Technologies Currently Used in Biomarker Testing for Lung Cancer

“The timing from the initial realization that something is wrong until having a treatment plan in hand can potentially be quite lengthy because there are a lot of moving parts,”

- Lynette M. Sholl, MD, chief of the Pulmonary Pathology Division and Associate Director, Center for Advanced Molecular Diagnostics at Brigham and Women’s Hospital

Methods for molecular testing in patients diagnosed with non-small cell lung cancer (NSCLC) are continually evolving, driven by the need for enhanced diagnostic accuracy. While use of programmed cell death ligand 1 (PD-L1) expression as a predictive biomarker in NSCLC has been recommended for metastatic NSCLC to find out if immunotherapy would be beneficial. It is worth noting that there is no single technique for testing and new technologies are evolving to improve detection sensitivity and ultimately targeted therapy.

Instead, different clinics and cancer centers may choose different techniques or a combination of techniques depending on

• Prompt delivery of results, with a turnaround time of less than two weeks. To achieve this, clinics opt for a semi or fully-automated detection tool
• Cost consideration- Payers (both Medicare and commercial insurers) recognize the importance of molecular testing. Refer to the Payer Coverage Policies of Tumor Biomarkers for tests covered by insurance. The number of covered molecular tests continues to expand based on
  • inclusion of test in guidelines like National Cancer Comprehensive Network (NCCN) or American Society for Clinical Oncology (ASCO)
  • Availability of new FDA-approved targeted therapy and companion diagnostics
• Ability to test different types of biopsy
• Availability of multiple skilled operators to ensure operation testing continuity

Examples of molecular tests in this article have received approval by the U.S. Food and Drug Administration (FDA) as Companion Diagnostics. Additionally, they are nationally reimbursed by Medicare and other commercial payers, making them accessible and financially viable options for patients.

Immunohistochemistry (IHC) has been an indispensable tool in cancer diagnosis for years. The principle of IHC is based on antigen-antibody interaction. Commercially-designed antibodies tagged with a dye bind to the specific antigen in tumor cells. In the case of cancer diagnostics, the stained antigens are biomarkers.

Molecular lung cancer testing started historically with direct gene sequencing at known locations in DNA. Based on reproduced scientific studies, we know where exactly the driver mutations are in the DNA (this is what allele-specific means) and the specific DNA sequence of the mutated genes. Companies design short DNA probes that recognize these sites. In a technique called polymerase chain reactions (PCR), the DNA probe binds to the targeted site to signal the site for amplification. PCR amplification will generate thousands to millions of DNA copies containing the gene mutation from the raw DNA (extracted from tissue specimen), just like a photocopier. A separate instrument sequences the generated DNA copies.

The PCR amplification provides a higher DNA yield for sequencing. Thus, a higher signal and sensitivity in the result is possible. This method is suitable for types of mutation like insertion, substitution, and deletion. The result can be obtained in a few days. Unlike next-generation sequencing, allele-specific testing cannot detect new abnormalities as it only identifies prespecified mutations.

Examples of DNA allele-specific tests:

• cobas® EGFR Mutation Test v2 (Roche Molecular Systems, Inc.)
• therascreen® KRAS RGQ PCR kit (Qiagen Manchester, Ltd.)

Next-generation sequencing (NGS) represents a leap in sequencing technology as it incorporates multiple digital transformation concepts in one platform. The computational data, specimen processing, and data storage are heavily automated in NGS, enabling high data throughput every run.

The speed and throughput of NGS offer the benefits of

• massive parallel sequencing of many DNA strands compared to the traditional capillary-based sequencing that processes one DNA strand at a time
• sequencing of the whole genome
• detection of multiple gene abnormalities
• quantitative results

Furthermore, NGS can detect gene rearrangements that historically can only be detected by FISH. It is now in routine clinical and diagnostic practice for the conveniences and cost-effective factors that NGS offers. The turnaround time is about two weeks to a month for NGS of tissue DNA, while the Oncomine^TM Dx Target Test for NSCLC promises an even shorter turnaround time – 5 days or less.

Examples of DNA or RNA next-generation sequencing:

• FoundationOne® CDx (Foundation Medicine, Inc.)
• Oncomine^TM Dx Target Test (Life Technologies Corporation)

Fluorescence in situ hybridization (FISH) is a powerful molecular biology technique used in biomarker testing and various other applications. It is based on the principle of nucleic acid hybridization.

This technique uses a labeled DNA or RNA probe to bind specifically to the complementary sequence in the target sample (e.g., cells or tissue sections). The probe is designed to target the specific biomarker of interest. If the probe has successfully bound to its target, it will emit a fluorescent signal that can be visualized as bright spots or patterns within the sample.

The pattern and intensity of the fluorescence signal can provide information about the presence, location, and quantity of the biomarker of interest. Researchers and clinicians can analyze the results to determine the biomarker's status, which may have diagnostic or prognostic significance.

Examples of FISH:

• Vysis ALK Break Apart FISH Probe Kit (Abbott Molecular Inc.)

The landscape of molecular testing for NSCLC is continuously changing. Flexibility and precision are paramount. The techniques and tests mentioned above are tailored for personalized cancer diagnosis and treatments. These advancements empower oncologists to make informed treatment decisions but also offer hope and a chance at a better quality of life for those battling NSCLC.

Read next: The Types of Lung Cancer Biomarker Tests