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Identifying large indels in targeted next generation sequencing assays for myeloid neoplasms: a cautionary tale of the ZRSR1 pseudogene
  1. Isaac KS Ng1,
  2. Christopher Ng2,
  3. Jia Jin Low3,
  4. Lily Chiu2,
  5. Elaine Seah4,
  6. Chin Hin Ng4,
  7. Wee-Joo Chng4,5,6,
  8. Benedict Yan2,
  9. Kenneth H K Ban1
  1. 1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
  2. 2 Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
  3. 3 Department of Statistics, National University of Singapore, Singapore
  4. 4 Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
  5. 5 Cancer Science Institute, National University of Singapore, Singapore
  6. 6 Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
  1. Correspondence to Dr Kenneth H K Ban, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Dr, Singapore 117596, Singapore; kenneth_ban{at}nuhs.edu.sg

Abstract

Targeted next generation sequencing platforms have been increasingly utilised for identification of novel mutations in myeloid neoplasms, such as acute myeloid leukaemia (AML), and hold great promise for use in routine clinical diagnostics. In this study, we evaluated the utility of an open source variant caller in detecting large indels in a targeted sequencing of AML samples. While we found that this bioinformatics pipeline has the potential to accurately capture large indels (>20 bp) in patient samples, we highlighted the pitfall of a confounding ZRSR1 pseudogene that led to an erroneous ZRSR2 variant call. We further discuss possible clinical implications of the ZRSR1 pseudogene in myeloid neoplasms based on its molecular features. Knowledge of the confounding ZRSR1 pseudogene in ZRSR2 sequencing assays could be particularly important in AML diagnostics because the detection of ZRSR2 in AML patients is highly specific for an s-AML diagnosis.

  • MOLECULAR PATHOLOGY
  • MOLECULAR GENETICS
  • HAEMATO-ONCOLOGY
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Footnotes

  • Handling editor Runjan Chetty

  • Contributors IKSN and JJL wrote the manuscript. IKSN, W-JC, BY and KB designed the study. ES and CHN organised the clinical samples. IKSN, CN and LC performed the experiments. IKSN, CN, JJL, W-JC, BY and KB contributed to data analysis and interpretation. The manuscript was reviewed by all of the authors.

  • Funding This work was partly supported by Singapore Cancer Syndicate Grant. This research was supported by the National Research Foundation Singapore and the Singapore Ministry of Education under the Research Centers of Excellence initiative. W-JC is supported by NMRC Clinician Scientist Investigator award.

  • Competing interests None declared.

  • Ethics approval The study was approved by the NUHS institutional review board (reference No 2015/00111).

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

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