julia N Bailey, Joseph Beyene, Rita M Cantor, Heather J Cordell, Robert C Culverhouse, Corinne D Engelman, David W Fardo, Saurabh Ghosh, Inke R König, Justo Lorenzo Bermejo, Phillip E Melton, Stephanie A Santorico, Glen A Satten, Lei Sun, Nathan L Tintle, Andreas Ziegler, Jean W MacCluer, Laura Almasy
Data for Genetic Analysis Workshop 18: human whole genome sequence, blood pressure, and simulated phenotypes in extended pedigrees
Laura Almasy, Thomas D Dyer, Juan M Peralta, Goo Jun, Andrew R Wood, Christian Fuchsberger, Marcio A Almeida, Jack W Kent Jr, Sharon Fowler, Tom W Blackwell, Sobha Puppala, Satish Kumar, Joanne E Curran, Donna Lehman, Goncalo Abecasis, Ravindranath Duggirala, John Blangero
Admixture mapping analysis in the context of GWAS with GAW18 data
Mengjie Chen, Can Yang, Cong Li, Lin Hou, Xiaowei Chen, Hongyu Zhao
Identifying cryptic population structure in multigenerational pedigrees in a Mexican American sample
Robert C Culverhouse, Anthony L Hinrichs, Brian K Suarez
Estimating and adjusting for ancestry admixture in statistical methods for relatedness inference, heritability estimation, and association testing
Timothy Thornton, Matthew P Conomos, Serge Sverdlov, Elizabeth M Blue, Charles YK Cheung, Christopher G Glazner, Steven M Lewis, Ellen M Wijsman
Use of admixture and association for detection of quantitative trait loci in the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) study
Daniel Yorgov, Karen L Edwards, Stephanie A Santorico
Considering interactive effects in the identification of influential regions with extremely rare variants via fixed bin approach
Michael Agne, Chien-Hsun Huang, Inchi Hu, Haitian Wang, Tian Zheng, Shaw-Hwa Lo
A comparison of two collapsing methods in different approaches
Carmen Dering, Arne Schillert, Inke R König, Andreas Ziegler
Evaluation of gene-based association tests for analyzing rare variants using Genetic Analysis Workshop 18 data
Andriy Derkach, Jerry F Lawless, Daniele Merico, Andrew D Paterson, Lei Sun
Rare variant analysis of blood pressure phenotypes in the Genetic Analysis Workshop 18 whole genome sequencing data using sequence kernel association test
Cates Mallaney, Yun Ju Sung
Genetic Analysis Workshop 18 single-nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation
Thomas Nalpathamkalam, Andriy Derkach, Andrew D Paterson, Daniele Merico
Whole genome sequence analysis of the simulated systolic blood pressure in Genetic Analysis Workshop 18 family data: long-term average and collapsing methods
Yun Ju Sung, Jacob Basson, Dabeeru C Rao
Small sample properties of rare variant analysis methods
Michael D Swartz, Taebeom Kim, Jiangong Niu, Robert K Yu, Sanjay Shete, Iuliana Ionita-Laza
Higher criticism approach to detect rare variants using whole genome sequencing data
Jing Xuan, Li Yang, Zheyang Wu
Analysis of homozygosity disequilibrium using whole-genome sequencing data
Hsin-Chou Yang, Han-Wei Li
Imputation in families using a heuristic phasing approach
August N Blackburn, Angela K Dean, Donna M Lehman
Genotypic discrepancies arising from imputation
Anthony L Hinrichs, Robert C Culverhouse, Brian K Suarez
Family-based association test using normal approximation to gene dropping null distribution
Yuan Jiang, Sarah Emerson, Lu Wang, Lujing Li, Yanming Di
Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses
Elizabeth Marchani Blue, Charles YK Cheung, Christopher G Glazner, Matthew P Conomos, Steven M Lewis, Serge Sverdlov, Timothy Thornton, Ellen M Wijsman
Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference
Sunah Song, Robert Shields, Xin Li, Jing Li
Using Mendelian inheritance errors as quality control criteria in whole genome sequencing data set
Valentina V Pilipenko, Hua He, Brad G Kurowski, Eileen S Alexander, Xue Zhang, Lili Ding, Tesfaye B Mersha, Leah Kottyan, David W Fardo, Lisa J Martin
