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Clinical validation of qPCR Target Selector™ assays using highly specific switch-blockers for rare mutation detection
  1. Lyle Arnold1,2,
  2. Vassilios Alexiadis1,
  3. Tim watanaskul1,
  4. Vahid Zarrabi3,
  5. Jason Poole1,
  6. Veena Singh4
  1. 1 Research and Development, Biocept Inc, San Diego, California, USA
  2. 2 Aegea Biotechnologies, San Diego, California, USA
  3. 3 Department of Molecular Pathology, UCLA, Los Angeles, California, USA
  4. 4 Clinical Laboratory, Biocept Inc, San Diego, California, USA
  1. Correspondence to Dr Veena Singh, Clinical Laboratory, Biocept Inc, San Diego, California, USA; vsingh{at}biocept.com

Abstract

Aims The identification of actionable DNA mutations associated with a patient’s tumour is critical for devising a targeted, personalised cancer treatment strategy. However, these molecular analyses are typically performed using tissue obtained via biopsy, which involves substantial risk and is often not feasible. In addition, biopsied tissue does not always reflect tumour heterogeneity, and sequential biopsies to track disease progression (eg, emergence of drug resistance mutations) are not well tolerated. To overcome these and other biopsy-associated limitations, we have developed non-invasive ‘liquid biopsy’ technologies to enable the molecular characterisation of a patient’s cancer using peripheral blood samples.

Methods The Target Selector ctDNA platform uses a real-time PCR-based approach, coupled with DNA sequencing, to identify cancer-associated genetic mutations within circulating tumour DNA. This is accomplished via a patented blocking approach suppressing wild-type DNA amplification, while allowing specific amplification of mutant alleles.

Results To promote the clinical uptake of liquid biopsy technologies, it is first critical to demonstrate concordance between results obtained via liquid and traditional biopsy procedures. Here, we focused on three genes frequently mutated in cancer: EGFR (Del19, L858, and T790), BRAF (V600) and KRAS (G12/G13). For each Target Selector assay, we demonstrated extremely high accuracy, sensitivity and specificity compared with results obtained from tissue biopsies. Overall, we found between 93% and 96% concordance to blinded tissue samples across 127 clinical assays.

Conclusions The switch-blocker technology reported here offers a highly effective method for non-invasively determining the molecular signatures of patients with cancer.

  • cancer genetics
  • genetics
  • laboratory tests
  • lung cancer
  • oncology
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Footnotes

  • Handling editor Runjan Chetty.

  • Contributors DF, JAM and CRTV are acknowledged for data compilation and review.

  • Funding All authors were employees of Aegea Biotechnologies or Biocept at the time this work was conducted.

  • Competing interests None declared.

  • Patient consent for publication Not required.

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

  • Data availability statement All data relevant to the study are included in the article or uploaded as supplementary information. The accurate clinical detection of actionable mutations in patients with cancer is essential for treatment decisions related to Food and Drug Administration-approved targeted therapies and other precision medicine applications. While traditional tissue biopsies have been considered as the gold standard for molecular profiling, insufficient tissue and tumour heterogeneity often pose barriers towards correct biomarker status determination. Liquid biopsy methodologies address these challenges and provide a complementary approach to tissue testing. However, assays with extremely high sensitivity are key for being able to inform on patients that present with low circulating tumour DNA mutant copy levels. The clinical validation studies presented in this paper demonstrate the utility of a highly sensitive PCR assay that enriches mutants of interest in 'hot-spot' regions of the genome. This assay has sensitivities in the range of 0.01%–0.02% minor allele frequency. In earlier studies, we demonstrated analytically the ability to detect down to single copy mutations. In this study, we report on the clinical validation of this assay, using tissue results as the 'gold standard' when carried out with blinded clinical samples. These assays are more sensitive than most previously reported assays, and do not require that they be allele specific. At the same time, these assays are more sensitive than a vast majority, if not all next-generation sequencing assays, and are comparable or more sensitive than allele-specific digital assays. The availability of these assays for informing on rare, cancer-associated, actionable alterations should be of interest to the broader medical community.

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