Jung-Ying Tzeng
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Works (67)
Updated: April 3rd, 2024 17:53
2023 journal article
The prediction of Alzheimer's disease through multi-trait genetic modeling
FRONTIERS IN AGING NEUROSCIENCE, 15.
author keywords: Alzheimer's disease; statistical genetics; genetic risk; risk scores; polygenic trait
TL;DR:
This work developed a joint genetic score, MetaGRS, to better capture the polygenic architecture of Alzheimer’s Disease, using information about multiple traits/risk factors associated with the target trait.
(via Semantic Scholar)
open access via doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 21, 2023
2023 journal article
Transfer learning with false negative control improves polygenic risk prediction
PLOS Genetics, 19(11), e1010597.
Ed(s): M. Epstein
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: March 4, 2024
2022 journal article
Duration of exposure to epidural anesthesia at delivery, DNA methylation in umbilical cord blood and their association with offspring asthma in Non-Hispanic Black women
ENVIRONMENTAL EPIGENETICS, 9(1).
author keywords: epidural anesthesia; labor analgesia; asthma; health disparities; DNA methylation; mediation analysis
TL;DR:
It is suggested that DNA methylation in immune-related pathways contributes to the effects of the duration of exposure to epidural anesthesia on childhood asthma risk in NHB offspring.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
5. Gender Equality
(Web of Science)
Source: Web Of Science
Added: February 13, 2023
2022 journal article
Phylogeny-guided microbiome OTU-specific association test (POST)
MICROBIOME, 10(1).
author keywords: Association test; Phylogenetic tree; Kernel machine regression
MeSH headings : Computational Biology / methods; Computer Simulation; Female; Humans; Infant, Newborn; Microbiota / genetics; Phylogeny; Premature Birth
TL;DR:
This work proposes a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST), and develops a user friendly R package POSTm, which can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 20, 2022
2021 journal article
An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data
FRONTIERS IN GENETICS, 12.
author keywords: co-localization; gene-level; integrative analysis; Taiwan Biobank; CNV; SNV; CNV-SNV cross-platform interaction; rare variant
TL;DR:
This study proposes an integrative approach that combines both single nucleotide variants (SNVs) and copy number variations (CNVs) in the same genomic unit to co-localize the concurrent effect and to deal with the sparsity due to rare variants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: December 6, 2021
2021 journal article
Gene-set integrative analysis of multi-omics data using tensor-based association test
BIOINFORMATICS, 37(16), 2259–2265.
TL;DR:
A tensor-based framework for variable-wise inference in multi-omics analysis is introduced and the variable-specific tensor test is derived, which will enhance computational efficiency of tensor modeling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: October 18, 2021
2021 journal article
SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data
FRONTIERS IN GENETICS, 12.
author keywords: gene-based GxE test for biobank data; GxE collapsing test for biobank data; GxE test for large-scale sequencing data; scalable GEI test; gene-environment variance component test; gene-environment kernel test; regional-based gene-environment test
TL;DR:
SEAGLE, a Scalable Exact AlGorithm for Large-scale set-based G×E tests, is presented to permit GxE VC tests for biobank-scale data to explore the interaction of gene and physical activity status on body mass index and demonstrates its utility by conducting genome-wide gene-basedG×E analysis on the Taiwan Biobank data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 29, 2021
2020 journal article
Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis
PLOS COMPUTATIONAL BIOLOGY, 16(5).
Ed(s): J. Ma n
MeSH headings : Algorithms; Area Under Curve; Computational Biology / methods; DNA Copy Number Variations / genetics; Genetic Predisposition to Disease / genetics; Genetic Variation / genetics; Genome, Human / genetics; Genome-Wide Association Study / methods; Genomics / methods; Humans; Polymorphism, Single Nucleotide / genetics; Spatial Analysis
TL;DR:
A new kernel-based test called CONCUR is developed that is free from a definition of locus and evaluates CNV-phenotype associations by comparing individuals’ copy number profiles across the genomic regions and is well powered to detect CNV effects in the Swedish Schizophrenia Study and the Taiwan Biobank.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: June 22, 2020
2020 journal article
Effective SNP ranking improves the performance of eQTL mapping
GENETIC EPIDEMIOLOGY, 44(6), 611–619.