Evaluating the concordance between sequencing, imputation and microarray genotype calls in the GAW18 data
Ally Rogers, Andrew Beck, Nathan L Tintle
PREST-plus identifies pedigree errors and cryptic relatedness in the GAW18 sample using genome-wide SNP data
Lei Sun, Apostolos Dimitromanolakis
De novo mutations discovered in 8 Mexican American families through whole genome sequencing
Heming Wang, Xiaofeng Zhu
A 2-step penalized regression method for family-based next-generation sequencing association studies
Xiuhua Ding, Shaoyong Su, Kannabiran Nandakumar, Xiaoling Wang, David W Fardo
On family-based genome-wide association studies with large pedigrees: observations and recommendations
David W Fardo, Xue Zhang, Lili Ding, Hua He, Brad Kurowski, Eileen S Alexander, Tesfaye B Mersha, Valentina Pilipenko, Leah Kottyan, Kannabiran Nandakumar, Lisa Martin
Comparing the power of family-based association tests for sequence data with applications in the GAW18 simulated data
Jing Huang, Yong Chen, Michael D Swartz, Iuliana Ionita-Laza
A generalized least-squares framework for rare-variant analysis in family data
Dalin Li, Jerome I Rotter,, Xiuqing Guo
Combined linkage and family-based association analysis improves candidate gene detection in Genetic Analysis Workshop 18 simulation data
Yi Li, Jia Nee Foo, Herty Liany, Hui-Qi Low, Jianjun Liu
Comparison of multilevel modeling and the family-based association test for identifying genetic variants associated with systolic and diastolic blood pressure using Genetic Analysis Workshop 18 simulated data
Jian Wang, Robert Yu, Sanjay Shete
Family-based tests applied to extended pedigrees identify rare variants related to hypertension
Mengyuan Xu, Harold Z Wang, Wei Guo, Haide Qin, Yin Y Shugart
Two-stage family-based designs for sequencing studies
Zhao Yang, Duncan C Thomas
A comparative analysis of family-based and population-based association tests using whole genome sequence data
Jin J Zhou, Wai-Ki Yip, Michael H Cho, Dandi Qiao, Merry-Lynn N McDonald, Nan M Laird
Combining information from linkage and association mapping for next-generation sequencing longitudinal family data
Brunilda Balliu, Hae-Won Uh, Roula Tsonaka, Stefan Boehringer, Quinta Helmer, Jeanine J Houwing-Duistermaat
Rare genetic variant analysis on blood pressure in related samples
Han Chen, Seung Hoan Choi, Jaeyoung Hong, Chen Lu, Jacqueline N Milton, Catherine Allard, Sean M Lacey, Honghuang Lin, Josée Dupuis
Evaluation of the power and type I error of recently proposed family-based tests of association for rare variants
Allison Hainline, Carolina Alvarez, Alexander Luedtke, Brian Greco, Andrew Beck, Nathan L Tintle
Family-based Bayesian collapsing method for rare-variant association study
Liang He, Janne M Pitkäniemi
A comparison of whole genome sequencing with exome sequencing for family-based association studies
Sean Lacey, Jae Yoon Chung, Honghuang Lin
Adjustment of familial relatedness in association test for rare variants
Cong Li, Can Yang, Mengjie Chen, Xiaowei Chen, Lin Hou, Hongyu Zhao
Extended T2 tests for longitudinal family data in whole genome sequencing studies
Yiwei Liu, Jing Xuan, Zheyang Wu
Kernel score statistic for dependent data
Dörthe Malzahn, Stefanie Friedrichs, Albert Rosenberger, Heike Bickeböller
Adjusting for population stratification and relatedness with sequencing data
Yiwei Zhang, Wei Pan
Analysis of Genetic Analysis Workshop 18 data with gene-based penalized regression
Kristin L Ayers, Heather J Cordell
Whole genome sequencing data from pedigrees suggests linkage disequilibrium among rare variants created by population admixture
Tao Feng, Xiaofeng Zhu
A Bayesian hierarchical gene model on latent genotypes for genome-wide association studies
Ian Johnston, Luis E Carvalho
