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Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton

  • Authors:
    • Mohiuddin M. Taher
    • Amal Ali Hassan
    • Muhammad Saeed
    • Raid A. Jastania
    • Tahani H. Nageeti
    • Hisham Alkhalidi
    • Ghida Dairi
    • Zainularifeen Abduljaleel
    • Mohammad Athar
    • Abdellatif Bouazzaoui
    • Wafa M. El‑Bjeirami
    • Faisal A. Al‑Allaf

  • View Affiliations

  • Published online on: September 19, 2019     https://doi.org/10.3892/ol.2019.10882
  • Pages: 5063-5076

  • Copyright: © Taher et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Choroid plexus papilloma (CPP) is a rare benign tumor of the central nervous system that is usually confined to the cerebral ventricles. According to the World Health Organization, CPP corresponds to a grade I atypical CPP (a‑CPP); however, it can become more aggressive and reach grade II, which can rarely undergo malignant transformation into a choroid plexus carcinoma (grade III). To the best of our knowledge, identification of these tumors mutations by next generation DNA sequencing (NGS) has not been yet reported. In the present study, NGS analysis of an a‑CPP case was performed. Data were analyzed using Advaita Bioinformatics i‑VariantGuide and Ion Reporter 5.6 programs. The results from NGS identified 12 novel missense mutations in the following genes: NOTCH1, ATM, STK36, MAGI1, DST, RECQL4, NUMA1, THBS1, MYH11, MALT1, SMARCA4 and CDH20. The PolyPhen score of six variants viz., DST, RECQL4, NUMA1, THBS1, MYHI1 and SMARCA4 were high, which suggested these variants represents pathogenic variants. Two novel insertions that caused frameshift were also found. Furthermore, two novel nonsense mutations and 14 novel intronic variants were identified in this tumor. The novel missense mutation detected in ATM gene was situated in c.5808A>T; p. (Leu1936Phe) in exon 39, and a known ATM mutation was in c.5948A>G; p. (Asn1983Ser). These novel mutations had not been reported in previous database. Subsequently, the quality statistics of these variants, including allele coverage, allele ratio, P‑value, Phred quality score, sequencing coverage, PolyPhen score and alleles frequency was performed. For all variants, P‑value was highly significant and the Phred quality score was high. In addition, the results from sequencing coverage demonstrated that 97.02% reads were on target and that 97.88% amplicons had at least 500 reads. These findings may serve at determining new strategies to distinguish the types of choroid plexus tumor, and at developing novel targeted therapies. Development of NGS technologies in the Kingdom of Saudi Arabia may be used in molecular pathology laboratories.
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November-2019
Volume 18 Issue 5

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Spandidos Publications style
Taher MM, Hassan AA, Saeed M, Jastania RA, Nageeti TH, Alkhalidi H, Dairi G, Abduljaleel Z, Athar M, Bouazzaoui A, Bouazzaoui A, et al: Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton. Oncol Lett 18: 5063-5076, 2019.
APA
Taher, M.M., Hassan, A.A., Saeed, M., Jastania, R.A., Nageeti, T.H., Alkhalidi, H. ... Al‑Allaf, F.A. (2019). Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton. Oncology Letters, 18, 5063-5076. https://doi.org/10.3892/ol.2019.10882
MLA
Taher, M. M., Hassan, A. A., Saeed, M., Jastania, R. A., Nageeti, T. H., Alkhalidi, H., Dairi, G., Abduljaleel, Z., Athar, M., Bouazzaoui, A., El‑Bjeirami, W. M., Al‑Allaf, F. A."Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton". Oncology Letters 18.5 (2019): 5063-5076.
Chicago
Taher, M. M., Hassan, A. A., Saeed, M., Jastania, R. A., Nageeti, T. H., Alkhalidi, H., Dairi, G., Abduljaleel, Z., Athar, M., Bouazzaoui, A., El‑Bjeirami, W. M., Al‑Allaf, F. A."Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton". Oncology Letters 18, no. 5 (2019): 5063-5076. https://doi.org/10.3892/ol.2019.10882