author keywords: HC ranking; hotspot; multivariate response; penalized regression; trans-eQTL
MeSH headings : Computer Simulation; Data Analysis; Gene Expression Regulation; Genome-Wide Association Study; Humans; Models, Genetic; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics
TL;DR:
This paper illustrates how the HC-based SNP ranking can effectively prioritize eQTL signals over noise, greatly reduce the burden of joint modeling, and improve the power for eZTL mapping.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 14, 2020
2020 journal article
FastLORS: Joint modelling for expression quantitative trait loci mapping in R
STAT, 9(1).
author keywords: block coordinate descent; eQTL mapping; low-rank approximation; proximal gradient descent; sparse regression
TL;DR:
FastLORS is a software package that implements a new algorithm to solve sparse multivariate regression for expression quantitative trait loci (eQTLs) mapping that reduces the computational cost compared with LORS.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 7, 2020
2020 journal article
Robust kernel association testing (RobKAT)
GENETIC EPIDEMIOLOGY, 44(3), 272–282.
author keywords: kernel association test; multimarker hypothesis test; robust regression; schizophrenia; semiparametric
MeSH headings : Algorithms; Computer Simulation; Genetic Association Studies; Humans; Models, Genetic; Polymorphism, Single Nucleotide / genetics; Selection, Genetic
TL;DR:
The proposed robust association test (RobKAT) is evaluated, which is a general and robust kernel association test with a flexible choice of the loss function, no distributional assumptions, and has SKAT and QRKM as special cases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: March 23, 2020
2020 journal article
The association between neuraxial anesthesia and the development of childhood asthma - a secondary analysis of the newborn epigenetics study cohort
CURRENT MEDICAL RESEARCH AND OPINION, 36(6), 1025–1032.
author keywords: Anesthesia; opioid analgesics; asthma; children; sex-specific
MeSH headings : Adult; Anesthesia, Epidural / adverse effects; Anesthesia, Obstetrical / adverse effects; Asthma / etiology; Cesarean Section / adverse effects; Child; Child, Preschool; Epigenesis, Genetic; Female; Humans; Infant, Newborn; Logistic Models; Male; Pregnancy; Retrospective Studies
TL;DR:
The data suggest that peripartum exposure to neuraxial anesthesia may reduce the risk of childhood asthma primarily in males.
(via Semantic Scholar)
Source: Web Of Science
Added: June 22, 2020
2019 journal article
Identifying individual risk rare variants using protein structure guided local tests (POINT)
PLOS COMPUTATIONAL BIOLOGY, 15(2).
MeSH headings : Angiopoietin-Like Protein 4 / genetics; Cholesterol Ester Transfer Proteins / genetics; Computational Biology / methods; Computer Simulation; Genetic Association Studies / methods; Genetic Predisposition to Disease / genetics; Genetic Variation / genetics; Humans; Models, Genetic; Proprotein Convertase 9 / genetics; Protein Structure, Tertiary; Risk Factors; Sequence Analysis, DNA / methods
TL;DR:
This work proposes a protein structure guided local test (POINT) to provide variant-specific association information using structure-guided aggregation of signal and assess the selection performance of POINT using simulations and illustrates how it can be used to prioritize individual rare variants in PCSK9, ANGPTL4 and CETP in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 25, 2019
2019 journal article
Reference equations for spirometry in healthy Asian children aged 5 to 18 years in Taiwan
WORLD ALLERGY ORGANIZATION JOURNAL, 12(11).
author keywords: Asian; Children; Prediction equations; Pulmonary function; Reference values; Spirometry
TL;DR:
Evidence is provided that the GLI-2012 reference equations are not properly matched to spirometric data in a contemporary Taiwanese child population, indicating the urgent need for an update of GLI reference values by inclusion of more data of non-Caucasian decent.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Source: Web Of Science
Added: January 13, 2020
2019 article
VARIANCE COMPONENT TEST FOR CROSS-DISORDER PATHWAY ANALYSIS
EUROPEAN NEUROPSYCHOPHARMACOLOGY, Vol. 29, pp. 1204–1205.
Sources: Web Of Science, NC State University Libraries
Added: August 12, 2019
2018 journal article
Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study
International Journal of Obesity, 42(7), 1285–1295.
