GLIMMERS: glioma molecular markers exploration using long-read sequencing

Wichayapat Thongrattana; Tantip Arigul; Bhoom Suktitipat; Manop Pithukpakorn; Sith Sathornsumetee; Thidathip Wongsurawat; Piroon Jenjaroenpun

doi:10.1093/bioadv/vbae058

GLIMMERS: glioma molecular markers exploration using long-read sequencing

Bioinform Adv. 2024 Apr 15;4(1):vbae058. doi: 10.1093/bioadv/vbae058. eCollection 2024.

Authors

Wichayapat Thongrattana^{1

2}, Tantip Arigul^{2

3}, Bhoom Suktitipat^{4

5}, Manop Pithukpakorn^{6

7}, Sith Sathornsumetee⁸, Thidathip Wongsurawat^{2

3

9}, Piroon Jenjaroenpun^{2

3

9}

Affiliations

¹ Master of Science Program in Medical Bioinformatics (International Program), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
² Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
³ Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁴ Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁵ Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakon Pathom 73000, Thailand.
⁶ Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁷ Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁸ Department of Medicine (Neurology), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁹ Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.

Abstract

Summary: The revised WHO guidelines for classifying and grading brain tumors include several copy number variation (CNV) markers. The turnaround time for detecting CNVs and alterations throughout the entire genome is drastically reduced with the customized read incremental approach on the nanopore platform. However, this approach is challenging for non-bioinformaticians due to the need to use multiple software tools, extract CNV markers and interpret results, which creates barriers due to the time and specialized resources that are necessary. To address this problem and help clinicians classify and grade brain tumors, we developed GLIMMERS: glioma molecular markers exploration using long-read sequencing, an open-access tool that automatically analyzes nanopore-based CNV data and generates simplified reports.

Availability and implementation: GLIMMERS is available at https://gitlab.com/silol_public/glimmers under the terms of the MIT license.