Identification of missense mutations in genes related to cancer pathways in glioma

Glioma is the most common primary brain tumour of the central nervous system. Many genetic alterations and mutations have been identified in glioma using various approaches. We performed DNA sequencing on the tumours of 16 patients with Grade I, II, III and IV glioma. The AmpliSeq Cancer Primers Poo...

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Main Authors:	Nor Azian Abdul Murad, Saiful Effendi Syafruddin, Muhiddin Ishak, Mohd Ridhwan Abdul Razak, Sri Noraima Othman, Soon, Bee Hong, Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Toh, Charng Jeng, Isa Mohamed Rose, Roslan Harun, Rahman Jamal
Format:	Article
Language:	English
Published:	Pusat Perubatan Universiti Kebangsaan Malaysia 2016
Online Access:	http://journalarticle.ukm.my/13240/ http://journalarticle.ukm.my/13240/ http://journalarticle.ukm.my/13240/1/25-54-1-SM.pdf

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recordtype	eprints
spelling	ukm-132402019-08-06T11:07:09Z http://journalarticle.ukm.my/13240/ Identification of missense mutations in genes related to cancer pathways in glioma Nor Azian Abdul Murad, Saiful Effendi Syafruddin, Muhiddin Ishak, Mohd Ridhwan Abdul Razak, Sri Noraima Othman, Soon, Bee Hong Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Toh, Charng Jeng Isa Mohamed Rose, Roslan Harun, Rahman Jamal, Glioma is the most common primary brain tumour of the central nervous system. Many genetic alterations and mutations have been identified in glioma using various approaches. We performed DNA sequencing on the tumours of 16 patients with Grade I, II, III and IV glioma. The AmpliSeq Cancer Primers Pool was used to generate the amplicons. The targeted-ion sphere particles were prepared using the Ion One Touch and Ion Enrichment systems. DNA sequencing was performed on the Ion Torrent Personal Genome Machine (PGM) and the data were analysed using the Torrent Suite Software. In total, 14 mutations were identified in the following genes: KDR (Q472H), MLH1 (V384D), MET (N375S), PTPN11 (E69K), BRAF (V600E), TP53 (D149E, E154K, V157F), IDH1 (R132H), PIK3CA (H1047R), CSF1R (c1061_1061 ins A), KIT (M541L), PTEN (c1373_1373 del A) and PDGFRA (E556V). In addition, there were four novel mutations identified; TP53 (E154K, and D149E), CSF1R (c1061_1061 ins A) and PDGFRA (E556V). The pathogenicity prediction showed that only three mutations were pathogenic: PTPN11 (E69K), BRAF (V600E) and Tp53 (E154K). These mutations result in changes of the proteins’ structure and could affect their functions. Pathway analyses suggested that these genes are closely related to the pathogenesis of GBM through several pathways such as proliferation and invasion, metabolism and angiogenesis. In conclusion, PGM in combination with the AmpliSeq Cancer Panel could be utilised as a potential molecular diagnostic tool not only for glioma but also for other cancers. Pusat Perubatan Universiti Kebangsaan Malaysia 2016 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/13240/1/25-54-1-SM.pdf Nor Azian Abdul Murad, and Saiful Effendi Syafruddin, and Muhiddin Ishak, and Mohd Ridhwan Abdul Razak, and Sri Noraima Othman, and Soon, Bee Hong and Azizi Abu Bakar, and Farizal Fadzil, and Jegan Thanabalan, and Toh, Charng Jeng and Isa Mohamed Rose, and Roslan Harun, and Rahman Jamal, (2016) Identification of missense mutations in genes related to cancer pathways in glioma. Asia-Pacific Journal of Molecular Medicine, 6 (1). pp. 1-10. ISSN 2232-0326 http://spaj.ukm.my/apjmm/index.php/apjmm/issue/view/10
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Kebangasaan Malaysia
building	UKM Institutional Repository
collection	Online Access
language	English
description	Glioma is the most common primary brain tumour of the central nervous system. Many genetic alterations and mutations have been identified in glioma using various approaches. We performed DNA sequencing on the tumours of 16 patients with Grade I, II, III and IV glioma. The AmpliSeq Cancer Primers Pool was used to generate the amplicons. The targeted-ion sphere particles were prepared using the Ion One Touch and Ion Enrichment systems. DNA sequencing was performed on the Ion Torrent Personal Genome Machine (PGM) and the data were analysed using the Torrent Suite Software. In total, 14 mutations were identified in the following genes: KDR (Q472H), MLH1 (V384D), MET (N375S), PTPN11 (E69K), BRAF (V600E), TP53 (D149E, E154K, V157F), IDH1 (R132H), PIK3CA (H1047R), CSF1R (c1061_1061 ins A), KIT (M541L), PTEN (c1373_1373 del A) and PDGFRA (E556V). In addition, there were four novel mutations identified; TP53 (E154K, and D149E), CSF1R (c1061_1061 ins A) and PDGFRA (E556V). The pathogenicity prediction showed that only three mutations were pathogenic: PTPN11 (E69K), BRAF (V600E) and Tp53 (E154K). These mutations result in changes of the proteins’ structure and could affect their functions. Pathway analyses suggested that these genes are closely related to the pathogenesis of GBM through several pathways such as proliferation and invasion, metabolism and angiogenesis. In conclusion, PGM in combination with the AmpliSeq Cancer Panel could be utilised as a potential molecular diagnostic tool not only for glioma but also for other cancers.
format	Article
author	Nor Azian Abdul Murad, Saiful Effendi Syafruddin, Muhiddin Ishak, Mohd Ridhwan Abdul Razak, Sri Noraima Othman, Soon, Bee Hong Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Toh, Charng Jeng Isa Mohamed Rose, Roslan Harun, Rahman Jamal,
spellingShingle	Nor Azian Abdul Murad, Saiful Effendi Syafruddin, Muhiddin Ishak, Mohd Ridhwan Abdul Razak, Sri Noraima Othman, Soon, Bee Hong Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Toh, Charng Jeng Isa Mohamed Rose, Roslan Harun, Rahman Jamal, Identification of missense mutations in genes related to cancer pathways in glioma
author_facet	Nor Azian Abdul Murad, Saiful Effendi Syafruddin, Muhiddin Ishak, Mohd Ridhwan Abdul Razak, Sri Noraima Othman, Soon, Bee Hong Azizi Abu Bakar, Farizal Fadzil, Jegan Thanabalan, Toh, Charng Jeng Isa Mohamed Rose, Roslan Harun, Rahman Jamal,
author_sort	Nor Azian Abdul Murad,
title	Identification of missense mutations in genes related to cancer pathways in glioma
title_short	Identification of missense mutations in genes related to cancer pathways in glioma
title_full	Identification of missense mutations in genes related to cancer pathways in glioma
title_fullStr	Identification of missense mutations in genes related to cancer pathways in glioma
title_full_unstemmed	Identification of missense mutations in genes related to cancer pathways in glioma
title_sort	identification of missense mutations in genes related to cancer pathways in glioma
publisher	Pusat Perubatan Universiti Kebangsaan Malaysia
publishDate	2016
url	http://journalarticle.ukm.my/13240/ http://journalarticle.ukm.my/13240/ http://journalarticle.ukm.my/13240/1/25-54-1-SM.pdf
first_indexed	2023-09-18T20:04:25Z
last_indexed	2023-09-18T20:04:25Z
_version_	1777407062257434624

Identification of missense mutations in genes related to cancer pathways in glioma

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