Comparison of structural variants detected by optical mapping with long-read next-generation sequencing

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989100%3A27240%2F21%3A10248614" target="_blank" >RIV/61989100:27240/21:10248614 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15110/21:73607268

Result on the web

<a href="https://academic.oup.com/bioinformatics/article-abstract/37/20/3398/6275264?redirectedFrom=fulltext" target="_blank" >https://academic.oup.com/bioinformatics/article-abstract/37/20/3398/6275264?redirectedFrom=fulltext</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btab359" target="_blank" >10.1093/bioinformatics/btab359</a>

Result language

angličtina

Original language name

Comparison of structural variants detected by optical mapping with long-read next-generation sequencing

Original language description

Motivation: Recent studies have shown the potential of using long-read whole-genome sequencing (WGS) approaches and optical mapping (OM) for the detection of clinically relevant structural variants (SVs) in cancer research. Three main long-read WGS platforms are currently in use: Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT) and 10x Genomics. Recently, whole-genome OM technology (Bionano Genomics) has been introduced into human diagnostics. Questions remain about the accuracy of these long-read sequencing platforms, how comparable/interchangeable they are when searching for SVs and to what extent they can be replaced or supplemented by OM. Moreover, no tool can effectively compare SVs obtained by OM and WGS. Results: This study compared optical maps of the breast cancer cell line SKBR3 with AnnotSV outputs from WGS platforms. For this purpose, a software tool with comparative and filtering features was developed. The majority of SVs up to a 50 kbp distance variance threshold found by OM were confirmed by all WGS platforms, and similar to 99% of translocations and similar to 80% of deletions found by OM were confirmed by both PacBio and ONT, with similar to 70% being confirmed by 10x Genomics in combination with PacBio and/or ONT. Interestingly, long deletions (&gt;100 kbp) were detected only by 10x Genomics. Regarding insertions, similar to 74% was confirmed by PacBio and ONT, but none by 10x Genomics. Inversions and duplications detected by OM were not detected by WGS. Moreover, the tool enabled the confirmation of SVs that overlapped in the same gene(s) and was applied to the filtering of disease-associated SVs.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10200 - Computer and information sciences

Project

<a href="/en/project/NU20-06-00269" target="_blank" >NU20-06-00269: Utility of cellular profiles and proteomics of synovial fluid and periprosthetic tissues for clinical decision making in knee osteoarthritis</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Volume of the periodical

37

Issue of the periodical within the volume

20

Country of publishing house

GB - UNITED KINGDOM

Number of pages

7

Pages from-to

3398-3404

UT code for WoS article

000733829400002

EID of the result in the Scopus database

—