Dense and accurate whole-chromosome haplotyping of individual genomes
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- Dense and accurate whole-chromosome haplotyping of individual genomes
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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.
Original language | English |
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Article number | 1293 |
Journal | Nature Communications |
Volume | 8 |
Number of pages | 10 |
ISSN | 2041-1723 |
DOIs | |
Publication status | Published - 2017 |
Externally published | Yes |
- Alleles, Chromosomes, Human/genetics, Diploidy, Gene Library, Genetic Variation, Genome, Human, Genomics/methods, Haplotypes, High-Throughput Nucleotide Sequencing/methods, Humans, Sequence Analysis, DNA/methods
Research areas
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