Kernel machine SNP-set testing under multiple candidate kernels.

PubWeight™: 1.04‹?› | Rank: Top 15%

🔗 View Article (PMC 3769109)

Published in Genet Epidemiol on March 07, 2013

Authors

Michael C Wu1, Arnab Maity, Seunggeun Lee, Elizabeth M Simmons, Quaker E Harmon, Xinyi Lin, Stephanie M Engel, Jeffrey J Molldrem, Paul M Armistead

Author Affiliations

1: Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7420, USA. mwu@bios.unc.edu

Articles citing this

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test. Am J Hum Genet (2015) 1.06

Test for rare variants by environment interactions in sequencing association studies. Biometrics (2015) 0.84

Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors. Genet Epidemiol (2014) 0.82

Statistical analysis for genome-wide association study. J Biomed Res (2014) 0.80

A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants. Am J Hum Genet (2016) 0.80

Analysis of gene-gene interactions using gene-trait similarity regression. Hum Hered (2014) 0.80

Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow. Curr Genomics (2015) 0.79

Rare variants detection with kernel machine learning based on likelihood ratio test. PLoS One (2014) 0.77

Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT). Stat Interface (2016) 0.76

A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction. Genet Epidemiol (2015) 0.76

A weighted U statistic for association analyses considering genetic heterogeneity. Stat Med (2016) 0.75

Prioritizing individual genetic variants after kernel machine testing using variable selection. Genet Epidemiol (2016) 0.75

Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-Analysis of Noncoding Variation in Metabochip Data. Am J Hum Genet (2017) 0.75

Articles cited by this

Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet (2006) 115.71

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68

A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet (2007) 52.68

Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet (2011) 18.88

A global test for groups of genes: testing association with a clinical outcome. Bioinformatics (2004) 10.82

Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet (2010) 6.60

So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. Am J Hum Genet (2007) 6.26

Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet (2012) 5.48

A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet (2008) 4.96

An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics (2004) 4.90

Optimal tests for rare variant effects in sequencing association studies. Biostatistics (2012) 4.69

Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics (2007) 4.66

Testing association between disease and multiple SNPs in a candidate gene. Genet Epidemiol (2007) 4.50

Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol (2009) 3.96

Generalized genomic distance-based regression methodology for multilocus association analysis. Am J Hum Genet (2006) 3.79

Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics (2008) 3.70

Comparison of statistical tests for disease association with rare variants. Genet Epidemiol (2011) 3.42

Haplotype-based association analysis via variance-components score test. Am J Hum Genet (2007) 2.93

Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol (2008) 2.40

Association tests using kernel-based measures of multi-locus genotype similarity between individuals. Genet Epidemiol (2010) 2.39

To permute or not to permute. Bioinformatics (2006) 2.33

Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations. Hum Hered (2010) 2.01

Vitamin D-related genetic variation, plasma vitamin D, and risk of lethal prostate cancer: a prospective nested case-control study. J Natl Cancer Inst (2012) 1.79

Genomic similarity and kernel methods II: methods for genomic information. Hum Hered (2010) 1.58

Gene-trait similarity regression for multimarker-based association analysis. Biometrics (2009) 1.44

Relationship between genomic distance-based regression and kernel machine regression for multi-marker association testing. Genet Epidemiol (2011) 1.41

Smoking and pregnancy outcome among African-American and white women in central North Carolina. Epidemiology (2001) 1.31

Kernel machine approach to testing the significance of multiple genetic markers for risk prediction. Biometrics (2011) 1.30

Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies. Genet Epidemiol (2011) 1.29

Multivariate phenotype association analysis by marker-set kernel machine regression. Genet Epidemiol (2012) 1.29

Test selection with application to detecting disease association with multiple SNPs. Hum Hered (2009) 1.14

Variation in folate pathway genes contributes to risk of congenital heart defects among individuals with Down syndrome. Genet Epidemiol (2010) 1.14

A Large-scale genetic association study of esophageal adenocarcinoma risk. Carcinogenesis (2010) 1.12

Tests of association between quantitative traits and haplotypes in a reduced-dimensional space. Ann Hum Genet (2005) 1.09

On distance-based permutation tests for between-group comparisons. Biometrics (2009) 1.07

Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies. Cancer Epidemiol Biomarkers Prev (2010) 1.05

Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test. Biostatistics (2012) 1.04

Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. Breast Cancer Res Treat (2010) 0.93

A unified framework for multi-locus association analysis of both common and rare variants. BMC Genomics (2011) 0.92

