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Discovery and genotyping of structural variation from long-read haploid genome sequence data
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural v...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411763/ https://www.ncbi.nlm.nih.gov/pubmed/27895111 http://dx.doi.org/10.1101/gr.214007.116 |
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author | Huddleston, John Chaisson, Mark J.P. Steinberg, Karyn Meltz Warren, Wes Hoekzema, Kendra Gordon, David Graves-Lindsay, Tina A. Munson, Katherine M. Kronenberg, Zev N. Vives, Laura Peluso, Paul Boitano, Matthew Chin, Chen-Shin Korlach, Jonas Wilson, Richard K. Eichler, Evan E. |
author_facet | Huddleston, John Chaisson, Mark J.P. Steinberg, Karyn Meltz Warren, Wes Hoekzema, Kendra Gordon, David Graves-Lindsay, Tina A. Munson, Katherine M. Kronenberg, Zev N. Vives, Laura Peluso, Paul Boitano, Matthew Chin, Chen-Shin Korlach, Jonas Wilson, Richard K. Eichler, Evan E. |
author_sort | Huddleston, John |
collection | PubMed |
description | In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection. |
format | Online Article Text |
id | pubmed-5411763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-54117632017-11-01 Discovery and genotyping of structural variation from long-read haploid genome sequence data Huddleston, John Chaisson, Mark J.P. Steinberg, Karyn Meltz Warren, Wes Hoekzema, Kendra Gordon, David Graves-Lindsay, Tina A. Munson, Katherine M. Kronenberg, Zev N. Vives, Laura Peluso, Paul Boitano, Matthew Chin, Chen-Shin Korlach, Jonas Wilson, Richard K. Eichler, Evan E. Genome Res Research In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection. Cold Spring Harbor Laboratory Press 2017-05 /pmc/articles/PMC5411763/ /pubmed/27895111 http://dx.doi.org/10.1101/gr.214007.116 Text en © 2017 Huddleston et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Research Huddleston, John Chaisson, Mark J.P. Steinberg, Karyn Meltz Warren, Wes Hoekzema, Kendra Gordon, David Graves-Lindsay, Tina A. Munson, Katherine M. Kronenberg, Zev N. Vives, Laura Peluso, Paul Boitano, Matthew Chin, Chen-Shin Korlach, Jonas Wilson, Richard K. Eichler, Evan E. Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title | Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title_full | Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title_fullStr | Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title_full_unstemmed | Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title_short | Discovery and genotyping of structural variation from long-read haploid genome sequence data |
title_sort | discovery and genotyping of structural variation from long-read haploid genome sequence data |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411763/ https://www.ncbi.nlm.nih.gov/pubmed/27895111 http://dx.doi.org/10.1101/gr.214007.116 |
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