ArticleGenome research2022
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Intrahost mutational dynamics parallel long-term genome evolution in endosymbionts.Molecular biology and evolution · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Integrative and accurate annotations enhance current nonsense-mediated mRNA decay rules.Nucleic acids research · 2025Article
- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals.PLoS biology · 2025Article
- Overcoming Limitations to Deep Learning in Domesticated Animals with TrioTrain.bioRxiv : the preprint server for biology · 2024Article
- Introgressions lead to reference bias in wheat RNA-seq analysis.BMC 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
- Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges.Archives of pharmacal research · 2023Review
- Improving variant calling using population data and deep learning.BMC bioinformatics · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus genome as a potential successor of the current reference genome and assessed its effect on the accuracy of RNA-seq read alignment. To find the best haploid genome representation, we constructed consensus genomes at the pan-human, superpopulation, and population levels, using variant information from The 1000 Genomes Project Consortium. Using personal haploid genomes as the ground truth, we compared mapping errors for real RNA-seq reads aligned to the consensus genomes versus the reference genome. For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of approximately two to three when the reference was replaced with the pan-human consensus genome. We also found that using more population-specific consensuses resulted in little to no increase over using the pan-human consensus, suggesting a limit in the utility of incorporating a more specific genomic variation. Replacing the reference with consensus genomes impacts functional analyses, such as differential expressions of isoforms, genes, and splice junctions.
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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.