Contributors: A. Green n, C. Hoyo n, C. Mattingly n , Y. Luo n, n, S. Murphy *, D. Buchwalter n , A. Planchart n
MeSH headings : Adipogenesis / drug effects; Animals; Cadmium / adverse effects; Cadmium / analysis; Cadmium / blood; Disease Models, Animal; Environmental Exposure / adverse effects; Environmental Exposure / analysis; Female; Humans; Infant, Newborn; Male; Maternal Exposure / adverse effects; Metals, Heavy / adverse effects; Metals, Heavy / analysis; Pediatric Obesity / blood; Pediatric Obesity / chemically induced; Pediatric Obesity / epidemiology; Pregnancy; Pregnant Women; Prenatal Exposure Delayed Effects / blood; Prenatal Exposure Delayed Effects / chemically induced; Prenatal Exposure Delayed Effects / epidemiology; Prospective Studies; Socioeconomic Factors; United States / epidemiology; Zebrafish / metabolism
TL;DR:
The findings identify Cd as a potential human obesogen, suggesting that the underlying mechanisms may be evolutionarily conserved, and that zebrafish may be a valuable model for uncovering pathways leading to Cd-mediated obesity in human populations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 7, 2019
2018 journal article
Efficient Signal Inclusion With Genomic Applications
Journal of the American Statistical Association, 114(528), 1–23.
author keywords: Dimension reduction; False-negative control; False-positive control; Ultrahigh dimension; Variable screening
TL;DR:
The signal missing rate (SMR) is proposed as a new measure for false-negative control to account for the variability offalse-negative proportion and novel data-adaptive procedures are developed to control SMR without incurring many unnecessary false positives under dependence.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, ORCID, NC State University Libraries
Added: February 21, 2020
2018 personal communication
Genetic loci determining total immunoglobulin E levels from birth through adulthood
Yao, T.-C., Chung, R.-H., Lin, C.-Y., Tsai, P.-C., Chang, W.-C., Yeh, K.-W., … Huang, J.-L. (2019, March).
MeSH headings : Age Factors; Female; Genetic Loci; Genetic Predisposition to Disease; Genome-Wide Association Study; Humans; Immunoglobulin E / blood; Immunoglobulin E / immunology; Pregnancy
TL;DR:
The whole metagenome profiling reveals skin microbiome‐dependent susceptibility to atopic dermatitis flare, and deep sequencing transcriptome analysis of murine wound healing: effects of a multicomponent, Multitarget Natural Product Therapy‐Tr14.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 11, 2019
2018 journal article
Inference on phenotype-specific effects of genes using multivariate kernel machine regression
GENETIC EPIDEMIOLOGY, 42(1), 64–79.
Contributors: A. Maity n , J. Zhao n, P. Sullivan * & n
author keywords: kernel machine; multivariate regression; mixed models; restricted maximum likelihood; variance components
MeSH headings : Age Factors; Antipsychotic Agents / therapeutic use; Computer Simulation; Genetic Markers / genetics; Humans; Likelihood Functions; Models, Genetic; Phenotype; Sex Factors
TL;DR:
An estimation method based on the penalized likelihood approach to estimate phenotype‐specific effects and their corresponding standard errors while accounting for possible correlation among the phenotypes is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples
GENETICS, 209(1), 105–113.
author keywords: cross-sample comparison; within-sample comparison; U-statistics
MeSH headings : Algorithms; Case-Control Studies; Computer Simulation; Genetic Association Studies / methods; Genetic Variation; Humans; Models, Genetic; Models, Statistical; Phenotype; Sample Size
TL;DR:
This work shows that for rare variants, comparison based on the two within-group measures can more effectively quantify the genetic difference between cases and controls, and proposes a dissimilarity test that compares the degree of SNP Dissimilarity within cases to that within controls to better characterize the difference between two disease phenotypes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
A Powerful Test for SNP Effects on Multivariate Binary Outcomes Using Kernel Machine Regression
Statistics in Biosciences, 10(1), 117–138.
Contributors: C. Davenport *, A. Maity n , P. Sullivan * & n
author keywords: Correlated binary responses; Generalized estimating equations; IBS kernel; Kernel machine; Non-parametric regression
TL;DR:
A score-based test using a non-parametric modeling framework that jointly models the global effect of the marker set and accounts for the non-linear effects and potentially complicated interaction between markers using reproducing kernels is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, ORCID
Added: September 4, 2019
2017 journal article
A new method for detecting associations with rare copy-number variants
European Neuropsychopharmacology, 27, S165–166.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Fast Bayesian variable screenings for binary response regressions with small sample size
JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION, 87(14), 2708–2723.
author keywords: g-prior; logistic regression; probit regression; sure independence screening
TL;DR:
A Bayesian screening procedure is introduced for the binary response models with logit and probit links by imposing a generalized g-prior on the regression coefficients to derive the analytical form of their posterior means and compute screening statistics without Markov chain Monte Carlo implementation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Maternal blood cadmium, lead and arsenic levels, nutrient combinations, and offspring birthweight
BMC Public Health, 17.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
On the substructure controls in rare variant analysis: Principal components or variance components?
