TY - JOUR

T1 - Dense and accurate whole-chromosome haplotyping of individual genomes

AU - Porubsky, David

AU - Garg, Shilpa

AU - Sanders, Ashley D.

AU - Korbel, Jan O.

AU - Guryev, Victor

AU - Lansdorp, Peter M.

AU - Marschall, Tobias

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - Alleles

KW - Chromosomes, Human/genetics

KW - Diploidy

KW - Gene Library

KW - Genetic Variation

KW - Genome, Human

KW - Genomics/methods

KW - Haplotypes

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Sequence Analysis, DNA/methods

U2 - 10.1038/s41467-017-01389-4

DO - 10.1038/s41467-017-01389-4

M3 - Journal article

C2 - 29101320

VL - 8

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 1293

ER -