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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 |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 8 |
| Number: | 1 |
| 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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