Cargando…

Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing

Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays...

Descripción completa

Detalles Bibliográficos
Autores principales: Sala-Torra, Olga, Reddy, Shishir, Hung, Ling-Hong, Beppu, Lan, Wu, David, Radich, Jerald, Yeung, Ka Yee, Yeung, Cecilia C. S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10497132/
https://www.ncbi.nlm.nih.gov/pubmed/37699001
http://dx.doi.org/10.1371/journal.pgph.0002267
_version_ 1785105243382480896
author Sala-Torra, Olga
Reddy, Shishir
Hung, Ling-Hong
Beppu, Lan
Wu, David
Radich, Jerald
Yeung, Ka Yee
Yeung, Cecilia C. S.
author_facet Sala-Torra, Olga
Reddy, Shishir
Hung, Ling-Hong
Beppu, Lan
Wu, David
Radich, Jerald
Yeung, Ka Yee
Yeung, Cecilia C. S.
author_sort Sala-Torra, Olga
collection PubMed
description Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays, trained technical support, and the availability of reliable electricity. Current fusion detection methods require a long turnaround time (7–10 days) or advance knowledge of the genes involved in the fusions. Recent technology developments have made sequencing possible without a sophisticated molecular laboratory, potentially making molecular diagnosis accessible to remote areas and low-income settings. We describe a long-read sequencing DNA assay designed with CRISPR guides to select and enrich for recurrent leukemia fusion genes, that does not need a priori knowledge of the abnormality present. By applying rapid sequencing technology based on nanopores, we sequenced long pieces of genomic DNA and successfully detected fusion genes in cell lines and primary specimens (e.g., BCR::ABL1, PML::RARA, CBFB::MYH11, KMT2A::AFF1) using cloud-based bioinformatics workflows with novel custom fusion finder software. We detected fusion genes in 100% of cell lines with the expected breakpoints and confirmed the presence or absence of a recurrent fusion gene in 12 of 14 patient cases. With our optimized assay and cloud-based bioinformatics workflow, these assays and analyses could be performed in under 8 hours. The platform’s portability, potential for adaptation to lower-cost devices, and integrated cloud analysis make this assay a candidate to be placed in settings like LMIC to bridge the need of bedside rapid molecular diagnostics.
format Online
Article
Text
id pubmed-10497132
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-104971322023-09-13 Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing Sala-Torra, Olga Reddy, Shishir Hung, Ling-Hong Beppu, Lan Wu, David Radich, Jerald Yeung, Ka Yee Yeung, Cecilia C. S. PLOS Glob Public Health Research Article Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays, trained technical support, and the availability of reliable electricity. Current fusion detection methods require a long turnaround time (7–10 days) or advance knowledge of the genes involved in the fusions. Recent technology developments have made sequencing possible without a sophisticated molecular laboratory, potentially making molecular diagnosis accessible to remote areas and low-income settings. We describe a long-read sequencing DNA assay designed with CRISPR guides to select and enrich for recurrent leukemia fusion genes, that does not need a priori knowledge of the abnormality present. By applying rapid sequencing technology based on nanopores, we sequenced long pieces of genomic DNA and successfully detected fusion genes in cell lines and primary specimens (e.g., BCR::ABL1, PML::RARA, CBFB::MYH11, KMT2A::AFF1) using cloud-based bioinformatics workflows with novel custom fusion finder software. We detected fusion genes in 100% of cell lines with the expected breakpoints and confirmed the presence or absence of a recurrent fusion gene in 12 of 14 patient cases. With our optimized assay and cloud-based bioinformatics workflow, these assays and analyses could be performed in under 8 hours. The platform’s portability, potential for adaptation to lower-cost devices, and integrated cloud analysis make this assay a candidate to be placed in settings like LMIC to bridge the need of bedside rapid molecular diagnostics. Public Library of Science 2023-09-12 /pmc/articles/PMC10497132/ /pubmed/37699001 http://dx.doi.org/10.1371/journal.pgph.0002267 Text en © 2023 Sala-Torra et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sala-Torra, Olga
Reddy, Shishir
Hung, Ling-Hong
Beppu, Lan
Wu, David
Radich, Jerald
Yeung, Ka Yee
Yeung, Cecilia C. S.
Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title_full Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title_fullStr Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title_full_unstemmed Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title_short Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
title_sort rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10497132/
https://www.ncbi.nlm.nih.gov/pubmed/37699001
http://dx.doi.org/10.1371/journal.pgph.0002267
work_keys_str_mv AT salatorraolga rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT reddyshishir rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT hunglinghong rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT beppulan rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT wudavid rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT radichjerald rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT yeungkayee rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing
AT yeungceciliacs rapiddetectionofmyeloidneoplasmfusionsusingsinglemoleculelongreadsequencing