GENETIC EPIDEMIOLOGY, 42(3), 276–287.
author keywords: population substructure; principal components analysis; rare variant association tests; variance components
MeSH headings : Computer Simulation; Confounding Factors, Epidemiologic; Genetic Association Studies; Genetic Variation; Humans; Models, Genetic; Principal Component Analysis
TL;DR:
Evaluating the performance of SKAT coupling with principal components (PC) or variance components (VC) based PS correction methods found that PC‐based methods can account for confounding effects in most scenarios except for admixture, although the number of sufficient PCs depends on the PS complexity and the type of variants used.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 personal communication
Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"
Kong, D., Maity, A., Hsu, F.-C., & Tzeng, J.-Y. (2018, June).
MeSH headings : Biomarkers; Models, Genetic; Models, Statistical
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 16, 2018
2016 journal article
Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression
GENETIC EPIDEMIOLOGY, 40(4), 333–340.
author keywords: DNA methylation; imputation; penalized functional regression; epigenome-wide association study
MeSH headings : CpG Islands / genetics; DNA Methylation; Epigenesis, Genetic; Genetic Association Studies / methods; Humans; Leukemia, Myeloid, Acute / genetics; Linear Models; Models, Genetic
TL;DR:
The findings indicate that the penalized functional regression model is a convenient and valuable imputation tool for methylation data, and it can boost statistical power in downstream epigenome‐wide association study (EWAS).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Rare variants association analysis in large-scale sequencing studies at the single locus level
PLoS Computational Biology, 12(6).
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction
GENETIC EPIDEMIOLOGY, 39(6), 456–468.
author keywords: multiple-kernel analysis; kernel machine regression; exon level association test; gene-environment interaction; gene-gene interactions
MeSH headings : Algorithms; Gene-Environment Interaction; Genetic Variation; Homocysteine / metabolism; Humans; Models, Genetic; Quantitative Trait Loci; Regression Analysis; Risk Factors; Software; Stroke / etiology; Vitamins / metabolism
TL;DR:
This work proposes a computationally efficient and statistically rigorous “fastKM” algorithm for multikernel analysis that is based on a low‐rank approximation to the nuisance effect kernel matrices and shows that it has similar performance to an EM‐based KM approach for quantitative traits while running much faster.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
A new method for detecting associations with rare copy-number variants
PLoS Genetics, 11(10).
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies
BIOMETRICS, 71(2), 529–537.
author keywords: Association analysis; Haplotype; Individualized medicine; Multiple comparisons; Penalized regression; Pharmacogenetics
MeSH headings : Antineoplastic Agents / adverse effects; Biometry; Computer Simulation; Female; Genes, bcl-2; Haplotypes; Humans; Likelihood Functions; Models, Statistical; Ovarian Neoplasms / drug therapy; Ovarian Neoplasms / genetics; Pharmacogenetics / statistics & numerical data; Regression Analysis
TL;DR:
This work proposes a penalized likelihood approach that is able to overcome the drawbacks of the standard approach and yield the desired personalized output and demonstrates the utility of the method by applying it to the Scottish Randomized Trial in Ovarian Cancer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression
Genetics, 199(3), 695-.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Detection of Gene-Gene Interactions Using Multistage Sparse and Low-Rank Regression
BIOMETRICS, 72(1), 85–94.
author keywords: Asymptotic normality; Gene-gene interactions; Low-rank approximation; Over-parametrization; Screen-and-Clean; Sparsity
MeSH headings : Algorithms; Computer Simulation; Data Interpretation, Statistical; High-Throughput Screening Assays / methods; Models, Statistical; Pattern Recognition, Automated / methods; Protein Interaction Mapping / methods; Regression Analysis; Reproducibility of Results; Sensitivity and Specificity
TL;DR:
The results suggest that the new procedure can identify main and interaction effects that would have been omitted by conventional screening methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder
The American Journal of Human Genetics, 96(2), 283–294.
MeSH headings : Bipolar Disorder / genetics; Depressive Disorder, Major / genetics; Genetic Testing / methods; Genetics, Medical / methods; Humans; Linear Models; Mental Disorders / genetics; Multifactorial Inheritance / genetics; Multivariate Analysis; Polymorphism, Single Nucleotide / genetics; Risk Assessment / methods; Schizophrenia / genetics
TL;DR:
The multivariate approach significantly increases the prediction accuracy for schizophrenia, bipolar disorder, and major depressive disorder in the discovery as well as in independent validation datasets and is a flexible and powerful tool to maximize prediction accuracy.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Module-based association analysis for omics data with network structure
PLoS One, 10(3).
