Frontiers in Molecular Biosciences (Sep 2022)

A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samples

  • Cedric Chuan-Young Ng,
  • Cedric Chuan-Young Ng,
  • Sandy Lim,
  • Abner Herbert Lim,
  • Abner Herbert Lim,
  • Nur Diyana Md Nasir,
  • Jingxian Zhang,
  • Vikneswari Rajasegaran,
  • Vikneswari Rajasegaran,
  • Jing Yi Lee,
  • Jing Yi Lee,
  • Jessica Sook Ting Kok,
  • Jessica Sook Ting Kok,
  • Aye Aye Thike,
  • Johnathan Xiande Lim,
  • Ruifen Weng,
  • Sidney Yee,
  • Yukti Choudhury,
  • Jason Yongsheng Chan,
  • Jason Yongsheng Chan,
  • Puay Hoon Tan,
  • Puay Hoon Tan,
  • Min-Han Tan,
  • Bin Tean Teh

DOI
https://doi.org/10.3389/fmolb.2022.963243
Journal volume & issue
Vol. 9

Abstract

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Introduction: A well-validated diagnostic assay with curated biomarkers complements clinicopathological factors to facilitate early diagnosis and ensure timely treatment delivery. This study focuses on an Asian-centric cancer diagnostic assay designed and thoroughly validated against commercially available standard references and a cohort of over 200 clinical specimens spanning 12 diverse Asian-centric cancer types.Methods: The assay uses hybrid-capture probes capable of profiling DNA aberrations from 572 cancer-related genes and 91 RNA fusion partners. The panel can detect clinically-tractable biomarkers such as microsatellite instability (MSI) and tumor mutation burden (TMB).Results: Analytical evaluation demonstrated 100% specificity and 99.9% sensitivity within a ≥5% VAF limit of detection (LoD) for SNV/Indels. RNA-based fusion features an LoD of ≥5 copies per nanogram input when evaluated against commercial references. Excellent linearity and concordance were observed when benchmarking against orthogonal methods in identifying MSI status, TMB scores and RNA fusions. Actionable genetic alterations were identified in 65% of the clinical samples.Conclusion: These results demonstrate a molecular diagnostic assay that accurately detects genomic alterations and complex biomarkers. The data also supports an excellent performance of this assay for making critical diagnoses and well-informed therapeutic decisions in Asian prevalent cancers.

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