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Dense and accurate whole-chromosome haplotyping of individual genomes

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Item Type:Article
Title:Dense and accurate whole-chromosome haplotyping of individual genomes
Creators Name:Porubsky, D. and Garg, S. and Sanders, A.D. and Korbel, J.O. and Guryev, V. and Lansdorp, P.M. and Marschall, T.
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.
Keywords:Alleles, Diploidy, DNA Sequence Analysis, Genomics, Gene Library, Genetic Variation, Haplotypes, Human Chromosomes, Human Genome, High-Throughput Nucleotide Sequencing
Source:Nature Communications
Publisher:Nature Publishing Group
Page Range:1293
Date:3 November 2017
Official Publication:https://doi.org/10.1038/s41467-017-01389-4
PubMed:View item in PubMed

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