Nature Search

Genome-wide identification of directed gene networks using large-scale population genomics data

Identification of causal drivers behind expression is essential for understanding gene function. Here authors develop a method for the large-scale inference of gene–gene interactions in observational population genomics data and characterize a network of trans-effects for 6600 genes.

René Luijk
Koen F. Dekkers
Diana van Heemst
ResearchOpen Access06 Aug 2018
Nature Communications

Volume: 9, P: 1-10
A characterization of cis- and trans-heritability of RNA-Seq-based gene expression

Klaasjan G. Ouwens
Rick Jansen
Dorret I. Boomsma
Research26 Sept 2019
European Journal of Human Genetics

Volume: 28, P: 253-263
Publisher Correction: Identification of 371 genetic variants for age at first sex and birth linked to externalising behavior

Melinda C. Mills
Felix C. Tropf
Felix R. Day
Amendments and Corrections28 Jul 2021
Nature Human Behaviour

Volume: 5, P: 1111
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Analyses of expression profiles from whole blood of 31,684 individuals identify cis-expression quantitative trait loci (eQTL) effects for 88% of genes and trans-eQTL effects for 37% of trait-associated variants.

Urmo Võsa
Annique Claringbould
Lude Franke
Research02 Sept 2021
Nature Genetics

Volume: 53, P: 1300-1310
Identification of 371 genetic variants for age at first sex and birth linked to externalising behaviour

This genome-wide study of age at first sexual intercourse and first birth identifies 371 signals driven by reproductive biology, externalising behaviour and environmental effects, with later onset associated with lower incidence of some diseases.

Melinda C. Mills
Felix C. Tropf
Felix R. Day
Research01 Jul 2021
Nature Human Behaviour

Volume: 5, P: 1717-1730
Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

Many genetic variants identified in genome-wide association studies are associated with gene expression. Here, Porcu et al. propose a transcriptome-wide summary statistics-based Mendelian randomization approach (TWMR) that, applied to 43 human traits, uncovers hundreds of previously unreported gene–trait associations.

Eleonora Porcu
Sina Rüeger
Zoltán Kutalik
ResearchOpen Access24 Jul 2019
Nature Communications

Volume: 10, P: 1-12
Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

In mammalian female germ cells, parent-specific epigenetic marks are erased and the X chromosome reactivated before entry into meiosis. Here, by combining parental haplotype reconstruction with single-cell transcriptomics of human female embryonic germ cells, the authors demonstrate that epigenetic reprogramming occurs in a heterogeneous fashion and during a broad time window up to week 14.

Ábel Vértesy
Wibowo Arindrarto
Susana M. Chuva de Sousa Lopes
ResearchOpen Access14 May 2018
Nature Communications

Volume: 9, P: 1-10
Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

Wibowo Arindrarto
Daniel M. Borràs
Hendrik Veelken
ResearchOpen Access03 Mar 2020
Leukemia

Volume: 35, P: 47-61
OTTERS: a powerful TWAS framework leveraging summary-level reference data

Here, the authors present a TWAS framework OTTERS that adapts multiple polygenic risk score methods to estimate eQTL weights from summary-level eQTL data. Both simulation and real studies show OTTERS is powerful across a wide range of genetic architectures.

Qile Dai
Geyu Zhou
Jingjing Yang
ResearchOpen Access07 Mar 2023
Nature Communications

Volume: 14, P: 1-13
Identification of context-dependent expression quantitative trait loci in whole blood

Bastiaan Heijmans, Peter ’t Hoen, Lude Franke and colleagues describe a strategy to identify context-dependent expression quantitative trait loci (eQTLs). They apply their method to peripheral blood RNA–seq data from 2,116 unrelated individuals and discover 23,060 significant cis-regulated genes, of which 12% showed context-dependent eQTL effects.