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 110(511), 962–974.
author keywords: ASE; eQTL study; Gene expression; Haplotype; Maximum likelihood
TL;DR:
This article provides a maximum-likelihood framework for cis-eQTL mapping with RNA-seq data that integrates the inference of haplotypes and the association analysis into a single stage, and is thus unbiased and statistically powerful.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways
Nature Neuroscience, 18(2), 199–209.
MeSH headings : Brain / immunology; Brain / metabolism; Databases, Genetic; Genetic Predisposition to Disease / genetics; Genome-Wide Association Study / methods; Histones / genetics; Histones / metabolism; Humans; Mental Disorders / etiology; Mental Disorders / genetics; Signal Transduction / genetics
TL;DR:
It is indicated that risk variants for psychiatric disorders aggregate in particular biological pathways and that these pathways are frequently shared between disorders.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: December 29, 2020
2015 journal article
Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways
Nature Neuroscience, 18(2), 199–209.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Testing and estimation in marker-set association study using semiparametric quantile regression kernel machine
BIOMETRICS, 72(2), 364–371.
author keywords: Bootstrap; Genetic marker-set association; Kernel machines; Permutation; Quantile regression; Semiparametric; Smoothing parameter; Testing
MeSH headings : Algorithms; Biomarkers; Biometry / methods; Clinical Trials as Topic; Computer Simulation; Genetic Association Studies; Homocysteine / blood; Humans; Linear Models; Models, Genetic; Models, Statistical; Polymorphism, Single Nucleotide; Regression Analysis
TL;DR:
An efficient algorithm is proposed to solve the corresponding optimization problem for estimating the effects of covariates and also a powerful test is introduced for detecting the overall effect of the marker set.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
Analysis of Gene-Gene Interactions Using Gene-Trait Similarity Regression
HUMAN HEREDITY, 78(1), 17–26.
author keywords: Gene-gene interactions; Gene-trait similarity; Similarity regression
MeSH headings : Algorithms; Computer Simulation; Epistasis, Genetic; Genotype; Humans; Models, Genetic; Polymorphism, Single Nucleotide; Principal Component Analysis; Regression Analysis
TL;DR:
A new similarity-based test to assess G×G at the gene level, which permits the study of epistasis at biologically functional units with amplified interaction signals and has satisfactory power and robustness under different genetic architecture when compared to existing gene-based interaction tests.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Complete Effect-Profile Assessment in Association Studies With Multiple Genetic and Multiple Environmental Factors
GENETIC EPIDEMIOLOGY, 39(2), 122–133.
Contributors: Z. Wang n, A. Maity n , Y. Luo n, M. Neely * & n
author keywords: factor-set association analysis; kernel machine regression; genetic-environmental interactions; joint and conditional tests
MeSH headings : Computer Simulation; Environment; Gene-Environment Interaction; Genetic Predisposition to Disease; Genome-Wide Association Study / methods; Humans; Models, Genetic; Software
TL;DR:
The issues encountered in constructing kernels for investigating interactions between two factor‐sets are illustrated, and a simple yet intuitive solution to construct the G×E kernel that retains the ease‐of‐interpretation of classic regression is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
GENE-LEVEL PHARMACOGENETIC ANALYSIS ON SURVIVAL OUTCOMES USING GENE-TRAIT SIMILARITY REGRESSION
ANNALS OF APPLIED STATISTICS, 8(2), 1232–1255.
author keywords: Association study; gene/pathway; pharmacogenetics; similarity regression; survival data; proportional odds model; proportional hazards model
TL;DR:
A gene-trait similarity regression for survival analysis to assess the effect of a gene or pathway on time-to-event outcomes and derives the equivalence between the similarity survival regression and a random effects model, which further unifies the current variance-component based methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Heritability and genomics of gene expression in peripheral blood
Nature Genetics, 46(5), 430–437.
MeSH headings : Blood / metabolism; Gene Expression Profiling; Gene Expression Regulation / genetics; Genotype; Humans; Inheritance Patterns / genetics; Likelihood Functions; Netherlands; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics
TL;DR:
Gen expression profiles in 2,752 twins were assessed, using a classic twin design, to quantify expression heritability and quantitative trait loci (eQTLs) in peripheral blood, providing a new resource toward understanding the genetic control of transcription.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: February 5, 2020
2014 journal article
Heritability and genomics of gene expression in peripheral blood
Nature Genetics, 46(5), 430–437.
