A web-based bioinformatic tool LYNX for targeted LYmphoid NeXt- generation sequencing data analysis and visualization for hematooncology.

REIGL, Tomáš, Jakub Paweł PORC, Veronika NAVRKALOVÁ, Jakub HYNŠT, Karol PÁL, Kamila STRÁNSKÁ, Jana KOTAŠKOVÁ, Šárka POSPÍŠILOVÁ and Karla PLEVOVÁ. A web-based bioinformatic tool LYNX for targeted LYmphoid NeXt- generation sequencing data analysis and visualization for hematooncology. In ESHG Conference 2023, Glasgow, Skotsko. 2023.

Basic information

• Original name: A web-based bioinformatic tool LYNX for targeted LYmphoid NeXt- generation sequencing data analysis and visualization for hematooncology.
• Authors: REIGL, Tomáš (203 Czech Republic, belonging to the institution), Jakub Paweł PORC (616 Poland, belonging to the institution), Veronika NAVRKALOVÁ (203 Czech Republic, belonging to the institution), Jakub HYNŠT (203 Czech Republic, belonging to the institution), Karol PÁL (703 Slovakia, belonging to the institution), Kamila STRÁNSKÁ (203 Czech Republic, belonging to the institution), Jana KOTAŠKOVÁ (203 Czech Republic, belonging to the institution), Šárka POSPÍŠILOVÁ (203 Czech Republic, guarantor, belonging to the institution) and Karla PLEVOVÁ (203 Czech Republic, belonging to the institution).
• Edition: ESHG Conference 2023, Glasgow, Skotsko, 2023.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• RIV identification code: RIV/00216224:14740/23:00132843
• Organization unit: Central European Institute of Technology
• Keywords in English: Next-generation sequencing; genetic markers; lymphoid malignancies; LYNX
• Tags: NÚVR_CEITEC, rivok
• Tags: International impact, Reviewed

Abstract

Next-generation sequencing (NGS) is one of the most rapidly expanding technologies in laboratory medicine. In routine diagnostics, a single NGS experiment can replace several laboratory tests and provide more information about the disease being tested. Commonly, the assistance of a qualified bioinformatician or a dedicated tool is necessary for the data analysis. Our team has created an integrative, targeted NGS panel that detects genetic markers common for most abundant lymphoid malignancies (PMID: 34082072). For this panel, we have developed a bioinformatic tool, LYNX, with a user interface (UI) that allows diagnosticians to easily analyze the data and interactively visualize the results. This facilitates data interpretation and speeds up diagnostic procedures.

Links

• LM2018140, research and development project: Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

• LX22NPO5102, research and development project: Name: Národní ústav pro výzkum rakoviny (Acronym: NÚVR)

Investor: Ministry of Education, Youth and Sports of the CR, National institute for cancer research, 5.1 EXCELES

• NU20-08-00314, research and development project: Name: Single cell analýza: moderní nástroj pro studium klonální evoluce u pacientů s chronickou lymfocytární leukémií s vysokým rizikem (Acronym: Single cell analysis of CLL cells)

Investor: Ministry of Health of the CR, Subprogram 1 - standard

• NU21-08-00237, research and development project: Name: Pokročilé sekvenační metody pro analýzu strukturních přestaveb nádorového genomu

Investor: Ministry of Health of the CR, Advanced sequencing methods for deciphering structural variants in cancer genome, Subprogram 1 - standard

• NU22-08-00227, research and development project: Name: Pokročilé molekulární analýzy pro komplexní diagnostiku a monitorování pacientů s difúzním velkobuněčným B-lymfomem: využití profilování genové exprese, tekutých biopsií a sekvenování třetí generace

Investor: Ministry of Health of the CR, Advanced molecular testing for aggregate diagnosis and management of DLBCL patients: engagement of gene expression profiling, liquid biopsy and long-read sequencing, Subprogram 1 - standard