One Reference Genome is Not Enough

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2019 May 26

PMID 31126314

Citations 37

Authors

Xiaofei Yang

Wan-Ping Lee

Kai Ye

Charles Lee

Affiliations

Soon will be listed here.

Abstract

A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome.

Citing Articles

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Assessing parasite genomes assembled using only Oxford Nanopore Technologies MinION data.

Herzog K, Wu R, Hawdon J, Nejsum P, Fauver J iScience. 2024; 27(9):110614.

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Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing.

Yang X, Zhao X, Qu S, Jia P, Wang B, Gao S Fundam Res. 2024; 2(6):946-953.

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Pangenome analysis reveals transposon-driven genome evolution in cotton.

He X, Qi Z, Liu Z, Chang X, Zhang X, Li J BMC Biol. 2024; 22(1):92.

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Dysregulated lncRNAs regulate human umbilical cord mesenchymal stem cell differentiation into insulin-producing cells by forming a regulatory network with mRNAs.

Xie T, Huang Q, Huang Q, Huang Y, Liu S, Zeng H Stem Cell Res Ther. 2024; 15(1):22.

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References

Rakocevic G, Semenyuk V, Lee W, Spencer J, Browning J, Johnson I . Fast and accurate genomic analyses using genome graphs. Nat Genet. 2019; 51(2):354-362. DOI: 10.1038/s41588-018-0316-4. View

Audano P, Sulovari A, Graves-Lindsay T, Cantsilieris S, Sorensen M, Welch A . Characterizing the Major Structural Variant Alleles of the Human Genome. Cell. 2019; 176(3):663-675.e19. PMC: 6438697. DOI: 10.1016/j.cell.2018.12.019. View

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F . The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016; 538(7624):201-206. PMC: 5161557. DOI: 10.1038/nature18964. View

Schneider V, Graves-Lindsay T, Howe K, Bouk N, Chen H, Kitts P . Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017; 27(5):849-864. PMC: 5411779. DOI: 10.1101/gr.213611.116. View

Chaisson M, Huddleston J, Dennis M, Sudmant P, Malig M, Hormozdiari F . Resolving the complexity of the human genome using single-molecule sequencing. Nature. 2014; 517(7536):608-11. PMC: 4317254. DOI: 10.1038/nature13907. View