Source: NC State University Libraries
Added: August 6, 2018
2014 journal article
Integrative gene set analysis of multi-platform data with sample heterogeneity
BIOINFORMATICS, 30(11), 1501–1507.
MeSH headings : Breast Neoplasms / genetics; DNA Copy Number Variations; DNA Methylation; Female; Gene Expression Profiling; Genes; Genomics / methods; Humans; Sequence Analysis, RNA; Statistics, Nonparametric
TL;DR:
The proposed multi-platform Mann-Whitney statistics method has higher power for heterogeneous samples and comparable performance for homogeneous samples when compared with the existing methods, and is able to identify novel pathways that are missed by other strategies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Pathway-Guided Identification of Gene-Gene Interactions
ANNALS OF HUMAN GENETICS, 78(6), 478–491.
author keywords: Pathway analysis; gene-gene interactions; bio-knowledge-guided
MeSH headings : Computer Simulation; Epistasis, Genetic; Genotype; Humans; Linear Models; Models, Genetic; Polymorphism, Single Nucleotide; Principal Component Analysis; Regression Analysis
TL;DR:
A regression model with pathway‐guided regularization for detecting interactions among genes using the principal components to summarize the SNP‐SNP interactions between a gene pair, and an L1 penalty that incorporates adaptive weights based on biological guidance and trait supervision to identify important main and interaction effects is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
A mega-analysis of genome-wide association studies for major depressive disorder
Molecular Psychiatry, 18(4), 497–511.
Source: NC State University Libraries
Added: August 6, 2018
2013 journal article
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
Nature Genetics, 45(9), 984–994.
MeSH headings : Adult; Attention Deficit Disorder with Hyperactivity / genetics; Bipolar Disorder / genetics; Child; Child Development Disorders, Pervasive / genetics; Crohn Disease / genetics; Depressive Disorder, Major / genetics; Genetic Heterogeneity; Genetic Predisposition to Disease; Genome, Human; Genome-Wide Association Study; Humans; Inheritance Patterns; Mental Disorders / genetics; Polymorphism, Single Nucleotide; Schizophrenia / genetics
TL;DR:
Empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: December 29, 2020
2013 journal article
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
Nature Genetics, 45(9), 984-.
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regression
GENETIC EPIDEMIOLOGY, 36(7), 686–695.
Contributors: A. Maity n , P. Sullivan * & n
author keywords: kernel machine regression; multivariate regression; multivariate phenotypes; score-based test
MeSH headings : Antipsychotic Agents / therapeutic use; Chromosomes, Human, Pair 6; Computer Simulation; Genetic Markers; Genome-Wide Association Study; Herpesviridae Infections / genetics; Herpesviridae Infections / immunology; Herpesviridae Infections / virology; Humans; Models, Genetic; Models, Statistical; Multivariate Analysis; Phenotype; Polymorphism, Single Nucleotide; Regression Analysis; Schizophrenia / drug therapy; Schizophrenia / genetics; Schizophrenia / virology
TL;DR:
A multivariate regression based on kernel machine is constructed to facilitate the joint evaluation of multimarker effects on multiple phenotypes and illustrates the utility of the multivariate kernel machine method through the Clinical Antipsychotic Trails of Intervention Effectiveness antibody study.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2011 journal article
Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies
BMC Genetics, 12.
Source: NC State University Libraries
Added: August 6, 2018
2011 journal article
Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression
AMERICAN JOURNAL OF HUMAN GENETICS, 89(2), 277–288.
MeSH headings : Chromosomes, Human, Pair 21 / genetics; Computer Simulation; Databases, Genetic; Environment; Genes / genetics; Genetic Markers; Humans; Models, Genetic; Mutation / genetics; Quantitative Trait, Heritable; Regression Analysis
TL;DR:
A similarity-based regression method for assessing the main genetic and interaction effects of a group of markers on quantitative traits and is an ideal tool for evaluating associations between phenotype and marker sets defined by linkage disequilibrium blocks, genes, or pathways in whole-genome analysis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
A quality control algorithm for filtering SNPs in genome-wide association studies
BIOINFORMATICS, 26(14), 1731–1737.
