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Dense and accurate whole-chromosome haplotyping of individual genomes
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| Zeitschriftentitel: | Nature Communications |
|---|---|
| Personen und Körperschaften: | , , , , , , |
| In: | Nature Communications, 8, 2017, 1 |
| Format: | E-Article |
| Sprache: | Englisch |
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Springer Science and Business Media LLC
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| author_facet |
Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias |
|---|---|
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Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias |
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Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias Nature Communications Dense and accurate whole-chromosome haplotyping of individual genomes General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry Multidisciplinary |
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porubsky, david |
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Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias 2041-1723 Springer Science and Business Media LLC General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry Multidisciplinary http://dx.doi.org/10.1038/s41467-017-01389-4 <jats:title>Abstract</jats:title><jats:p>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.</jats:p> Dense and accurate whole-chromosome haplotyping of individual genomes Nature Communications |
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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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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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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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dense and accurate whole-chromosome haplotyping of individual genomes |
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General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry Multidisciplinary |
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<jats:title>Abstract</jats:title><jats:p>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.</jats:p> |
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| description | <jats:title>Abstract</jats:title><jats:p>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.</jats:p> |
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| spelling | Porubsky, David Garg, Shilpa Sanders, Ashley D. Korbel, Jan O. Guryev, Victor Lansdorp, Peter M. Marschall, Tobias 2041-1723 Springer Science and Business Media LLC General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry Multidisciplinary http://dx.doi.org/10.1038/s41467-017-01389-4 <jats:title>Abstract</jats:title><jats:p>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.</jats:p> Dense and accurate whole-chromosome haplotyping of individual genomes Nature Communications |
| spellingShingle | Porubsky, David, Garg, Shilpa, Sanders, Ashley D., Korbel, Jan O., Guryev, Victor, Lansdorp, Peter M., Marschall, Tobias, Nature Communications, Dense and accurate whole-chromosome haplotyping of individual genomes, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary |
| title | Dense and accurate whole-chromosome haplotyping of individual genomes |
| title_full | Dense and accurate whole-chromosome haplotyping of individual genomes |
| title_fullStr | Dense and accurate whole-chromosome haplotyping of individual genomes |
| title_full_unstemmed | Dense and accurate whole-chromosome haplotyping of individual genomes |
| title_short | Dense and accurate whole-chromosome haplotyping of individual genomes |
| title_sort | dense and accurate whole-chromosome haplotyping of individual genomes |
| title_unstemmed | Dense and accurate whole-chromosome haplotyping of individual genomes |
| topic | General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary |
| url | http://dx.doi.org/10.1038/s41467-017-01389-4 |