Tumor Genetic Profiling for Cancer Patients

Cancers or malignant lesions are a products of accumulating mutations in the biological tissues. Under normal circumstances, human body has a unique and fool-proof system to check for abnormal cells in order to catch genetic mutations before the damage sets in. For example, genetic signaling molecules especially protein kinases are known to activate the death or suicide-cascade in newly formed cells that are terminally damaged beyond the point of repair. However, certain congenital or acquired irregularities in the normal functioning of immune system may compromise the integrity of this screening process; thereby aggravating the risk of malignant lesions. Other indications of conducting an extensive tumor genetic profile in certain high risk patients are:

• Certain genetic mutations run in the families or are inherited from either set of the parents at the time of birth. Conducting extensive genetic tumor profiling helps in parental counseling and may reduce the risk of certain life threatening cancers in the offspring.
• Some inherited or acquired genetic mutations can increase the risk of malignancies later in life. Knowing the type of genetic mutation via extensive profiling can aid in early detection or even prevention of these cancers.
• Study reported by John D. Hainsworth and associates (1) highlighted another application of tumor genetic profiling. Investigators suggested that use of genetic profiling and molecular studies can play a vital role in the identification of primary site in the diagnosis of carcinoma of unknown primary site (CUP).
• Tumor profiling is also needed to determine the efficacy and therapeutic efficiency of certain anti-tumor therapies. For example, study reported in Journal of Clinical Oncology (3) suggested that physicians are now relying on designing personalized anti-cancer treatment regimens for the management of non-small cell lung carcinomas. Based on the data and clinical results, specific tyrosine kinase inhibitor drugs that targets anaplastic lymphoma kinase (ALK) gene and epidermal growth factor receptor (EGFR) gene have yield promising results in the management of non-small cell carcinoma in selected patients.

There are several other indications and benefits of tumor genetic profiling in cancer patients.

What are some genetic alterations that are linked to carcinogenesis?

The genetic alterations that are known to contribute in cancer development are:

• The substitution of a single nitrogenous base in a nucleotide may result in a complete change of the amino acid sequence (encoding for a specific protein). This phenomena is referred to as single nucleotide variant and is regarded as the most common form of genetic mutation.
• Insertion or deletion of multiple nucleotides can cause premature truncation of the proteins.
• The change in exon or gene copies quantity completely affects the functional domains of proteins formed.
• Structural changes in the genetic makeup such as translocation or inversion of the entire or part of gene.

The molecular testing for tumor ranges from simple to complex testing. Detection of one type of mutation is the domain of simple testing while detection of multiple mutations at a time is a function of complex testing. Following are a few testing techniques that are frequently used for tumor genetic profiling:

1-Allelle Specific PCR:

• Variants detected: Detects mainly SNVs (or single nucleotide variant).

• Method: The fluorescent reporter probe is used along with the PCR in which the reporter probe detects the allele of interest. One wild type and one mutant type are added to the reaction mixture, causing extension of the genomic DNA by DNA polymerase, hence amplifies the signals to be read precisely.
• Time to complete test: 1-2 days.
• Pros: Sensitive. It can detect mutations in DNA up to 1-5% with no special equipment required.
• Cons: It is specific for SNV and cannot detect any other mutation.

2-Pyrosequencing:

• Variants detected: Different types of mutations, in a specific area to be targeted.
• Method: In the presence of ATP sulfurylase, luciferase, apyrase and other enzymes, the sequencing primer is formed to the PCR product, generating pyrophosphate. After a series of reactions a light is also generated, hence the intensity of the light and order of dNTP additions determine the sequence.
• Time to complete test: 2-3 days.
• Pros: Fast and sensitive.
• Cons: Requires special instrumentation.

3-Single Base Extension Assay:

• Variants detected: Specific SNVs (or single nucleotide variants).
• Method: Multiplex PCR combined with capillary electrophoresis can detect 1-100+ SNVs. These tests detects for mutations of interest as they are customized in such way.
• Time to complete test: 2-3 days.
• Pros: Sensitive and reliable up to 5-10%.
• Cons: It is specific for SNV and cannot detect any other mutation.

4- Fluorescence In Situ Hybridization (FISH)

• Variants detected: Targeted genes and SNVs.
• Method: Fluorescence microscopy is used to detect the sequences.
• Time to complete test: 2-3 days.
• Pros: Detects the sequence easily as compared to other techniques.
• Cons: paraffin-embedded tissue on slides required.

There are many other testing techniques such as Sanger Dideoxy Sequencing, Mass Spectrometry- MS, Multiplex Ligation-Dependent Probe Amplification-MLPA, Next Generation Sequencing-Amplicon Capture, Next Generation Sequencing-Hybridization Capture, Next Generation Sequencing-Whole Exome Sequencing and Next Generation Sequencing-Whole Genome Sequencing are used for molecular cancer detection.

References:

1. Hainsworth, J. D., Rubin, M. S., Spigel, D. R., Boccia, R. V., Raby, S., Quinn, R., & Greco, F. A. (2013). Molecular gene expression profiling to predict the tissue of origin and direct site-specific therapy in patients with carcinoma of unknown primary site: a prospective trial of the Sarah Cannon research institute. Journal of Clinical Oncology, 31(2), 217-223.

2. Dawson, S. J., Tsui, D. W., Murtaza, M., Biggs, H., Rueda, O. M., Chin, S. F., ... & Rosenfeld, N. (2013). Analysis of circulating tumor DNA to monitor metastatic breast cancer. New England Journal of Medicine, 368(13), 1199-1209.

3. Li, T., Kung, H. J., Mack, P. C., & Gandara, D. R. (2013). Genotyping and genomic profiling of non–small-cell lung cancer: Implications for current and future therapies. Journal of Clinical Oncology, 31(8), 1039-1049.

4. Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., ... & Yelensky, R. (2013). Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature biotechnology, 31(11), 1023-1031.