MeSH headings : Algorithms; Genome; Genome-Wide Association Study / methods; Genome-Wide Association Study / standards; Polymorphism, Single Nucleotide; Quality Control
TL;DR:
An algorithm that is based on principal component analysis and clustering analysis to identify low-quality SNPs and suggests that with the same or fewer SNPs excluded, the proposed algorithm tends to give a similar or lower value of lambda, a reduced number of false associations, and retains all true associations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Evaluating Haplotype Effects in Case-Control Studies via Penalized-Likelihood Approaches: Prospective or Retrospective Analysis?
GENETIC EPIDEMIOLOGY, 34(8), 892–911.
author keywords: haplotype-based association analysis; variable selection; regularized regression; prospective likelihood; retrospective likelihood
MeSH headings : Algorithms; Case-Control Studies; Computer Simulation; Genes, Dominant; Genes, Recessive; Genotype; Haplotypes / genetics; Humans; Likelihood Functions; Models, Genetic; Prospective Studies; Regression Analysis; Retrospective Studies
TL;DR:
The results suggest that the impact of prospective analyses depends on (1) the underlying genetic mode and (2) the genetic model adopted in the analysis, and when the correct genetic model is used, the difference between the two analyses is negligible for additive and slight for dominant haplotype effects.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Haplotype-Based Pharmacogenetic Analysis for Longitudinal Quantitative Traits in the Presence of Dropout
JOURNAL OF BIOPHARMACEUTICAL STATISTICS, 20(2), 334–350.
author keywords: Adaptive LASSO; Haplotype-based association analysis; Haplotype-treatment interaction; Missing data; Repeated outcome; Variable selection
MeSH headings : Antipsychotic Agents / therapeutic use; Computer Simulation; Data Interpretation, Statistical; Genetic Predisposition to Disease; Haplotypes; Humans; Likelihood Functions; Longitudinal Studies; Models, Statistical; Patient Dropouts / statistics & numerical data; Pharmacogenetics / statistics & numerical data; Phenotype; Quantitative Trait, Heritable; Randomized Controlled Trials as Topic / statistics & numerical data; Reproducibility of Results; Schizophrenia / drug therapy; Schizophrenia / genetics; Treatment Outcome
TL;DR:
The inverse probability weights are used to handle the outcome-dependent dropouts under the missing-at-random assumption, and the weighted L 1 penalty is incorporated to select important main and interaction effects with high dimensionality.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2009 journal article
A Regression-based Association Test for Case-control Studies that Uses Inferred Ancestral Haplotype Similarity
ANNALS OF HUMAN GENETICS, 73, 520–526.
author keywords: Case-control studies; haplotype similarity; haplotype sharing; haplotype-based association test; covariates; regression-based association analysis
MeSH headings : Case-Control Studies; Computer Simulation; Gene Frequency; Genetic Techniques; Genome, Human; Haplotypes; Humans; Linkage Disequilibrium; Models, Genetic; Polymorphism, Single Nucleotide; Regression Analysis
TL;DR:
A new regression‐based HS association method for case‐control studies that incorporates covariate information and combines the advantages of the two classes of approaches by using inferred ancestral haplotypes is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2009 journal article
A comprehensive approach to haplotype-specific analysis by penalized likelihood
European Journal of Human Genetics, 18(1), 95–103.
MeSH headings : Computer Simulation; Haplotypes / genetics; Humans; Likelihood Functions; Models, Statistical; Quantitative Trait, Heritable
TL;DR:
Simulation studies reveal the better abilities of the proposed method to identify the haplotype effect structure compared with the traditional haplotype association methods, demonstrating the informativeness and powerfulness of the propose method.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2009 journal article
Erratum: Genomewide association for schizophrenia in the CATIE study: results of stage 1
Molecular Psychiatry, 14(12), 1144–1144.
Source: Crossref
Added: February 24, 2020
2009 journal article
Gene-Trait Similarity Regression for Multimarker-Based Association Analysis
Biometrics, 65(3), 822–832.
MeSH headings : Chromosome Mapping / methods; Computer Simulation; Genetic Linkage / genetics; Genetic Markers / genetics; Haplotypes / genetics; Humans; Models, Genetic; Models, Statistical; Quantitative Trait Loci / genetics; Regression Analysis
TL;DR:
The proposed similarity‐based regression method to detect associations between traits and multimarker genotypes allows for covariates, uses phase‐independent similarity measures to bypass the needs to impute phase information, and is applicable to traits of general types.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: NC State University Libraries, NC State University Libraries, Crossref
Added: August 6, 2018
2009 review
Genome-wide association for major depressive disorder: A possible role for the presynaptic protein piccolo
[Review of ]. Molecular Psychiatry, 14(4), 359–375.
