Dense and accurate whole-chromosome haplotyping of individual genomes

David Porubsky, Shilpa Garg, Ashley D. Sanders, Jan O. Korbel, Victor Guryev, Peter M. Lansdorp and Tobias Marschall ()
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David Porubsky: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen
Shilpa Garg: Center for Bioinformatics, Saarland University
Ashley D. Sanders: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Jan O. Korbel: European Molecular Biology Laboratory (EMBL), Genome Biology Unit
Victor Guryev: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen
Peter M. Lansdorp: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen
Tobias Marschall: Center for Bioinformatics, Saarland University

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different technologies represents an attractive solution to chart the genetic variation of diploid genomes.

Date: 2017
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DOI: 10.1038/s41467-017-01389-4

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