Detecting BRAF (V600E) Mutation in FFPE or Blood Samples | DiaCarta, Inc.

Detecting BRAF (V600E) Mutation in FFPE or Blood Samples

by | Aug 7, 2018 | Blog

When mutated, oncogenes can convert normal cells to cancer cells. BRAF is one of the oncogenes that controls transduction of chemical signal from outside the cells to nucleus. As a member of the RAS/MAPK pathway, the BRAF gene product, the B-Raf protein, regulates cell growth and division.

BRAF (V600E) mutation, the most common BRAF mutation, has been found in different types of cancer including melanoma, colon cancer, and hairy cell leukemia. BRAF mutations occur between 40 and 60% of melanoma and 90% of these mutations are V600E. It has been shown BRAF (V600E) is more sensitive to BRAF inhibitors and some of these inhibitors have demonstrated clinical efficacy for malignant melanoma metastasis and increase patient overall survival. Identification of the BRAF (V600E) mutation may provide benefits to the patients who are selected for BRAF inhibitor therapy.

Using the XNA technology, we have developed gene mutation detection kits to identify BRAF (V600E) and other important cancer driver genes using a simple and fast qPCR assay that regular qPCR can’t do. We recently have also celebrated our 7th anniversary and reward our researchers with these mutation kits.

Lead Source

Confirmation of NGS for False-negative Variants Using XNA Technology

Next-generation sequencing (NGS) is a powerful tool that has seen a fast increase in clinical labs although only a few NGS tests have been approved by the FDA. However, there have been a lot of debate on if variants from NGS sequencing should be confirmed either by Sanger sequencing, the gold standard, or other techniques such as quantitative PCR, or the combination, or other methods.

Evaluation of a novel liquid biopsy-based ColoScape assay for mutational analysis of colorectal neoplasia and triage of FIT+ patients: a pilot study

Abstract: Circulating cell free tumour derived nucleic acids are becoming recognised as clinically significant and extremely usef ul biomarkers for detection of cancer and for monitoring the progression of targeted drug therapy and immunotherapy. Screening programmes for colorectal cancer in Europe use the Fetal Immunochemical Test (FIT) test as a primary screener. FIT+ patients are referred to immediate colonoscopy and the positive predictive value (PPV) is usually 25%. In this article, we report a study employing the ColoScape assay panel to detect mutations in the APC, KRAS, BRAF and CTNNB1 genes, in order to collect preliminary performance indicators and plan a future, larger population study. The assay was evaluated on 52 prospectively collected whole-blood samples obtained from FIT+ patients enrolled in the CRC screening programme of ASL NAPOLI 3 SUD, using colonoscopy as confirmation. The assay’s sensitivity for advanced adenomas was 53.8% and the specificity was 92.3%. The PPV was 70.0% and negative predicitive value (NPV) was 85.7%. Workflow optimisation is essential to maximise sensitivity. Of note, four of the six positive cases missed by ColoScape had a less than suboptimal DNA input (data not shown). Had they been ruled out as inadequate, sensitivity would have increased from 53.8% to 69%. However, as stated previously, this is not a clinical trial, but rather an initial, preliminary technical evaluation. In conclusion this study shows that ColoScape is a promising tool and further studies are warranted in order to validate its use for the triage of FIT+ patients.
Authors: Mauro Scimia, Jinwei Du, Francesco Pepe, Maria Antonia Bianco, Silvana Russo Spena, Farah Patell-Socha, Qing Sun, Michael J Powell, Umberto Malapelle, Giancarlo Troncone
Source: Clin Pathol 2018;0:1–4. doi:10.1136/jclinpath-2018-205412

XNA Molecular Clamps Help Identify False-positive T790M Mutation

Eighty five percent of the lung cancer patients are non-small cell lung cancer (NSCLC) patients. Among this population, patients with exon 19 deletion and L858R mutations respond well to the first (such as erlotinib and gefitinib) and second generation (such as afatinib and dacomitinib) of tyrosine kinase inhibitors (TKIs). However, all the respondents develop resistance after 9 to 14-month period and more than 50% of the resistance cases are due to the single point mutation at exon 20, T790M.

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