Sample Types

The most relevant sample types that can generate insights about solid tumor features are:

• Fresh-frozen (FF) or formalin-fixed paraffin-embedded (FFPE) sample tissues obtained through biopsy or excision of the malignant mass for staining or immunohistochemical analysis
• FF or FFPE tissue specimens for profiling through molecular, biochemical, proteomic, and metabolic studies
• Urine and whole blood (serum and plasma) for biomarker analysis

Worldwide, FFPE tissue samples tissue samples are commonly used for immuno-histological or molecular profiling for various types of cancer (e.g., prostate, breast, colon, brain). By using the FFPE method for tissue archiving, researchers are empowered to investigate and analyze the excised biopsies. To achieve a more in-depth view of the proteins or to study morphology from FFPE tissue samples, one can employ immunohistochemistry (IHC) techniques (using antibodies or fluorescent-labeled antibodies) to visualize specific proteins present in individual cancerous cells within the excised tissue.

Proteomic studies of the native form of non-denatured proteins and the preservation of DNA and RNA information come with particular challenges due to formalin-induced cross-linking in FFPE samples. Frozen tissue can be suitable for keeping the genomic, proteomic, and transcriptomic features unaltered. Furthermore, scientists are paying closer attention to the uncovering of fundamental multi-omics approaches to understand the tumor's complexity and unique signature better.

Detecting the mutational levels in solid tumors can be challenging, especially in samples that have non-small malignancies of the lungs, colon and melanomas. For example, common characteristics that are studied include the histological form (adenocarcinoma vs. squamous cell carcinoma) and mutational state of the protein, C-K-RAS (KRAS) and the epidermal growth factor receptor (EGFR) gene. When considering the whole cancer genome, taking into consideration the preponderance of DNA alteration or specific mutations is the key to describing and quantifying the onco-genes and tumorigenic suppressor genes. When it comes to gene insertions or deletions of a single base pair, namely point mutations, the RAS gene family (HRAS, KRAS, NRAS) is associated with malignancies like colon, lung, or pancreatic cancer. These specific point mutations enable researchers to optimally study a multi-layered phenotype or a complex cancer type.

DNA sequencing or denaturing high-performance liquid chromatography (dHPLC), qRT-PCR, or SYBR Green PCR and melting temperature analysis are used for point mutation profiling and discovery. They provide accuracy, sensitivity, reproducibility, and high production capabilities.

Taken together, testing of a solid tumor's genetic profile and decoding the specific genes from formalin-fixed malignant samples still represent a challenge due to the limited tumor content and the quality of the histological samples. Besides the existing challenges of FFPE tissue samples, researchers are developing strategies and multi-omics approaches to make use of the entire DNA concentration from these sample types. Repeating some genomics experiments can increase the chances of achieving the most accurate cancer type.