With the development of gene sequencing technology, cancer has become the largest market for gene sequencing. The benefits of genetic testing are obvious and provide a reference for patients to develop individualized treatment plans. However, the results of genetic testing are not the gold standard, there may be errors, and if an inaccurate test report is used to guide patients on medication, the results may not be optimistic. Today we share with you a report in JTO magazine about the problem of missorcing exon 14 of the MET gene.
Figure 1. False positive reports of MET gene 14 exon jump mutations
There are two types of errors in genetic testing, false negatives and false positives.
False negative error: The genetic mutation was not detected
False negative means that there is a genetic mutation in the tumor, but it is not detected. There are generally two reasons for this:
First: the patient's sample has a problem, for example, when the tumor is punctured, not enough cancer cells are taken; or if the blood test is taken, the patient has a large number of normal cell gene fragments in the blood after chemotherapy, interfering with the gene fragment signal of the tumor cells.
Second: the problem of gene sequencing technology, genetic testing companies have weak bioinformatic analysis capabilities, and do not have a comprehensive and accurate interpretation of the test results, which is more common in smaller gene companies.
False positive error: something out of nothing
False positive means that the patient does not have a certain genetic mutation, but the test report gives the type of genetic mutation and recommends the targeted drug. There are generally two reasons for this:
First: The gene sequencing company did not test at all, but falsified a genetic test report according to the characteristics of the patient's condition. As long as the patients who go to the test are "present" mutations, all drugs are available, and "everyone is happy". This is an extremely bad practice, some mercenary companies, taking advantage of the patient's eagerness to seek medical treatment, making money with a conscience, not only allowing patients to spend money in vain, but more seriously delaying the patient's later treatment. I once met a lung cancer patient in her 40s who had mutations in 6 of the 10 genes she tested, including the KRAS gene. At that time, experts from a well-known hospital in Beijing were consulted, and experts recommended the direct use of expensive imported drugs based on the test report. Patients expressed skepticism because, according to basic common sense of tumor gene mutations, it is impossible for a tumor to have as many driver gene mutations. After consideration, the patient performed a confirmatory test at two other well-known genetic companies, and the results showed that none of the previous six genes were detected, and only the 20 exon insertion mutations of the EGFR gene were present, that is, the original genetic test report was forged. Without the subsequent validation testing, patients go directly to buy expensive but symptomatic drugs, and even if they dump their family property, they will not be able to treat them.
Second; it is also a problem of sequencing technology, and a formal professional genetic test result is not completely the truth, it may just be close to the truth. During the inspection process, errors can occur due to the detection of samples or other reasons, which may also produce incorrect results. For example, the following "JTO" magazine reported that the MET gene exon jump mutation is the case.
MET gene 14 exon jump mutation
Oncomine DxTT uses second-generation gene sequencing technology, which was approved by the US FDA for pre-treatment diagnosis of lung cancer and has been used worldwide. Of the 568 samples tested by Oncomine DxTT sequencing technology, the investigators selected 50 samples for repeated testing. Of the 50 samples, 26 were judged positive by Oncomine DxTT as positive for exon jump mutations in META gene 14 and 24 by Oncomine DxTT as negative for exon jump mutations in MET gene 14. For these 50 samples, Archer MET and RT-PCR techniques were used for verification. Archer MET is an accompanying kit used to detect exon-jump mutations in the MET gene 14. RT-PCR is a traditional molecular detection technique in the laboratory.
Figure 2. Comparison of results from three detection techniques
The results showed that the Archer MET and RT-PCR test results were consistent, but the test results of 8 samples were different from those of Oncomine DxTT. Using Oncomine DxTT technology, the 8 samples were "present" with exon 14 mutations in the MET gene, but the results of the Archer MET and RT-PCR verification tests were negative. Oncomine DxTT is a second-generation gene sequencing technology approved by the US FDA to be applied to the world, and this error can even occur, in some patients, "out of nothing", the original non-existent EXON 14 mutation of the MET gene was detected. This problem may be caused by the homogenization error of the Donor Site of the Oncomine DxTT splicing donor, the technical terminology here is more complicated, interested friends can download the reference to learn more.
Figure 3. Possible causes of false positives for second-generation gene sequencing techniques
The results of genetic testing can only be referenced, not absolutized
Due to the mixed domestic genetic testing market and the uneven level of gene sequencing companies, the SEquencing error of EXON 14 of the MET gene should be more common. We can't deny the value of second-generation gene sequencing technology, but we should not absolutize the test results, no matter how advanced the technology has the possibility of error, not to mention there are many uncontrollable factors. Patients should be cautious about the results of the first genetic test report before determining the use of a targeted drug, and may consider performing a confirmatory test to ensure accuracy. For more genetic testing knowledge, welcome to the cancer app to exchange and learn.
参考文献：Takashi Teishikata, MD, et al., An Alert to Possible False Positives With a Commercial Assay for MET Exon 14 Skipping，Journal of Thoracic Oncology Vol. 16 No. 12: 2133–2138