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Evaluation of the Oncomine Comprehensive Assay v3 panel for the detection of 1p/19q codeletion in oligodendroglial tumours
  1. Rola H Ali1,2,
  2. Mona Alateeqi3,
  3. Hiba Jama3,
  4. Noor Alrumaidhi3,
  5. Ali Alqallaf2,
  6. Eiman Mahmoud Mohammed3,
  7. Maryam Almurshed4,
  8. Shakir Bahzad3
  1. 1Department of Pathology, Kuwait University, Jabriya, Kuwait
  2. 2Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
  3. 3Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
  4. 4Department of Pathology, Al Sabah Hospital, Shuwaikh, Kuwait
  1. Correspondence to Dr Rola H Ali, Department of Pathology, Kuwait University, Jabriya 13110, Kuwait; rola.ali{at}ku.edu.kw

Abstract

Aims Accurate assessment of 1p/19q codeletion status in diffuse gliomas is of paramount importance for diagnostic, prognostic and predictive purposes. While targeted next generation sequencing (NGS) has been widely implemented for glioma molecular profiling, its role in detecting structural chromosomal variants is less well established, requiring supplementary informatic tools for robust detection. Herein, we evaluated a commercially available amplicon-based targeted NGS panel (Oncomine Comprehensive Assay v3) for the detection of 1p/19q losses in glioma tissues using an Ion Torrent platform and the standard built-in NGS data analysis pipeline solely.

Methods Using as little as 20 ng of DNA from formalin-fixed paraffin-embedded tissues, we analysed 25 previously characterised gliomas for multi-locus copy number losses (CNLs) on 1p and 19q, including 11 oligodendrogliomas (ODG) and 14 non-oligodendroglial (non-ODG) controls. Fluorescence in-situ hybridisation (FISH) was used as a reference standard.

Results The software confidently detected combined contiguous 1p/19q CNLs in 11/11 ODGs (100% sensitivity), using a copy number cut-off of ≤1.5 and a minimum of 10 amplicons covering the regions. Only partial non-specific losses were identified in non-ODGs (100% specificity). Copy number averages of ODG and non-ODG groups were significantly different (p<0.001). NGS was concordant with FISH and was superior to it in distinguishing partial from contiguous losses indicative of whole-arm chromosomal deletion.

Conclusions This commercial NGS panel, along with the standard Ion Torrent algorithm, accurately detected 1p/19q losses in ODG samples, obviating the need for specialised custom-made informatic analyses. This can easily be incorporated into routine glioma workflow as an alternative to FISH.

  • pathology
  • molecular
  • microscopy
  • fluorescence
  • medical oncology

Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information.

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Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information.

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Footnotes

  • Handling editor Runjan Chetty.

  • Twitter @DrRolaAli

  • Contributors RHA: conceptualisation, planning, data collection, data analysis, manuscript writing and editing, figure preparation, responsible for overall content; MAla: investigation, data collection, technical assistance, writing; HJ: investigation, technical assistance; NA: investigation, technical assistance; AA: investigation, technical assistance; EMM: investigation, technical assistance; MAlm: investigation, review and editing; SB: conceptualisation, review and editing, supervision.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.

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