Chromosome-scale, haplotype-resolved assembly of human genomes

Shilpa Garg^{1

2

3}, Arkarachai Fungtammasan⁴, Andrew Carroll⁵, Mike Chou⁶, Anthony Schmitt⁷, Xiang Zhou⁷, Stephen Mac⁷, Paul Peluso⁸, Emily Hatas⁸, Jay Ghurye⁹, Jared Maguire⁹, Medhat Mahmoud¹⁰, Haoyu Cheng^{11

12}, David Heller¹³, Justin M Zook¹⁴, Tobias Moemke¹⁵, Tobias Marschall^{15

16}, Fritz J Sedlazeck¹⁰, John Aach⁶, Chen-Shan Chin¹⁷, George M Church¹⁸, Heng Li^{19

20}

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
² Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
³ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
⁴ DNAnexus, Mountain View, CA, USA.
⁵ Google, Mountain View, CA, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA, USA.
⁷ Arima Genomics, San Diego, CA, USA.
⁸ Pacific Biosciences, Menlo Park, CA, USA.
⁹ Dovetail Genomics, Scotts Valley, CA, USA.
¹⁰ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
¹¹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
¹² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹³ Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁴ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
¹⁵ Saarland University, Saarbrücken, Germany.
¹⁶ Max Planck Institute for Informatics, Saarbrücken, Germany.
¹⁷ DNAnexus, Mountain View, CA, USA. jchin@dnanexus.com.
¹⁸ Department of Genetics, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu.
¹⁹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA. hli@ds.dfci.harvard.edu.
²⁰ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. hli@ds.dfci.harvard.edu.

PMID: 33288905
PMCID: PMC7954703
DOI: 10.1038/s41587-020-0711-0

Chromosome-scale, haplotype-resolved assembly of human genomes

Shilpa Garg et al. Nat Biotechnol. 2021 Mar.

. 2021 Mar;39(3):309-312.

doi: 10.1038/s41587-020-0711-0. Epub 2020 Dec 7.

Authors

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
² Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
³ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. shilpa_garg@hms.harvard.edu.
⁴ DNAnexus, Mountain View, CA, USA.
⁵ Google, Mountain View, CA, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA, USA.
⁷ Arima Genomics, San Diego, CA, USA.
⁸ Pacific Biosciences, Menlo Park, CA, USA.
⁹ Dovetail Genomics, Scotts Valley, CA, USA.
¹⁰ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
¹¹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
¹² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹³ Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁴ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
¹⁵ Saarland University, Saarbrücken, Germany.
¹⁶ Max Planck Institute for Informatics, Saarbrücken, Germany.
¹⁷ DNAnexus, Mountain View, CA, USA. jchin@dnanexus.com.
¹⁸ Department of Genetics, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu.
¹⁹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA. hli@ds.dfci.harvard.edu.
²⁰ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. hli@ds.dfci.harvard.edu.

PMID: 33288905
PMCID: PMC7954703
DOI: 10.1038/s41587-020-0711-0

Abstract

Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98-99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.

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Conflict of interest statement

F.J.S. obtained a Pacbio SMRT grant in 2019 and had multiple travels sponsored by Pacific Biosciences and Oxford Nanopore Technologies. E.H. and P.P. are employees of Pacific Biosciences. C.-S.C. and A.F. are employees of DNAnexus. A.S., X.Z. and S.M. are employees of Arima Genomics. J.G. and J.M. are employees of Dovetail Genomics. A.C. is an employee of Google. H.L. is a consultant of Integrated DNA Technologies, Inc. and on the Scientific Advisory Boards of Sentieon, Inc., BGI and OrigiMed. G.M.C. is a cofounder of Editas Medicine and has other financial interests, listed at http://arep.med.harvard.edu/gmc/tech.html.

Figures

**Fig. 1. Outline of the phased assembly algorithm, DipAsm.**
Assemble HiFi reads into unphased contigs using Peregrine (1); group and order contigs into scaffolds with Hi-C data using HiRise/3D-DNA (3D de novo assembly) (2); map HiFi reads to scaffolds and call heterozygous SNPs using DeepVariant (3); phase heterozygous SNP calls with both HiFi and Hi-C data using WhatsHap plus HapCUT2 (4); partition reads based on their phase using WhatsHap (5); assemble partitioned reads into phased contigs using Peregrine (6).

**Fig. 2. Applications of phased assemblies.**
a, Local sequence divergence in comparison to the reference HLA haplotypes (top) and to the KIR haplotypes (bottom) regions in GRCh38. b, SV density (per 100 kb) on chromosome 1 for HG002 (inner), NA12878 (middle) and PGP1 (outer).

See this image and copyright information in PMC

References

1. Tewhey R, Bansal V, Torkamani A, Topol EJ, Schork NJ. The importance of phase information for human genomics. Nat. Rev. Genet. 2011;12:215–223. doi: 10.1038/nrg2950. - DOI - PMC - PubMed
1. Vinson JP, et al. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 2005;15:1127–1135. doi: 10.1101/gr.3722605. - DOI - PMC - PubMed
1. Chin C-S, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods. 2016;13:1050–1054. doi: 10.1038/nmeth.4035. - DOI - PMC - PubMed
1. Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB. Direct determination of diploid genome sequences. Genome Res. 2017;27:757–767. doi: 10.1101/gr.214874.116. - DOI - PMC - PubMed
1. Garg S, et al. A graph-based approach to diploid genome assembly. Bioinformatics. 2018;34:i105–i114. doi: 10.1093/bioinformatics/bty279. - DOI - PMC - PubMed

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Chromosome-scale, haplotype-resolved assembly of human genomes

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Chromosome-scale, haplotype-resolved assembly of human genomes

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Research Materials

Miscellaneous