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RNA-Seq in 296 phased trios provides a high resolution map of genomic imprinting

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00109-006-0131-8openalex-snapshot

Elevated placental expression of the imprinted PHLDA2 gene is associated with low birth weight

inferredcites →https://doi.org/10.1007/s00439-002-0891-3openalex-snapshot

The novel imprinted carboxypeptidase A4 gene (CPA4) in the 7q32 imprinting domain

inferredcites →https://doi.org/10.1007/s00439-003-0966-9openalex-snapshot

Increased variation in mtDNA in patients with familial sensorineural hearing impairment

inferredcites →https://doi.org/10.1016/j.ajhg.2009.11.004openalex-snapshot

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

inferredcites →https://doi.org/10.1016/j.ajhg.2013.08.008openalex-snapshot

Reliable Identification of Genomic Variants from RNA-Seq Data

inferredcites →https://doi.org/10.1016/j.ajhg.2016.06.032openalex-snapshot

DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome

inferredcites →https://doi.org/10.1016/j.ceb.2007.04.013openalex-snapshot

Mechanisms regulating imprinted genes in clusters

inferredcites →https://doi.org/10.1016/j.celrep.2015.07.017openalex-snapshot

Noncanonical Genomic Imprinting Effects in Offspring

inferredcites →https://doi.org/10.1016/s0168-9525(98)01432-2openalex-snapshot

Imprinting in Prader–Willi and Angelman syndromes

inferredcites →https://doi.org/10.1016/s0896-6273(00)80492-4openalex-snapshot

Three period Homologs in Mammals: Differential Light Responses in the Suprachiasmatic Circadian Clock and Oscillating Transcripts Outside of Brain

inferredcites →https://doi.org/10.1038/42706openalex-snapshot

Evidence from Turner's syndrome of an imprinted X-linked locus affecting cognitive function

inferredcites →https://doi.org/10.1038/nature08516openalex-snapshot

Origins and functional impact of copy number variation in the human genome

inferredcites →https://doi.org/10.1038/ng.187openalex-snapshot

Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57

inferredcites →https://doi.org/10.1038/ng.3021openalex-snapshot

Whole-genome sequence variation, population structure and demographic history of the Dutch population

inferredcites →https://doi.org/10.1038/ng.3721openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng.3737openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng0794-433openalex-snapshot

Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour

inferredcites →https://doi.org/10.1038/ng0997-12openalex-snapshot

Imprinting of the Angelman syndrome gene, UBE3A, is restricted to brain

inferredcites →https://doi.org/10.1038/ng1094-203bopenalex-snapshot

Erratum: Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour

inferredcites →https://doi.org/10.1038/ng1567openalex-snapshot

Identification of a cluster of X-linked imprinted genes in mice

inferredcites →https://doi.org/10.1038/ng1577openalex-snapshot

Xlr3b is a new imprinted candidate for X-linked parent-of-origin effects on cognitive function in mice

inferredcites →https://doi.org/10.1038/nmeth.3582openalex-snapshot

WASP: allele-specific software for robust molecular quantitative trait locus discovery

inferredcites →https://doi.org/10.1073/pnas.1600039113openalex-snapshot

A PERIOD3 variant causes a circadian phenotype and is associated with a seasonal mood trait

inferredcites →https://doi.org/10.1086/302712openalex-snapshot

Isoform-Specific Imprinting of the Human PEG1/MEST Gene

inferredcites →https://doi.org/10.1086/519795openalex-snapshot

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

inferredcites →https://doi.org/10.1086/521987openalex-snapshot

Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

inferredcites →https://doi.org/10.1093/bfgp/elq020openalex-snapshot

Identification and resolution of artifacts in the interpretation of imprinted gene expression

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/hmg/ddm041openalex-snapshot

Tissue-specific imprinting of the ZAC/PLAGL1 tumour suppressor gene results from variable utilization of monoallelic and biallelic promoters

inferredcites →https://doi.org/10.1093/hmg/ddp435openalex-snapshot

Multilocus methylation analysis in a large cohort of 11p15-related foetal growth disorders (Russell Silver and Beckwith Wiedemann syndromes) reveals simultaneous loss of methylation at paternal and maternal imprinted loci

inferredcites →https://doi.org/10.1101/cshperspect.a002592openalex-snapshot

Mammalian Genomic Imprinting

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1101/gr.192278.115openalex-snapshot

The landscape of genomic imprinting across diverse adult human tissues

inferredcites →https://doi.org/10.1111/j.1467-9868.2008.00700.xopenalex-snapshot

Approximate Bayesian Inference for Latent Gaussian models by using Integrated Nested Laplace Approximations

inferredcites →https://doi.org/10.1126/science.1190830openalex-snapshot

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

inferredcites →https://doi.org/10.1126/science.270.5242.1610openalex-snapshot

Gametic Imprinting in Mammals

inferredcites →https://doi.org/10.1126/science.289.5477.297openalex-snapshot

An Inherited Functional Circadian Clock in Zebrafish Embryos

inferredcites →https://doi.org/10.1128/mcb.19.2.1262openalex-snapshot

A Family of Insulin-Like Growth Factor II mRNA-Binding Proteins Represses Translation in Late Development

inferredcites →https://doi.org/10.1136/jmg.39.8.575openalex-snapshot

Characterisation of the growth regulating gene IMP3, a candidate for Silver-Russell syndrome

inferredcites →https://doi.org/10.1158/0008-5472.can-05-2959openalex-snapshot

Loss of Imprinting ofIGF2: A Common Epigenetic Modifier of Intestinal Tumor Risk

inferredcites →https://doi.org/10.1186/1471-2105-15-116openalex-snapshot

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

inferredcites →https://doi.org/10.1186/1471-2164-9-169openalex-snapshot

Overlapping genes in the human and mouse genomes

inferredcites →https://doi.org/10.1186/gb-2011-12-3-106openalex-snapshot

The role of imprinted genes in humans

inferredcites →https://doi.org/10.1186/gb-2011-12-3-r25openalex-snapshot

Genome-wide assessment of imprinted expression in human cells

inferredcites →https://doi.org/10.1186/s13059-015-0762-6openalex-snapshot

Tools and best practices for data processing in allelic expression analysis

inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot

Second-generation PLINK: rising to the challenge of larger and richer datasets

inferredcites →https://doi.org/10.1371/journal.pgen.1002600openalex-snapshot

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

inferredcites →https://doi.org/10.1371/journal.pone.0003839openalex-snapshot

Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.4161/15592294.2014.970052openalex-snapshot

Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41586-025-09357-5openalex-snapshot

Parent-of-origin effects on complex traits in up to 236,781 individuals

inferred← citeshttps://doi.org/10.1038/s41592-022-01731-9openalex-snapshot

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

inferred← citeshttps://doi.org/10.1101/2023.10.25.564046openalex-snapshot

Ornaments for Accurate and Efficient Allele-Specific Expression Estimation with Bias Correction

inferred← citeshttps://doi.org/10.1101/732792openalex-snapshot

A statistical method for joint estimation of cis -eQTLs and parent-of-orign effects using an orthogonal framework with RNA-seq data

inferred← citeshttps://doi.org/10.1111/joim.13306openalex-snapshot

Connecting the epigenome, metabolome and proteome for a deeper understanding of disease

inferred← citeshttps://doi.org/10.1186/s13148-019-0655-8openalex-snapshot

Novel parent-of-origin-specific differentially methylated loci on chromosome 16

inferred← citeshttps://doi.org/10.3892/etm.2023.12150openalex-snapshot

Single‑nucleotide polymorphism rs6592645 confers asthma risk through regulating LRRC32 expression

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