Inside Molecular Oncology: Understanding Cancer Through DNA and RNA

3. Tumour RNA analysis: gene expression, pathways and response mechanisms

DNA indicates which genomic alterations may be present. RNA provides a different perspective by showing which genes are being transcribed.

RNA analysis can support research into tumour subtypes, pathway activity, splice variants, fusion transcripts, tumour-microenvironment signals and treatment response. Methods such as RT-qPCR, targeted expression panels, microarrays and RNA sequencing each answer different questions and have different requirements for RNA quantity and integrity.

RNA is particularly sensitive to pre-analytical handling. Endogenous RNases can degrade RNA rapidly after tissue collection. If fresh tissue cannot be processed or frozen immediately, RNA stabilisation can provide an important bridge between collection and extraction. Prompt stabilisation helps preserve RNA integrity during handling, storage and transport.

FFPE workflows require a different approach. RNA extracted from FFPE tissue is often fragmented because of formalin fixation and storage conditions. It can still be useful, but downstream methods should be selected with this in mind. Shorter RT-qPCR targets and library-preparation methods designed for degraded RNA are common examples.

For both fresh and FFPE material, RNA must suit the downstream method, taking into account the limitations imposed by the original specimen.

4. Matched tumour–normal analysis: distinguishing somatic and inherited variants

A variant identified in tumour tissue may be somatic, germline or, in some cases, difficult to classify without additional information. Matched tumour–normal analysis addresses this question by comparing DNA from the tumour with DNA from a non-tumour source, such as blood, saliva or a buccal swab.

This approach is particularly useful in research studies that aim to distinguish changes acquired by the cancer from inherited variants. It can also support a more complete view of tumour evolution and genomic complexity.

The workflow requires consistent handling of both samples. Tumour tissue presents its own challenges, including tissue heterogeneity and variable tumour-cell content. The matched normal sample requires a reliable source of host genomic DNA. The two preparations should then be assessed within the same defined analytical strategy.

5. Virus-associated cancers: detecting the infectious component

Several viruses are associated with cancer development.

High-risk human papillomavirus, or HPV, is the most familiar example. Persistent infection with high-risk HPV types is strongly associated with cervical cancer and also contributes to anal, vulvar, vaginal, penile and a proportion of head-and-neck cancers [3]. Molecular HPV detection and genotyping are therefore important in screening, epidemiology and research.

Other oncogenic viruses include Epstein–Barr virus, hepatitis B virus, hepatitis C virus and human herpesvirus 8. Depending on the virus and clinical setting, laboratories may investigate viral DNA or RNA in swabs, blood-derived samples, tissue or other supported specimen types.

Detection of viral nucleic acid indicates the presence of a viral target. It does not, by itself, diagnose cancer. Cancer diagnosis and risk assessment require the complete clinical pathway, which may include screening history, cytology, histopathology, imaging or other biomarkers.

6. Biomarker-specific assays: primers, probes and defined controls

Extraction is only one part of a molecular workflow. Once DNA or RNA has been prepared, the analytical method needs sequence-specific components. PCR, qPCR and digital PCR, for example, rely on primers and probes designed for the relevant biomarker.

Custom oligonucleotides can support the development and implementation of such assays. Depending on the application, this may include primers for a known cancer-associated variant, hydrolysis probes for qPCR, molecular beacons, sequencing primers or oligonucleotides for targeted research methods.

Defined synthetic DNA can also be useful during assay development. Custom double-stranded DNA fragments may be used as defined control materials depending on the assay design and validation requirements. They can help laboratories assess assay performance, optimise conditions and investigate defined sequence variants without relying solely on limited biological material.

For functional cancer research, custom gene synthesis has a different role. Cloned genes and variant-containing constructs can support reporter assays, gene-expression studies, variant characterisation and the development of cellular research models. These applications sit primarily within research rather than routine diagnostic testing, but they are important for understanding the biological relevance of cancer-associated changes.

How Invitek Diagnostics can support oncology workflows

The oncology workflow extends from sample collection to molecular analysis. The table below maps Invitek Diagnostics products and services to workflow stages, subject to the applicable product documentation and workflow requirements.

Cancer research and molecular diagnostics depend on decisions made throughout the workflow. The choice of sample, the timing of stabilisation, the extraction method and the downstream assay all influence the quality and relevance of the final result.

Breast Cancer Awareness Month is a reminder that progress in oncology depends on both scientific insight and dependable laboratory practice. Reliable molecular workflows help laboratories investigate the biology of cancer, develop and validate biomarker assays, and generate reliable data for cancer research and, within appropriately validated clinical workflows, support clinical decision-making.

Working with challenging samples in molecular oncology?

Whether you're processing FFPE tissue, working with limited biopsy material or preserving RNA integrity, our team can help you identify suitable sample preparation and nucleic acid extraction solutions for your application.

👉 Discuss your workflow with our team