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Related Experiment Video

Updated: Aug 23, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq.

Vincent C T Hanlon¹, David Porubsky², Peter M Lansdorp^3,4

¹Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada. vhanlon@bccrc.ca.

Methods in Molecular Biology (Clifton, N.J.)

|November 6, 2022

Summary

Strand-seq technology, combined with local haplotype data, enables the creation of complete chromosome-length haplotypes. This study demonstrates phasing single nucleotide variants (SNVs) using the StrandPhaseR R package.

Keywords:

Genome in a Bottle Haplotype Phasing Strand-seq StrandPhaseR

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Last Updated: Aug 23, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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Published on: June 23, 2012

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Dense local haplotypes are extractable from sequencing data, but struggle to form chromosome-length haplotypes.
Strand-seq is a single-cell sequencing method capturing global phase information via DNA strand orientation.
Combining Strand-seq with local haplotypes can achieve complete chromosome-length phasing.

Purpose of the Study:

To demonstrate the utility of Strand-seq for obtaining chromosome-length haplotype information.
To apply the StrandPhaseR R package for phasing single nucleotide variants (SNVs).
To validate the method using publicly available Genome in a Bottle data.

Main Methods:

Utilized long-read or droplet-based sequencing data for local haplotype extraction.
Employed Strand-seq to capture sparse global phase information from single DNA strands.
Applied the StrandPhaseR R package to phase SNVs in sample HG005.

Main Results:

Successfully phased SNVs using Strand-seq data and the StrandPhaseR package.
Demonstrated the ability to combine local haplotype blocks into chromosome-length haplotypes.
Validated the phasing accuracy with publicly available reference data.

Conclusions:

Strand-seq is a valuable tool for generating complete chromosome-length haplotypes.
The StrandPhaseR R package effectively facilitates SNV phasing with Strand-seq data.
This approach overcomes limitations in current haplotype phasing methods.