Gene-based analysis of rare and common variants to determine association with blood pressure
Xiaofeng Liu, Joseph Beyene
A dual-clustering framework for association screening with whole genome sequencing data and longitudinal traits
Ying Liu, ChienHsun Huang, Inchi Hu, Shaw-Hwa Lo, Tian Zheng
Comparison of several sequence-based association methods in pedigrees
George Mathew, Varghese George, Hongyan Xu
A variance component-based gene burden test
Juan M Peralta, Marcio Almeida, Jack W Kent Jr, John Blangero
Collapsing singletons may boost signal for associating rare variants in sequencing study
Wei Wang, Zhi Wei
A goodness-of-fit association test for whole genome sequencing data
Li Yang, Jing Xuan, Zheyang Wu
Detection of imprinting effects for hypertension based on general pedigrees utilizing all affected and unaffected individuals
Fangyuan Zhang, Shili Lin
Application of noncollapsing methods to the gene-based association test: a comparison study using Genetic Analysis Workshop 18 data
Tian-Xiao Zhang, Yi-Ran Xie, John P Rice
Evaluation of logistic Bayesian LASSO for identifying association with rare haplotypes
Swati Biswas, Charalampos Papachristou
Population structure at different minor allele frequency levels
Omar De la Cruz, Paola Raska
Identifying rare variants associated with hypertension using the C-alpha test
Anna Faino, Amber Powell, André Williams, Lori Silveira
Haplotype approach for association analysis on hypertension
Xiaowei Shen, Osvaldo Espin-Garcia, Xin Qiu, Yonathan Brhane, Geoffrey Liu, Wei Xu
Identifying rare variant associations in population-based and family-based designs
Asuman S Turkmen, Shili Lin
Testing optimally weighted combination of variants for hypertension
Xingwang Zhao, Qiuying Sha, Shuanglin Zhang, Xuexia Wang
A partition-based approach to identify gene-environment interactions in genome wide association studies
Ruixue Fan, Chien-Hsun Huang, Inchi Hu, Haitian Wang, Tian Zheng, Shaw-Hwa Lo
A powerful statistical method identifies novel loci associated with diastolic blood pressure triggered by nonlinear gene-environment interaction
Honglang Wang, Tao He, Cen Wu, Ping-Shou Zhong, Yuehua Cui
Discovering pure gene-environment interactions in blood pressure genome-wide association studies data: a two-step approach incorporating new statistics
Maggie Haitian Wang, Chien-Hsun Huang, Tian Zheng, Shaw-Hwa Lo, Inchi Hu
Single-marker and multi-marker mixed models for polygenic score analysis in family-based data
Nora Bohossian, Mohamad Saad, Andrés Legarra, Maria Martinez
Genotype imputation accuracy with different reference panels in admixed populations
Guan-Hua Huang, Yi-Chi Tseng
Practical investigation of the performance of robust logistic regression to predict the genetic risk of hypertension
Miriam Kesselmeier, Carine Legrand, Barbara Peil, Maria Kabisch, Christine Fischer, Ute Hamann, Justo Lorenzo Bermejo
Evaluation of estimated genetic values and their application to genome-wide investigation of systolic blood pressure
Ellen E Quillen, V Saroja Voruganti, Geetha Chittoor, Rohina Rubicz, Juan M Peralta, Marcio AA Almeida, Jack W Kent Jr, Vincent P Diego, Thomas D Dyer, Anthony G Comuzzie, Harald HH Göring, Ravindranath Duggirala, Laura Almasy, John Blangero
A penalized linear mixed model for genomic prediction using pedigree structures
Can Yang, Cong Li, Mengjie Chen, Xiaowei Chen, Lin Hou, Hongyu Zhao
Prediction of genetic contributions to complex traits using whole genome sequencing data
Chen Yao, Ning Leng, Kent A Weigel, Kristine E Lee, Corinne D Engelman, Kristin J Meyers
Modeling of multivariate longitudinal phenotypes in family genetic studies with Bayesian multiplicity adjustment
Lili Ding, Brad G Kurowski, Hua He, Eileen S Alexander, Tesfaye B Mersha, David W Fardo, Xue Zhang, Valentina V Pilipenko, Leah Kottyan, Lisa J Martin
Genetic association analysis for common variants in the Genetic Analysis Workshop 18 data: a Dirichlet regression approach
Osvaldo Espin-Garcia, Xiaowei Shen, Xin Qiu, Yonathan Brhane, Geoffrey Liu, Wei Xu
A novel transmission-based test of association for multivariate phenotypes: an application to systolic and diastolic blood pressure levels
Tanushree Haldar, Indranil Mukhopadhyay, Saurabh Ghosh
Bivariate genetic association analysis of systolic and diastolic blood pressure by copula models
Stefan Konigorski, Yildiz E Yilmaz, Shelley B Bull
Penalized multivariate linear mixed model for longitudinal genome-wide association studies
Jin Liu, Jian Huang, Shuangge Ma
Association mapping of blood pressure levels in a longitudinal framework using binomial regression
Arunabha Majumdar, Indranil Mukhopadhyay, Saurabh Ghosh
Bivariate linear mixed model analysis to test joint associations of genetic variants on systolic and diastolic blood pressure
Binod Neupane, Joseph Beyene
Genetic association analysis using weighted false discovery rate approach on Genetic Analysis Workshop 18 data
Xin Qiu, Xiaowei Shen, Osvaldo Espin-Garcia, Abul Kalam Azad, Geoffrey Liu, Wei Xu
Using a Bayesian latent variable approach to detect pleiotropy in the Genetic Analysis Workshop 18 data
Lizhen Xu, Radu V Craiu, Andriy Derkach, Andrew D Paterson, Lei Sun
Prediction of hypertension based on the genetic analysis of longitudinal phenotypes: a comparison of different modeling approaches for the binary trait of hypertension
Yun-Hee Choi, Rafiqul Chowdhury, Balakumar Swaminathan
Accounting for relatedness in family-based association studies: application to Genetic Analysis Workshop 18 data
Jakris Eu-ahsunthornwattana, Richard AJ Howey, Heather J Cordell
Analysis of baseline, average, and longitudinally measured blood pressure data using linear mixed models
Ahmed Hossain, Joseph Beyene
Mapping genes with longitudinal phenotypes via Bayesian posterior probabilities
Anthony Musolf, Alejandro Q Nato Jr, Douglas Londono, Lisheng Zhou, Tara C Matise, Derek Gordon
Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis
Qihua Tan, Jacob V B Hjelmborg, Mads Thomassen, Andreas Kryger Jensen, Lene Christiansen, Kaare Christensen, Jing Hua Zhao, Torben A Kruse
Analysis of the progression of systolic blood pressure using imputation of missing phenotype values
Tatsiana Vaitsiakhovich, Dmitriy Drichel, Marina Angisch, Tim Becker, Christine Herold, André Lacour
Comparing baseline and longitudinal measures in association studies
Shuai Wang, Wei Gao, Julius Ngwa, Catherine Allard, Ching-Ti Liu, L Adrienne Cupples
Detecting longitudinal effects of haplotypes and smoking on hypertension using B-splines and Bayesian LASSO
Shuang Xia, Shili Lin
A multi-level model for analyzing whole genome sequencing family data with longitudinal traits
Taoye Chen, Patchara Santawisook, Zheyang Wu
Mixed-effects models for GAW18 longitudinal blood pressure data
Wonil Chung, Fei Zou
Gene analysis for longitudinal family data using random-effects models
Jeanine J Houwing-Duistermaat, Quinta Helmer, Bruna Balliu, Erik van den Akker, Roula Tsonaka, Hae-Won Uh
Association analysis of whole genome sequencing data accounting for longitudinal and family designs
Yijuan Hu, Qin Hui, Yan V Sun
Bivariate association analysis of longitudinal phenotypes in families
Phillip E Melton, Laura A Almasy
Detecting association of rare and common variants by testing an optimally weighted combination of variants with longitudinal data
Shuaicheng Wang, Shurong Fang, Qiuying Sha, Shuanglin Zhang
Mixed-effects models for joint modeling of sequence data in longitudinal studies
Yan Yan Wu, Laurent Briollais
Fast genome-wide pedigree quantitative trait loci analysis using MENDEL
Hua Zhou, Jin Zhou, Eric M Sobel, Kenneth Lange
Does the inclusion of rare variants improve risk prediction?
