Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

doi:10.1007/978-1-0716-2819-5_12

. 2023:2590:183-200.

doi: 10.1007/978-1-0716-2819-5_12.

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

Vincent C T Hanlon^#¹, David Porubsky^#², Peter M Lansdorp^{3

4}

Affiliations

¹ Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada. vhanlon@bccrc.ca.
² Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. porubsky@uw.edu.
³ Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.
⁴ Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

^# Contributed equally.

PMID: 36335500
DOI: 10.1007/978-1-0716-2819-5_12

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

Vincent C T Hanlon et al. Methods Mol Biol. 2023.

. 2023:2590:183-200.

doi: 10.1007/978-1-0716-2819-5_12.

Authors

Vincent C T Hanlon^#¹, David Porubsky^#², Peter M Lansdorp^{3

4}

Affiliations

¹ Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada. vhanlon@bccrc.ca.
² Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. porubsky@uw.edu.
³ Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.
⁴ Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

^# Contributed equally.

PMID: 36335500
DOI: 10.1007/978-1-0716-2819-5_12

Abstract

Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.

Keywords: Genome in a Bottle; Haplotype; Phasing; Strand-seq; StrandPhaseR.

PubMed Disclaimer

Cited by

Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B. Lorig-Roach R, et al. bioRxiv [Preprint]. 2023 Feb 22:2023.02.21.529152. doi: 10.1101/2023.02.21.529152. bioRxiv. 2023. Update in: Genome Res. 2024 Apr 25;34(3):454-468. doi: 10.1101/gr.278268.123 PMID: 36865218 Free PMC article. Updated. Preprint.
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.
Henglin M, Ghareghani M, Harvey WT, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. Henglin M, et al. Genome Biol. 2024 Oct 10;25(1):265. doi: 10.1186/s13059-024-03409-1. Genome Biol. 2024. PMID: 39390579 Free PMC article.
The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA.
Logsdon GA, Eichler EE. Logsdon GA, et al. Genes (Basel). 2022 Dec 28;14(1):92. doi: 10.3390/genes14010092. Genes (Basel). 2022. PMID: 36672831 Free PMC article. Review.
Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen HE, McNulty B, Porubsky D, Montague TG, Lucas JK, Condon C, Eizenga JM, Juul S, McKenzie SK, Simmonds SE, Park J, Asri M, Koren S, Eichler EE, Axel R, Martin B, Carnevali P, Miga KH, Paten B. Lorig-Roach R, et al. Genome Res. 2024 Apr 25;34(3):454-468. doi: 10.1101/gr.278268.123. Genome Res. 2024. PMID: 38627094 Free PMC article.
Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.
Henglin M, Ghareghani M, Harvey W, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. Henglin M, et al. bioRxiv [Preprint]. 2024 Jun 20:2024.02.15.580432. doi: 10.1101/2024.02.15.580432. bioRxiv. 2024. Update in: Genome Biol. 2024 Oct 10;25(1):265. doi: 10.1186/s13059-024-03409-1 PMID: 38529499 Free PMC article. Updated. Preprint.

References

1. Porubský D, Sanders AD, van Wietmarschen N et al (2016) Direct chromosome-length haplotyping by single-cell sequencing. Genome Res 26:1565–1574. https://doi.org/10.1101/gr.209841.116 - DOI - PubMed - PMC
1. Falconer E, Hills M, Naumann U et al (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9:1107–1112. https://doi.org/10.1038/nmeth.2206 - DOI - PubMed - PMC
1. Porubský D (2017) Haplotype resolved genomes: computational challenges and applications. Dissertation, University of Groningen
1. van Wietmarschen N, Lansdorp PM (2016) Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells. Nucleic Acids Res 44:6787–6793. https://doi.org/10.1093/nar/gkw422 - DOI - PubMed - PMC
1. Porubsky D, Sanders AD, Taudt A et al (2020) breakpointR: an R/Bioconductor package to localize Strand state changes in Strand-seq data. Bioinformatics 36:1260–1261. https://doi.org/10.1093/bioinformatics/btz681 - DOI - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

PJT-159787/CIHR/Canada

LinkOut - more resources

Full Text Sources
- Springer

[1] Porubský D, Sanders AD, van Wietmarschen N et al (2016) Direct chromosome-length haplotyping by single-cell sequencing. Genome Res 26:1565–1574. https://doi.org/10.1101/gr.209841.116 - DOI - PubMed - PMC

[2] Porubský D, Sanders AD, van Wietmarschen N et al (2016) Direct chromosome-length haplotyping by single-cell sequencing. Genome Res 26:1565–1574. https://doi.org/10.1101/gr.209841.116 - DOI - PubMed - PMC

[3] Falconer E, Hills M, Naumann U et al (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9:1107–1112. https://doi.org/10.1038/nmeth.2206 - DOI - PubMed - PMC

[4] Falconer E, Hills M, Naumann U et al (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9:1107–1112. https://doi.org/10.1038/nmeth.2206 - DOI - PubMed - PMC

[5] Porubský D (2017) Haplotype resolved genomes: computational challenges and applications. Dissertation, University of Groningen

[6] Porubský D (2017) Haplotype resolved genomes: computational challenges and applications. Dissertation, University of Groningen

[7] van Wietmarschen N, Lansdorp PM (2016) Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells. Nucleic Acids Res 44:6787–6793. https://doi.org/10.1093/nar/gkw422 - DOI - PubMed - PMC

[8] van Wietmarschen N, Lansdorp PM (2016) Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells. Nucleic Acids Res 44:6787–6793. https://doi.org/10.1093/nar/gkw422 - DOI - PubMed - PMC

[9] Porubsky D, Sanders AD, Taudt A et al (2020) breakpointR: an R/Bioconductor package to localize Strand state changes in Strand-seq data. Bioinformatics 36:1260–1261. https://doi.org/10.1093/bioinformatics/btz681 - DOI - PubMed

[10] Porubsky D, Sanders AD, Taudt A et al (2020) breakpointR: an R/Bioconductor package to localize Strand state changes in Strand-seq data. Bioinformatics 36:1260–1261. https://doi.org/10.1093/bioinformatics/btz681 - DOI - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

Affiliations

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

Authors

Affiliations

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources