This case study describes a 48-year-old female patient diagnosed with anaplastic/poorly differentiated thyroid carcinoma in 2018, accompanied by minor lung and brain metastases. The initial treatment plan involved chemotherapy, with a projected life expectancy of two months without it. Seeking a second opinion, the patient underwent next-generation sequencing (NGS) testing at Oncode, which revealed an ALK gene fusion alteration—a biomarker indicating the potential effectiveness of ALK inhibitors.

Considering the rarity of ALK fusion in anaplastic thyroid carcinoma, Oncode team suggested the possibility of the cancer originating from the lungs. Nonetheless, identification of ALK fusion in a non-NSCLC tumor could offer benefits from ALK inhibitors. This new insight influenced the diagnosis. Following targeted drug treatment, the patient experienced significant health improvement and continues to surpass initial expectations in terms of survival.

This case study highlights the power of precision medicine in uncovering the complex nature of cancer and providing more accurate treatment options. By leveraging genomic testing and targeted therapies, the patient’s prognosis drastically changed from a projected two-month life expectancy to over six years (last interview with patient was at early 2023), exemplifying the potential of genetic testing and targeted therapies to transform patients’ outcomes.

In October 2021, a PCR test revealed the patient’s EGFR positivity but absence of the BRAF mutation, indicating the potential efficacy of EGFR inhibitors (EGFR TKI). Surprisingly, the patient failed to respond to both EGFR TKI and second-line chemotherapy.

In January 2023, Oncode conducted a liquid biopsy NGS test on the patient’s sample, which showed a positive result for both EGFR and BRAF mutations. The presence of the BRAF gene mutation is known to render EGFR targeted therapy ineffective.

There are two possible explanations for the initial negative BRAF result. Firstly, the initial negative BRAF result could be the emergence of a new mutation, however, the mutation may have been present from the beginning and contributed to the lack of response to the treatment. Secondly, it is believable that the limited sensitivity of the PCR test (typically 95% compared to NGS’s 99.9% LOD) may have resulted in the earlier detection failure of low allele frequency BRAF mutations.

This case highlights the critical importance of testing sensitivity to avoid missed diagnoses or misdiagnoses, thereby ensuring that patients receive appropriate and effective targeted therapies.

The patient underwent PCR testing, and the KRAS test result came back negative, indicating a potentially better response to anti-EGFR therapies. However, despite treatment with oxaliplatin, irinotecan, cetuximab, and bevacizumab, the patient did not show any improvement, and her condition continued to worsen.

In light of this, the doctor decided to pursue a liquid biopsy NGS test with Oncode. The test revealed a positive KRAS gene mutation with a mutant allele frequency of 0.7%, which is below the limit of detection (LOD) for most PCR and some NGS tests.

It is well-established that colorectal cancer with KRAS mutations should not be treated with cetuximab or panitumumab due to the activation of alternate signaling pathways and/or structural changes in the EGFR protein.

This case underscores the importance of sufficient sensitivity in detection methods. Insufficient sensitivity may lead to false-negative results, resulting in misdiagnosis or delayed treatment.

In 2019, the patient received a diagnosis of NSCLC with an EGFR L858R mutation and underwent first-line treatment with EGFR TKIs. In 2022, the doctor performed a liquid biopsy NGS with Oncode to monitor the patient’s treatment response. Despite a low allele frequency of only 0.1%, the liquid biopsy NGS successfully detected the presence of the EGFR T790M mutation. This finding is significant as the T790M mutation is known to be associated with acquired resistance to first-generation EGFR TKIs. Approximately 50% of patients initially respond to treatment but eventually develop resistance, often within 9-14 months. The early detection of the T790M mutation through a highly sensitive test offers valuable information to the doctor, enabling prompt modification of the treatment plan to achieve better outcomes.

Multiple EGFR mutations, including T790M and C797S, were identified in a 35-year-old NSCLC patient who had failed third-line EGFR-TKI treatment, using the Oncode NGS test.

It is noteworthy that both the T790M and C797S variants were detected in the same allele in a cis configuration, indicating resistance to all EGFR-TKIs.

In T790M-positive NSCLCs that exhibit resistance to erlotinib and subsequently acquire a C797S mutation following third-generation TKI treatment, the configuration of these two mutations plays a crucial role in determining the response to therapy. If the mutations are in trans (on separate alleles), a combination of first- and third-generation TKIs may restore EGFR inhibition. However, if the mutations are in cis (on the same allele), the cancer cells become unresponsive to all EGFR TKIs, including the combination of first- and third-generation inhibitors.

It is important to note that the assessment of cis versus trans configurations can be determined by specific NGS approaches, although not all assays and bioinformatics pipelines can accurately distinguish between them. Nevertheless, identifying the cis or trans configuration of T790M and C797S mutations is crucial information that provides valuable insights into treatment indications for patients.

The patient underwent both PCR and NGS testing in different labs to determine the status of the FLT3-ITD gene. The PCR test indicated that FLT3-ITD was positive, while the NGS test showed it as negative. In order to obtain confirmation, sample was sent to Oncode for further analysis confirmation. Upon examination, both Oncode’s PCR and NGS tests confirmed that FLT3-ITD was indeed positive. It is worth noting that depending on the specific assay design used by individual laboratories, FLT3-ITD detection by NGS can sometimes be missed.

As FLT3-ITD is recognized as a challenging marker to detect accurately using NGS, it holds significant importance as a risk marker that directly impacts prognosis, treatment decisions, and overall clinical management in acute myeloid leukemia (AML). Therefore, it is crucial to thoroughly assess the performance of FLT3-ITD detection and accurately classify its allelic ratio to prevent missed diagnoses.

To ensure comprehensive examination and coverage of tests offered, Oncode conducts PCR and Fragment Analysis in parallel with NGS for all panels involving the FLT3 gene. This additional quality control step aims to provide a complete assessment of FLT3-ITD status and enhance the accuracy of the testing process.