Erin Austin, Wei Pan, Xiaotong Shen
Testing for associations between systolic blood pressure and single-nucleotide polymorphism profiles obtained from sparse principal component analysis
Ashley Bonner, Binod Neupane, Joseph Beyene
Comparing logistic regression, support vector machines, and permanental classification methods in predicting hypertension
Hsin-Hsiung Huang, Tu Xu, Jie Yang
Entropy-based method for assessing the influence of genetic markers and covariates on hypertension: application to Genetic Analysis Workshop 18 data
Jun Liu, Joseph Beyene
Identifying rare-variant associations in parent-child trios using a Gaussian support vector machine
Ake T Lu, Rita M Cantor
Gaussian graphical models for phenotypes using pedigree data and exploratory analysis using networks with genetic and nongenetic factors based on Genetic Analysis Workshop 18 data
Rajesh Talluri, Sanjay Shete
Pedigree-based random effect tests to screen gene pathways
Marcio Almeida, Juan M Peralta, Vidya Farook, Sobha Puppala, John W Kent Jr, Ravindranath Duggirala, John Blangero
Pathway-based analysis of rare and common variants to test for association with blood pressure
Huda Alsulami, Xiaofeng Liu, Joseph Beyene
Estimating proportions of explained variance: a comparison of whole genome subsets
Stella Aslibekyan, Howard W Wiener, Guodong Wu, Degui Zhi, Sadeep Shrestha, Gustavo de los Campos, Ana I Vazquez
Pathway analysis for genetic association studies: to do, or not to do? That is the question
Line Dufresne, Karim Oualkacha, Vincenzo Forgetta, Celia MT Greenwood
Integrated statistical and pathway approach to next-generation sequencing analysis: a family-based study of hypertension
Jeremy S Edwards, Susan R Atlas, Susan M Wilson, Candice F Cooper, Li Luo, Christine A Stidley
Application of family-based tests of association for rare variants to pathways
Brian Greco, Alexander Luedtke, Allison Hainline, Carolina Alvarez, Andrew Beck, Nathan L Tintle
Dynamic pathway analysis of genes associated with blood pressure using whole genome sequence data
Pingzhao Hu, Andrew D Paterson
An exploration of heterogeneity in genetic analysis of complex pedigrees: linkage and association using whole genome sequencing data in the MAP4 region
Shelley B Bull, Zhijian Chen, Kuan-Rui Tan, Julia Poirier
Multiphase analysis by linkage, quantitative transmission disequilibrium, and measured genotype: systolic blood pressure in complex Mexican American pedigrees
Zhijian Chen, Kuan-Rui Tan, Shelley B Bull
Identification of rare variants for hypertension with incorporation of linkage information
Yen-Feng Chiu, Ren-Hua Chung, Chun-Yi Lee, Hui-Yi Kao, Lin Hou, Fang-Chi Hsu
False-positive rates in two-point parametric linkage analysis
Silke Szymczak, Claire L Simpson, Cheryl D Cropp, Joan E Bailey-Wilson
Next-generation linkage and association methods applied to hypertension: a multifaceted approach to the analysis of sequence data
William CL Stewart, Yungui Huang, David A Greenberg, Veronica J Vieland
Erratum to: A dual clustering framework for association screening with whole genome sequencing data and longitudinal traits
Ying Liu, Chien Hsun Huang, Inchi Hu, Shaw-Hwa Lo, Tian Zheng