XNA Molecular Clamps Help Identify False-positive T790M Mutation

Common EGFR Mutations in Non-Small Cell Lung Cancer

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. Patients who develop T790M mutation responds to the third generation of TKIs, such as osimertinib. But another mutation in the same exon C797S is further developed in the T790M population and may or may not cause resistance to a mixture of different generations of TKIs depending on the cis/trans configurations.

False-positive T790M Mutations in Formalin-fixed Lung Tumors

It is reported that some of TKI-naïve patients carry the T790M mutations detected using formalin-fixed samples. In some formalin-fixed lung tumor samples, high frequency of T790M mutations are detected at high frequency (more than 40%) not only in the tumor cells, but in the adjacent tissues as well. In contrast, the same mutation is only detected in freshly frozen samples at low frequency (2.8%). Some of these T790M mutations have been reported to be false-negative. The XNA molecular clamps (blockers) have been used to verify these false-negative mutations (see the hyperlinked paper). The XNA clamps or blockers enrich the T790M mutant allele in the experiment (see Figure 1 of the paper), facilitating detection of the artifactual T790M mutation.

XNA technology and its application in cancer mutation detection

Developed at DiaCarta by Dr. Mike Powell, XNA technology uses xenonucleic acid sequence that is 100% complementary to the wild-type target DNA sequence to tightly bind the wild-type sequence like a clamp. As a result, the amplification of the wild-type sequence is blocked in a PCR reaction. However, mismatch in the mutant target DNA:XNA clamp duplex causes instability in binding and therefore XNA falls off the mutant target sequence during the PCR reaction, selectively allowing amplification of the mutant sequence.

One of the challenges in cancer mutation detection is the low sensitivity for the detection methodology, such as traditional Sanger Sequencing. Because of insufficient sensitivity, mutations in a small population of tumor cells among a big population of wild-type (normal) DNA are missed and a wrong conclusion can be made based on the unreliable testing.

Use of XNA technology can suppress the wild-type sequence but pick up the mutant detection even when the mutant alleles are present in a small population (0.1 to 0.5% sensitivity in FFPE and plasma samples). The above example of artificial T790M detection confirmed by XNA technology shows how XNA technology can be used for cancer mutation detection.

XNA is used for EGFR mutation detection

XNA molecular clamps are successfully used to detect cancer mutations such as EGFR, KRAS, NRAS, and BRAF. The current EGFR mutation detection covers mutations in and near EGFR codon 719 in exon 18, exon 19 deletions, codon 790 in exon 20 and codon 858 and codon 861 in Exon 21 and are applied for FFPE and plasma samples.