Daria V Zhernakova
Patrick Deelen
Lude Franke
Research05 Dec 2016
Nature Genetics

Volume: 49, P: 139-145
Disease variants alter transcription factor levels and methylation of their binding sites

Peter 't Hoen, Lude Franke, Bastiaan Heijmans and colleagues present a combined analysis of methylome and transcriptome data from a large collection of whole-blood samples to infer the downstream effects of disease-associated variants. They identify a large number of trait-associated SNPs influencing methylation of CpG sites in trans, providing insights into the downstream functional effects of many disease-associated variants.

Marc Jan Bonder
René Luijk
Bastiaan T Heijmans
Research05 Dec 2016
Nature Genetics

Volume: 49, P: 131-138
Genetic and environmental influences interact with age and sex in shaping the human methylome

Differential impact of genetic and environmental influences on DNA methylation may result in sex- and age-related physiological variation and disease susceptibility. By analysing DNA methylome of 2,603 individuals from twin families, here, the authors establish a catalogue of between-individual variation in DNA methylation.

Jenny van Dongen
Michel G. Nivard
Dorret I. Boomsma
ResearchOpen Access07 Apr 2016
Nature Communications

Volume: 7, P: 1-13
Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

DNA methylation is critically involved in X chromosome inactivation (XCI) and dosage compensation, yet some X-chromosomal genes escape XCI. Here, Lujik et al. identify three autosomal genetic loci that associate with differential DNA methylation near genes that variably escape XCI in females.

René Luijk
Haoyu Wu
Bastiaan T. Heijmans
ResearchOpen Access14 Sept 2018
Nature Communications

Volume: 9, P: 1-9
DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan

Jenny van Dongen
Fiona A. Hagenbeek
Dorret I. Boomsma
ResearchOpen Access08 Jan 2021
Molecular Psychiatry

Volume: 26, P: 2148-2162
DNA methylation signatures of educational attainment

Jenny van Dongen
Marc Jan Bonder
Bastiaan T. Heijmans
ResearchOpen Access23 Mar 2018
npj Science of Learning

Volume: 3, P: 1-14
Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2

Richard JLF Lemmers
Patrick J van der Vliet
Silvère M van der Maarel
ResearchOpen Access21 Nov 2017
European Journal of Human Genetics

Volume: 26, P: 94-106
A linear mixed-model approach to study multivariate gene–environment interactions

StructLMM is a new method to identify genotype–environment interactions (G×E) that involve multiple exposures or environments. When applied to UK Biobank and eQTL data, StructLMM discovers new G×E signals.

Rachel Moore
Francesco Paolo Casale
Oliver Stegle
Research26 Nov 2018
Nature Genetics

Volume: 51, P: 180-186
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data

Arno van Hilten
Jeroen van Rooij
Gennady V. Roshchupkin
ResearchOpen Access02 Aug 2024
npj Systems Biology and Applications

Volume: 10, P: 1-10
DNA methylation in peripheral tissues and left-handedness

Veronika V. Odintsova
Matthew Suderman
Jenny van Dongen
ResearchOpen Access04 Apr 2022
Scientific Reports

Volume: 12, P: 1-16
Skewed X-inactivation is common in the general female population

Ekaterina Shvetsova
Alina Sofronova
C Wijmenga
ResearchOpen Access14 Dec 2018
European Journal of Human Genetics

Volume: 27, P: 455-465

Search

Genome-wide identification of directed gene networks using large-scale population genomics data

A characterization of cis- and trans-heritability of RNA-Seq-based gene expression

Publisher Correction: Identification of 371 genetic variants for age at first sex and birth linked to externalising behavior

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Identification of 371 genetic variants for age at first sex and birth linked to externalising behaviour

Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

OTTERS: a powerful TWAS framework leveraging summary-level reference data

Identification of context-dependent expression quantitative trait loci in whole blood

Disease variants alter transcription factor levels and methylation of their binding sites

Genetic and environmental influences interact with age and sex in shaping the human methylome

Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan

DNA methylation signatures of educational attainment

Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2

A linear mixed-model approach to study multivariate gene–environment interactions

Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data

DNA methylation in peripheral tissues and left-handedness

Skewed X-inactivation is common in the general female population

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