Building complete chromosomal haplotypes using single-cell sequencing
- David Porubsky1,
- Ashley D Sanders2,
- Niek van Wietmarschen1,
- Ester Falconer2,
- Mark Hills2,
- Diana C.J. Spierings1,
- Marianna R Bevova1,
- Victor Guryev1 and
- Peter Michael Lansdorp2,3
- ↵* Corresponding author; email: plansdor{at}bccrc.ca
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 HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference. Using 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 as well as 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.
- Received May 29, 2016.
- Accepted September 15, 2016.
- Published by Cold Spring Harbor Laboratory Press
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