A Draft Human Pangenome Reference

Published

May 10, 2023

Author(s)

Wen-Wei Liao, Mobin Asri, Jana Ebler, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Erik Garrison, Tobias Marschall, Ira Hall, Heng Li, Benedict Paten

Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Citation

Nature

Volume

617

Pub Type

Journals

Download Paper

https://doi.org/10.1038/s41586-023-05896-x

Local Download

Keywords

pangenome graph, genome assembly

Citation

Liao, W. , Asri, M. , Ebler, J. , McDaniel, J. , Olson, N. , Wagner, J. , Zook, J. , Garrison, E. , Marschall, T. , Hall, I. , Li, H. and Paten, B. (2023), A Draft Human Pangenome Reference, Nature, [online], https://doi.org/10.1038/s41586-023-05896-x, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=935182 (Accessed October 8, 2025)