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Article
Improving the Power to Detect Indirect Effects in Mediation Analysis
Causal mediation analysis seeks to determine whether an independent variable affects a response variable directly or whether it does so indirectly, by way of a mediator. The existing statistical tests to deter...
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Article
Open AccessA computational method for cell type-specific expression quantitative trait loci map** using bulk RNA-seq data
Map** cell type-specific gene expression quantitative trait loci (ct-eQTLs) is a powerful way to investigate the genetic basis of complex traits. A popular method for ct-eQTL map** is to assess the interac...
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Article
Cell-type-aware analysis of RNA-seq data
Most tissue samples are composed of different cell types. Differential expression analysis without accounting for cell-type composition cannot separate the changes due to cell-type composition or cell type-spe...
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Article
Open AccessStatistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies
Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two m...
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Article
Genetic analyses of diverse populations improves discovery for complex traits
Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are b...
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Article
Open AccessAssociating somatic mutations to clinical outcomes: a pan-cancer study of survival time
We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale associat...
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Article
Open AccessI-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms
We propose a statistical boosting method, termed I-Boost, to integrate multiple types of high-dimensional genomics data with clinical data for predicting survival time. I-Boost provides substantially higher pr...
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Article
Open AccessAuthor Correction: Transitions from Ideal to Intermediate Cholesterol Levels may vary by Cholesterol Metric
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper
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Article
Open AccessTransitions from Ideal to Intermediate Cholesterol Levels may vary by Cholesterol Metric
To examine the ability of total cholesterol (TC), a low-density lipoprotein cholesterol (LDL-C) proxy widely used in public health initiatives, to capture important population-level shifts away from ideal and ...
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Article
Open AccessPreMeta: a tool to facilitate meta-analysis of rare-variant associations
Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perf...
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Article
Genetic variation in estrogen and progesterone pathway genes and breast cancer risk: an exploration of tumor subtype-specific effects
To determine whether associations between estrogen pathway-related single nucleotide polymorphisms (SNPs) and breast cancer risk differ by molecular subtype, we evaluated associations between SNPs in cytochrom...
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Article
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
Erik Ingelsson and colleagues report a large-scale genome-wide meta-analysis for associations to the extremes of anthropometric traits, including body mass index, height, waist-to-hip ratio and clinical obesit...
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Article
Common genetic variation in adiponectin, leptin, and leptin receptor and association with breast cancer subtypes
Adipocytokines are produced by visceral fat, and levels may be associated with breast cancer risk. We investigated whether single nucleotide polymorphisms (SNPs) in adipocytokine genes adiponectin (ADIPOQ), lepti...