Source: NC State University Libraries
Added: August 6, 2018
2008 journal article
Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo
Molecular Psychiatry, 14(4), 359–375.
author keywords: major depressive disorder; genome-wide association; Netherlands study of depression and anxiety; Netherlands twin registry
MeSH headings : Adult; Case-Control Studies; Cohort Studies; Cytoskeletal Proteins / genetics; Depressive Disorder, Major / genetics; Female; Genetic Linkage; Genetic Predisposition to Disease; Genome-Wide Association Study / methods; Humans; Male; Middle Aged; Neuropeptides / genetics; Polymorphism, Single Nucleotide / genetics
TL;DR:
A genome-wide association study of single nucleotide polymorphisms genotyped in 1738 MDD cases and 1802 controls selected to be at low liability for MDD found 11 signals localized to a 167 kb region overlapping the gene piccolo, whose protein product localizes to the cytomatrix of the presynaptic active zone and is important in monoaminergic neurotransmission in the brain.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: August 28, 2020
2008 journal article
Genomewide association for schizophrenia in the CATIE study: results of stage 1
Molecular Psychiatry, 13(6), 570–584.
author keywords: schizophrenia; genomewide association; CATIE
MeSH headings : Antipsychotic Agents / therapeutic use; Case-Control Studies; Computational Biology; DNA / genetics; DNA / isolation & purification; Genetic Markers; Genetic Variation; Genome, Human; Genotype; Humans; National Institute of Mental Health (U.S.); Polymorphism, Single Nucleotide; Schizophrenia / drug therapy; Schizophrenia / genetics; United States
TL;DR:
These data do not provide evidence for the involvement of any genomic region with schizophrenia detectable with moderate sample size, however, a planned genomewide association study for response phenotypes and inclusion of individual phenotype and genotype data from this study in meta-analyses hold promise for eventual identification of susceptibility and protective variants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref
Added: August 6, 2018
2007 journal article
Haplotype-based association analysis via variance-components score test
AMERICAN JOURNAL OF HUMAN GENETICS, 81(5), 927–938.
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; Computer Simulation; Databases, Genetic; Genetic Predisposition to Disease; Haplotypes; Humans; Likelihood Functions; Models, Genetic; Polymorphism, Single Nucleotide / genetics; Quantitative Trait, Heritable
TL;DR:
The broad coverage and the fast and easy implementation of this method make the VC strategy an effective tool for haplotype analysis, even in modern genomewide association studies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2006 journal article
A two-stage design for multiple testing in large-scale association studies
JOURNAL OF HUMAN GENETICS, 51(6), 523–532.
author keywords: association studies; cost-effectiveness; false positive rate; multiple testing; two-stage design
MeSH headings : Cost-Benefit Analysis; Data Interpretation, Statistical; False Positive Reactions; Genetic Markers; Genetic Techniques; Genotype; Humans; Hyperlipoproteinemia Type IV / genetics; Models, Genetic; Polymorphism, Single Nucleotide
TL;DR:
The main principle is to reduce the total number of tests by removing clearly unassociated markers in the first-stage test, which may be useful in guiding study design to achieve a high TPR while retaining the desired FPR.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2006 journal article
Likelihood-based inference on haplotype effects in genetic association studies - Comment
Journal of the American Statistical Association, 101(473), 111–114.
Source: NC State University Libraries
Added: August 6, 2018
2006 journal article
Regression-based association analysis with clustered haplotypes through use of genotypes
AMERICAN JOURNAL OF HUMAN GENETICS, 78(2), 231–242.
MeSH headings : Apolipoprotein A-V; Apolipoproteins A / genetics; Cluster Analysis; Computer Simulation; Genetic Linkage; Genotype; Haplotypes / genetics; Humans; Hypertriglyceridemia / genetics; Regression Analysis
TL;DR:
This study developed a regression-based approach using clustered haplotypes to assess haplotype-phenotype association and generalized the probabilistic clustering methods of Tzeng to the generalized linear model (GLM) framework established by Schaid et al.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Evolutionary-based grouping of haplotypes in association analysis
GENETIC EPIDEMIOLOGY, 28(3), 220–231.
author keywords: evolutionary-based clustering; dimension reduction of haplotypes; haplotype tests for association
MeSH headings : Algorithms; Genetic Predisposition to Disease / genetics; Genotype; Haplotypes / genetics; Humans; Models, Genetic; Polymorphism, Single Nucleotide / genetics
TL;DR:
This work adapts the evolutionary concepts of cladistic analyses and proposes a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes, and performs association analysis based on groups of haplotypes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
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