Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

David Porubsky; Peter Ebert; Peter A Audano; Mitchell R Vollger; William T Harvey; Pierre Marijon; Jana Ebler; Katherine M Munson; Melanie Sorensen; Arvis Sulovari; Marina Haukness; Maryam Ghareghani; Human Genome Structural Variation Consortium; Peter M Lansdorp; Benedict Paten; Scott E Devine; Ashley D Sanders; Charles Lee; Mark J P Chaisson; Jan O Korbel; Evan E Eichler; Tobias Marschall

doi:10.1038/s41587-020-0719-5

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Nat Biotechnol. 2021 Mar;39(3):302-308. doi: 10.1038/s41587-020-0719-5. Epub 2020 Dec 7.

Authors

David Porubsky^#¹, Peter Ebert^#², Peter A Audano¹, Mitchell R Vollger¹, William T Harvey¹, Pierre Marijon², Jana Ebler², Katherine M Munson¹, Melanie Sorensen¹, Arvis Sulovari¹, Marina Haukness³, Maryam Ghareghani^{2

4}; Human Genome Structural Variation Consortium; Peter M Lansdorp^{5

6}, Benedict Paten³, Scott E Devine⁷, Ashley D Sanders⁸, Charles Lee^{9

10

11}, Mark J P Chaisson¹², Jan O Korbel⁸, Evan E Eichler^{13

14}, Tobias Marschall¹⁵

Affiliations

¹ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
² Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany.
³ UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁴ Center for Bioinformatics, Saarland University, and Max Planck Institute for Informatics, Saarbrücken, Germany.
⁵ Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
⁶ Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
⁷ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
⁸ European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
⁹ The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
¹⁰ The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
¹¹ Department of Life Science, Ewha Womans University, Seoul, Republic of Korea.
¹² Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
¹³ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. eee@gs.washington.edu.
¹⁴ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. eee@gs.washington.edu.
¹⁵ Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany. tobias.marschall@hhu.de.

^# Contributed equally.

Abstract

Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing^1,2 with continuous long-read or high-fidelity³ sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Genome, Human*
Haplotypes
High-Throughput Nucleotide Sequencing / methods*
Humans
Parents*
Puerto Rico / ethnology
Sequence Analysis, DNA / methods*
Single-Cell Analysis / methods*

Abstract

Publication types

MeSH terms

Grants and funding