Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Jasmine: Population-scale structural variant comparison and analysis

View ORCID ProfileMelanie Kirsche, View ORCID ProfileGautam Prabhu, View ORCID ProfileRachel Sherman, View ORCID ProfileBohan Ni, View ORCID ProfileSergey Aganezov, View ORCID ProfileMichael C. Schatz
doi: https://doi.org/10.1101/2021.05.27.445886
Melanie Kirsche
1Department of Computer Science, Johns Hopkins University, Baltimore MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Melanie Kirsche
Gautam Prabhu
1Department of Computer Science, Johns Hopkins University, Baltimore MD
2Department of Biology, Johns Hopkins University, Baltimore, MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gautam Prabhu
Rachel Sherman
1Department of Computer Science, Johns Hopkins University, Baltimore MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Rachel Sherman
Bohan Ni
1Department of Computer Science, Johns Hopkins University, Baltimore MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bohan Ni
Sergey Aganezov
1Department of Computer Science, Johns Hopkins University, Baltimore MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sergey Aganezov
  • For correspondence: sergeyaganezovjr@gmail.com mschatz@cs.jhu.edu
Michael C. Schatz
1Department of Computer Science, Johns Hopkins University, Baltimore MD
2Department of Biology, Johns Hopkins University, Baltimore, MD
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael C. Schatz
  • For correspondence: sergeyaganezovjr@gmail.com mschatz@cs.jhu.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes.

Competing Interest Statement

S.A. has become an employee at Oxford Nanopore. R.S. has become an employee at Illumina.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted May 28, 2021.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Jasmine: Population-scale structural variant comparison and analysis
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Jasmine: Population-scale structural variant comparison and analysis
Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Sergey Aganezov, Michael C. Schatz
bioRxiv 2021.05.27.445886; doi: https://doi.org/10.1101/2021.05.27.445886
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Jasmine: Population-scale structural variant comparison and analysis
Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Sergey Aganezov, Michael C. Schatz
bioRxiv 2021.05.27.445886; doi: https://doi.org/10.1101/2021.05.27.445886

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3607)
  • Biochemistry (7581)
  • Bioengineering (5529)
  • Bioinformatics (20809)
  • Biophysics (10338)
  • Cancer Biology (7988)
  • Cell Biology (11647)
  • Clinical Trials (138)
  • Developmental Biology (6611)
  • Ecology (10217)
  • Epidemiology (2065)
  • Evolutionary Biology (13630)
  • Genetics (9550)
  • Genomics (12854)
  • Immunology (7925)
  • Microbiology (19555)
  • Molecular Biology (7668)
  • Neuroscience (42147)
  • Paleontology (308)
  • Pathology (1258)
  • Pharmacology and Toxicology (2203)
  • Physiology (3269)
  • Plant Biology (7051)
  • Scientific Communication and Education (1294)
  • Synthetic Biology (1952)
  • Systems Biology (5429)
  • Zoology (1119)