Direct chromosome-length haplotyping by single-cell sequencing
- David Porubský1,
- Ashley D. Sanders2,
- Niek van Wietmarschen1,
- Ester Falconer2,
- Mark Hills2,
- Diana C.J. Spierings1,
- Marianna R. Bevova1,
- Victor Guryev1 and
- Peter M. Lansdorp1,2,3
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands;
- 2Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada;
- 3Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Corresponding author: p.m.lansdorp{at}umcg.nl
Abstract
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for a HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference. By use of this approach, we mapped all meiotic recombination events in a family trio with high resolution (median range ∼14 kb) and phased larger structural variants like deletions, indels, and balanced rearrangements like inversions. Lastly, the single-cell resolution of Strand-seq allowed us to observe loss of heterozygosity regions in a small number of cells, a significant advantage for studies of heterogeneous cell populations, such as cancer cells. We conclude that Strand-seq is a unique and powerful approach to completely phase individual genomes and map inheritance patterns in families, while preserving haplotype differences between single cells.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.209841.116.
- Received May 29, 2016.
- Accepted September 15, 2016.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