SNP-set analysis replicates acute lung injury genetic risk factors. BMC Med Genet (2012) 0.86

Bayesian semiparametric regression models for evaluating pathway effects on continuous and binary clinical outcomes. Stat Med (2012) 0.84

Association between polymorphisms in cancer-related genes and early onset of esophageal adenocarcinoma. Neoplasia (2011) 0.84

Articles by these authors

Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet (2011) 18.88

Monoculture-derived T lymphocytes specific for multiple viruses expand and produce clinically relevant effects in immunocompromised individuals. Nat Med (2006) 4.42

Cord-blood engraftment with ex vivo mesenchymal-cell coculture. N Engl J Med (2012) 3.39

Functionally active virus-specific T cells that target CMV, adenovirus, and EBV can be expanded from naive T-cell populations in cord blood and will target a range of viral epitopes. Blood (2009) 3.27

Prenatal phenol and phthalate exposures and birth outcomes. Environ Health Perspect (2008) 3.11

Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet (2011) 3.02

Sequence kernel association tests for the combined effect of rare and common variants. Am J Hum Genet (2013) 2.41

Delayed immune reconstitution after cord blood transplantation is characterized by impaired thymopoiesis and late memory T-cell skewing. Blood (2007) 2.16

An anti-PR1/HLA-A2 T-cell receptor-like antibody mediates complement-dependent cytotoxicity against acute myeloid leukemia progenitor cells. Blood (2011) 2.10

PD-L1 expression in triple-negative breast cancer. Cancer Immunol Res (2014) 2.06

Display technologies: application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev (2006) 1.92

Phosphatidylinositol 3-kinase mediates bronchioalveolar stem cell expansion in mouse models of oncogenic K-ras-induced lung cancer. PLoS One (2008) 1.72

Endocrine disruptors and childhood social impairment. Neurotoxicology (2010) 1.71

CD25 expression on donor CD4+ or CD8+ T cells is associated with an increased risk for graft-versus-host disease after HLA-identical stem cell transplantation in humans. Blood (2003) 1.65

Donor-specific anti-HLA Abs and graft failure in matched unrelated donor hematopoietic stem cell transplantation. Blood (2011) 1.61

Serum concentrations of polychlorinated biphenyls in relation to in vitro fertilization outcomes. Environ Health Perspect (2011) 1.60

Validity of pre-eclampsia registration in the medical birth registry of norway for women participating in the norwegian mother and child cohort study, 1999-2010. Paediatr Perinat Epidemiol (2014) 1.58

Family-based association tests for sequence data, and comparisons with population-based association tests. Eur J Hum Genet (2013) 1.55

Selective depletion of donor alloreactive T cells without loss of antiviral or antileukemic responses. Blood (2003) 1.55

Project TENDR: Targeting Environmental Neuro-Developmental Risks The TENDR Consensus Statement. Environ Health Perspect (2016) 1.50

Nonparametric Bayesian variable selection with applications to multiple quantitative trait loci mapping with epistasis and gene-environment interaction. Genetics (2010) 1.48

Cytomegalovirus reactivation following allogeneic stem cell transplantation is associated with the presence of dysfunctional antigen-specific CD8+ T cells. Blood (2002) 1.39

Peripheral blood cytokine profiling during pregnancy and post-partum periods. Am J Reprod Immunol (2010) 1.37

Detecting rare variant effects using extreme phenotype sampling in sequencing association studies. Genet Epidemiol (2012) 1.35

Reduced Rank Mixed Effects Models for Spatially Correlated Hierarchical Functional Data. J Am Stat Assoc (2010) 1.30

A phase II trial of doxorubicin and gemcitabine in renal cell carcinoma with sarcomatoid features: ECOG 8802. Med Oncol (2011) 1.30

Loss of T-lymphocyte clonal dominance in patients with myelodysplastic syndrome responsive to immunosuppression. Blood (2002) 1.26

Quantification of population structure using correlated SNPs by shrinkage principal components. Hum Hered (2010) 1.24

Test for interactions between a genetic marker set and environment in generalized linear models. Biostatistics (2013) 1.20

Functional assessment and specific depletion of alloreactive human T cells using flow cytometry. Blood (2004) 1.18

Exposure to airborne particulate matter is associated with methylation pattern in the asthma pathway. Epigenomics (2013) 1.17

Maternal ethnicity and pre-eclampsia in New York City, 1995-2003. Paediatr Perinat Epidemiol (2011) 1.17

