Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Background: The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acut...

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Main Authors: Tan, Jaymi *, Chow, Yock Ping, Norzila, Zainul Abidin, Chang, Kian Meng, Veena, Selvaratnam, Nor Rafeah, Tumian, Poh, Yang Ming, Abhi, Veerakumarasivam *, Laffan, Michael Arthur, Wong, Chieh Lee
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Language:English
Published: BMC 2022
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Online Access:http://eprints.sunway.edu.my/2949/1/Abhi%20Veerakumarasivam_Analysis%20of%20genetic%20variants%20in%20myeloproliferative%20neoplasms.pdf
http://eprints.sunway.edu.my/2949/
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-021-01145-0
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spelling my.sunway.eprints.29492024-08-02T07:39:58Z http://eprints.sunway.edu.my/2949/ Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel Tan, Jaymi * Chow, Yock Ping Norzila, Zainul Abidin Chang, Kian Meng Veena, Selvaratnam Nor Rafeah, Tumian Poh, Yang Ming Abhi, Veerakumarasivam * Laffan, Michael Arthur Wong, Chieh Lee QH Natural history RC Internal medicine Background: The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods: The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results: The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions: The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL. BMC 2022 Article PeerReviewed text en cc_by_4 http://eprints.sunway.edu.my/2949/1/Abhi%20Veerakumarasivam_Analysis%20of%20genetic%20variants%20in%20myeloproliferative%20neoplasms.pdf Tan, Jaymi * and Chow, Yock Ping and Norzila, Zainul Abidin and Chang, Kian Meng and Veena, Selvaratnam and Nor Rafeah, Tumian and Poh, Yang Ming and Abhi, Veerakumarasivam * and Laffan, Michael Arthur and Wong, Chieh Lee (2022) Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel. BMC Medical Genomics, 15 (1). ISSN 1755-8794 https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-021-01145-0 10.1186/s12920-021-01145-0
institution Sunway University
building Sunway Campus Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Sunway University
content_source Sunway Institutional Repository
url_provider http://eprints.sunway.edu.my/
language English
topic QH Natural history
RC Internal medicine
spellingShingle QH Natural history
RC Internal medicine
Tan, Jaymi *
Chow, Yock Ping
Norzila, Zainul Abidin
Chang, Kian Meng
Veena, Selvaratnam
Nor Rafeah, Tumian
Poh, Yang Ming
Abhi, Veerakumarasivam *
Laffan, Michael Arthur
Wong, Chieh Lee
Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
description Background: The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods: The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results: The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions: The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL.
format Article
author Tan, Jaymi *
Chow, Yock Ping
Norzila, Zainul Abidin
Chang, Kian Meng
Veena, Selvaratnam
Nor Rafeah, Tumian
Poh, Yang Ming
Abhi, Veerakumarasivam *
Laffan, Michael Arthur
Wong, Chieh Lee
author_facet Tan, Jaymi *
Chow, Yock Ping
Norzila, Zainul Abidin
Chang, Kian Meng
Veena, Selvaratnam
Nor Rafeah, Tumian
Poh, Yang Ming
Abhi, Veerakumarasivam *
Laffan, Michael Arthur
Wong, Chieh Lee
author_sort Tan, Jaymi *
title Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
title_short Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
title_full Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
title_fullStr Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
title_full_unstemmed Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
title_sort analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel
publisher BMC
publishDate 2022
url http://eprints.sunway.edu.my/2949/1/Abhi%20Veerakumarasivam_Analysis%20of%20genetic%20variants%20in%20myeloproliferative%20neoplasms.pdf
http://eprints.sunway.edu.my/2949/
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-021-01145-0
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