ArticleGenome biology2020
Personalized and graph genomes reveal missing signal in epigenomic data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 68 citations in OpenAlex.
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
- Insights into natural neocentromere evolution from a cattle T2T X chromosome.Nature communications · 2025Article
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.Genome research · 2025Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- Efficient indexing and querying of annotations in a pangenome graph.bioRxiv : the preprint server for biology · 2024Article
- Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.Annual review of genomics and human genetics · 2024Review
- Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls.Nature communications · 2024Article
- Measuring, visualizing, and diagnosing reference bias with biastools.Genome biology · 2024Article
- Measuring, visualizing and diagnosing reference bias with biastools.bioRxiv : the preprint server for biology · 2024Article
- STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads.bioRxiv : the preprint server for biology · 2024Article
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
Abstract
backgroundEpigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results.
resultsWe show that accounting for genetic variation using a modified reference genome or a de novo assembled genome can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls either by creating new personal peaks or by the loss of reference peaks. Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered, and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. We show that using a graph personalized genome represents a reasonable compromise between modified reference genomes and de novo assembled genomes. We demonstrate that altered peaks have a genomic distribution typical of other peaks.
conclusionsAnalyzing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.