Characterizing the pregnancy immune phenotype: results of the viral immunity and pregnancy (VIP) study. J Clin Immunol (2011) 1.16

Prenatal exposure to environmental phenols: concentrations in amniotic fluid and variability in urinary concentrations during pregnancy. Environ Health Perspect (2013) 1.16

GEE-based SNP set association test for continuous and discrete traits in family-based association studies. Genet Epidemiol (2013) 1.14

Optimal Exposure Biomarkers for Nonpersistent Chemicals in Environmental Epidemiology. Environ Health Perspect (2015) 1.13

Breast cancer cell uptake of the inflammatory mediator neutrophil elastase triggers an anticancer adaptive immune response. Cancer Res (2012) 1.12

Co-stimulation through 4-1BB/CD137 improves the expansion and function of CD8(+) melanoma tumor-infiltrating lymphocytes for adoptive T-cell therapy. PLoS One (2013) 1.12

Neonatal genome-wide methylation patterns in relation to birth weight in the Norwegian Mother and Child Cohort. Am J Epidemiol (2014) 1.11

Pocket-sized ultrasound as an aid to physical diagnosis for internal medicine residents: a randomized trial. J Gen Intern Med (2014) 1.11

Maternal ethnic ancestry and adverse perinatal outcomes in New York City. Am J Obstet Gynecol (2009) 1.10

In utero exposure to maternal tobacco smoke and subsequent obesity, hypertension, and gestational diabetes among women in the MoBa cohort. Environ Health Perspect (2011) 1.10

Comment on a simple and improved correction for population stratification. Am J Hum Genet (2008) 1.09

Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. Proc Natl Acad Sci U S A (2011) 1.09

Mitochondrial DNA sequence variation in single cells from leukemia patients. Blood (2006) 1.05

Localized mucosal response to intranasal live attenuated influenza vaccine in adults. J Infect Dis (2012) 1.03

The effect of maternal PTSD following in utero trauma exposure on behavior and temperament in the 9-month-old infant. Ann N Y Acad Sci (2006) 1.01

Immunotherapy of hematologic malignancy. Hematology Am Soc Hematol Educ Program (2003) 1.00

Immunogenicity of trivalent inactivated influenza vaccination received during pregnancy or postpartum. Obstet Gynecol (2012) 0.99

Efficient Semiparametric Marginal Estimation for the Partially Linear Additive Model for Longitudinal/Clustered Data. Stat Biosci (2009) 0.98

Automated capillary electrophoresis system for fast single-cell analysis. Anal Chem (2013) 0.97

LFA-1 affinity regulation is necessary for the activation and proliferation of naive T cells. J Biol Chem (2009) 0.97

Immunotherapeutic peptide vaccination with leukemia-associated antigens. Curr Opin Immunol (2006) 0.97

Parametrically Guided Generalized Additive Models with Application to Mergers and Acquisitions Data. J Nonparametr Stat (2013) 0.96

Predictors and variability of repeat measurements of urinary phenols and parabens in a cohort of Shanghai women and men. Environ Health Perspect (2014) 0.96

A novel HLA-A*0201 restricted peptide derived from cathepsin G is an effective immunotherapeutic target in acute myeloid leukemia. Clin Cancer Res (2012) 0.95

Comparison of polyfluoroalkyl compound concentrations in maternal serum and amniotic fluid: a pilot study. Reprod Toxicol (2012) 0.95

A novel strategy for rapid and efficient isolation of human tumor-specific CD4(+) and CD8(+) T-cell clones. J Immunol Methods (2007) 0.95

PR1-specific T cells are associated with unmaintained cytogenetic remission of chronic myelogenous leukemia after interferon withdrawal. PLoS One (2010) 0.95

LFA-1 regulates CD8+ T cell activation via T cell receptor-mediated and LFA-1-mediated Erk1/2 signal pathways. J Biol Chem (2009) 0.95

The role of antigen cross-presentation from leukemia blasts on immunity to the leukemia-associated antigen PR1. J Immunother (2012) 0.94

Transcriptome atlases of mouse brain reveals differential expression across brain regions and genetic backgrounds. G3 (Bethesda) (2012) 0.92

Measurement of Total and Free Urinary Phenol and Paraben Concentrations over the Course of Pregnancy: Assessing Reliability and Contamination of Specimens in the Norwegian Mother and Child Cohort Study. Environ Health Perspect (2015) 0.92

Prenatal Phthalate Exposures and Childhood Fat Mass in a New York City Cohort. Environ Health Perspect (2015) 0.91

Detection and characterization of a novel subset of CD8⁺CD57⁺ T cells in metastatic melanoma with an incompletely differentiated phenotype. Clin Cancer Res (2012) 0.91

Adoptive transfer of PR1 cytotoxic T lymphocytes associated with reduced leukemia burden in a mouse acute myeloid leukemia xenograft model. Cytotherapy (2010) 0.91

SIMEX and standard error estimation in semiparametric measurement error models. Electron J Stat (2009) 0.91

CD13-positive bone marrow-derived myeloid cells promote angiogenesis, tumor growth, and metastasis. Proc Natl Acad Sci U S A (2013) 0.91

Perfluoroalkyl substances and lipid concentrations in plasma during pregnancy among women in the Norwegian Mother and Child Cohort Study. Environ Int (2013) 0.90

Blocking LFA-1 activation with lovastatin prevents graft-versus-host disease in mouse bone marrow transplantation. Biol Blood Marrow Transplant (2009) 0.90

Prepregnancy body mass index, smoking during pregnancy, and infant birth weight. Ann Epidemiol (2011) 0.90

Chemokine receptor CCR5 mediates alloimmune responses in graft-versus-host disease. Biol Blood Marrow Transplant (2009) 0.90

Descriptive epidemiology of chronic hypertension, gestational hypertension, and preeclampsia in New York State, 1995-2004. Matern Child Health J (2014) 0.90

Prenatal Phthalate Exposures and Body Mass Index Among 4- to 7-Year-old Children: A Pooled Analysis. Epidemiology (2016) 0.89

Power of a reproducing kernel-based method for testing the joint effect of a set of single-nucleotide polymorphisms. Genetica (2012) 0.88

Semi-automated scoring of triple-probe FISH in human sperm: methods and further validation. Cytometry A (2011) 0.87

Broad cross-presentation of the hematopoietically derived PR1 antigen on solid tumors leads to susceptibility to PR1-targeted immunotherapy. J Immunol (2012) 0.87

Optimization of peptide separations by differential ion mobility spectrometry. J Am Soc Mass Spectrom (2014) 0.86

Design and analysis issues in gene and environment studies. Environ Health (2012) 0.86

Alpha-defensins 1-3 release by dendritic cells is reduced by estrogen. Reprod Biol Endocrinol (2011) 0.85

A human Mix-like homeobox gene MIXL shows functional similarity to Xenopus Mix.1. Blood (2002) 0.85

Vitamin D receptor upregulation in alloreactive human T cells. Hum Immunol (2012) 0.85

Common minor histocompatibility antigen discovery based upon patient clinical outcomes and genomic data. PLoS One (2011) 0.84

Polymorphisms in inflammatory genes are associated with term small for gestational age and preeclampsia. Am J Reprod Immunol (2014) 0.84

Microfluidic chemical cytometry of peptide degradation in single drug-treated acute myeloid leukemia cells. Anal Chem (2013) 0.84

Targeting human B-cell malignancies through Ig light chain-specific cytotoxic T lymphocytes. Clin Cancer Res (2011) 0.84

Associations of adherence to the New Nordic Diet with risk of preeclampsia and preterm delivery in the Norwegian Mother and Child Cohort Study (MoBa). Eur J Epidemiol (2014) 0.84

Global analysis of methylation profiles from high resolution CpG data. Genet Epidemiol (2014) 0.83

On the complex relationship between genes and environment in the etiology of autism. Epidemiology (2011) 0.83

Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study. Environ Health (2014) 0.83

Differential ion mobility spectrometry coupled to tandem mass spectrometry enables targeted leukemia antigen detection. J Proteome Res (2014) 0.82

Association of hexachlorobenzene (HCB), dichlorodiphenyltrichloroethane (DDT), and dichlorodiphenyldichloroethylene (DDE) with in vitro fertilization (IVF) outcomes. Environ Health Perspect (2011) 0.82

Perfluoroalkyl substances during pregnancy and validated preeclampsia among nulliparous women in the Norwegian Mother and Child Cohort Study. Am J Epidemiol (2014) 0.82

Protein-templated gold nanoclusters: size dependent inversion of fluorescence emission in the presence of molecular oxygen. Nanoscale (2012) 0.82

Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors. Genet Epidemiol (2014) 0.82

Prenatal Exposure to Organophosphorous Pesticides and Fetal Growth: Pooled Results from Four Longitudinal Birth Cohort Studies. Environ Health Perspect (2015) 0.81