The Genetics of Cancer

Published on: Wednesday, August 12th, 2015 View all Articles

By: Mandar Kulkarni, Chief Technology Officer, Cancer Genetics India

Published on Healthcare Executive on August 13, 2015

The human body packs in approximately 100 trillion cells that are carefully coordinated for optimized functioning, including voluntary and involuntary actions. Each cell is constructed with a few distinct classes of macromolecular building blocks (e.g. proteins, carbohydrates, nucleic acids, fats, etc.). The functional unit of each cell is a protein molecule, which is built by connecting subunits (amino acids) in a specific order governed by the sequence of deoxyribonucleic acid (DNA) present in the cell’s nucleus. Collectively, all the DNA in each cell is organized into 23 pairs of chromosomes, which harbor distinct stretches of sequences referred to as genes.

Although two copies of each gene are present in each cell, information from only one copy is transcribed into the encoded “macromolecular gene product” that ultimately affects protein function either by changing the order of subunits or by regulating the amount of protein molecules produced. Therefore, certain changes in the DNA sequence (genetic variation) can impact either the structure or the amount of expressed protein, resulting in variation, enhancement or impairment of the specific cellular function carried out by the protein. The outcome of some genetic variations is readily discernible e.g. eye color, height, hair texture, while that of others is more subtle e.g. blood group, Red/Green colorblindness. Many such variations, and consequently physical and physiological traits, are inherited by offspring through the process of combining maternal (egg) and paternal (sperm) DNA during fertilization.

The first direct “cause-effect” relationship between altered protein (hemoglobin) and human disease (sickle cell anemia) was established in 1956 while the first cancer causing gene (oncogene), the sarcoma causing Src (pronounced sarc), was discovered in 1970. Genetic studies have continued to discover genes that contribute to specific traits and define underlying mutational landscapes causing various diseases. Over the last 45 years, since 1970, we have come to appreciate the complexity of genetics and human diseases. Mutations in a single gene may cause several diseases while several mutations across multiple genes may contribute to a single disease. Moreover, some mutations maybe inherited while others may arise due to various extraneous factors i.e. stress, diet, behavior, exposure to changing environment etc. Cancerous transformation requires accumulation of mutations in multiple genes. The combination of mutations offers specific advantages to tumor cells in terms of uncontrolled growth, continued growth in low-nutrient environments, accelerated cell division, increased self-renewal capabilities etc.

Higher incidence of cancers in related individuals has uncovered an inheritance pattern in underlying genetic lesions. For example, if multiple women on one side of a family have developed breast cancer it may indicate the presence of inherited mutations in BRCA-1 or BRCA-2 genes. If more than two individuals in a single family have developed medullary thyroid carcinoma, it may indicate presence of mutations in the multiple endocrine neoplasia type-2 (MEN2/RET) gene. Inherited cancers represent 5% to 10% of all cancers and the inherited mutations are generally not sufficient for cancer development but increase the risk or predispose the carrier individuals to cancer.

A family history of such cancers often prompts the physician to recommend genetic testing to design effective pathological risk management strategies. Appropriate patient sample collection

and storage, performing relevant tests, ensuring high quality standards for accuracy, clinical interpretation, and adequate knowledge guided counseling are critical parameters for the success of genetic testing and counseling. Choosing the relevant bodily source (e.g. blood, bone marrow, sputum, tumor biopsy etc.) for collecting an adequate amount of tissue/material and ensuring storage in conditions that preserve the genetic material until testing may commence is a clinical challenge. Several established protocols based on different scientific principles can interrogate different aspects of genetic aberrations. For example, a technique called fluorescence in-situ hybridization allows detection of larger scale genetic aberrations, while polymerase chain reaction based assays can detect minute changes in DNA. In the postgenomic era (since 2001, when the first human genome draft was published), great advances in DNA sequencing has led to the development of highly accurate assessment of gene sequences at an affordable cost. This has also given rise to population-wide genetic analyses and establishment of guidelines for clinical interpretation of observed mutations in individual samples. The fast pace of generating clinically significant information makes it challenging for genetic counselors to keep up with most up to date knowledge. Despite such challenges, the overall process of genetic testing that detects inherited abnormalities, combined with careful genetic counseling of carrier individuals, is an invaluable tool for guiding “high risk” individuals.

New frontiers

 

Lab-Pan-2

Until the 21st century, Sanger’s method was the sequencing platform of choice because of its high accuracy and mature technology however; it presented two major challenges in the rapidly changing technological landscape. Firstly, representation of various types of tumor cells in the collected clinical specimens, also known as tumor heterogeneity, led to detection of a relatively higher number of normal gene sequences. Although a sample containing only tumor tissue is ideal for detection of mutations, tumor sampling techniques such as tumor biopsy and malignancies of myeloid and lymphoid origin leads to the presence of multiple cell types within the collected tumor sample. Sequencing of such “mixed tumor” tissue by the Sanger method fails to report all the mutations present in the sample. Therefore, the sensitivity of the Sanger sequencing method is in an insurmountable limitation for comprehensive mutational analysis of clinical samples. Secondly, several sequencing events are required to determine the mutational profile of a single tumor tissue sample. In other words, the data throughput of Sanger sequencing is not compatible with the demand of having to determine the sequence of approximately 50 genes from each clinical sample. This automatically feeds into the cost of DNA sequencing which renders it cost prohibitive. Nonetheless, high accuracy, a well-established protocol, and the ease of interpretation makes Sanger sequencing the platform of choice for single-gene or single-mutation tests.

Simultaneously, development of massively-parallel or next-generation sequencing (NGS) led to a sharp decline in DNA sequencing cost, vastly improved sensitivity, and the ability to sequence multiple genes in parallel. In the context of cancer, which is driven by genetic aberrations in multiple genes, this presents great advantages over the traditional sequencing technology. Several public and private initiatives quickly adopted the new NGS platforms to establish mutational landscapes of several tumor types by sequencing the entire genomic DNA content of tumor tissues. Intuitively, the scale of this research has created a data deluge that many people continue to sift through to categorize the mutations into four relatively distinct classes of mutations

  • Germline versus somatic mutations – because > 90% cancers arise due to acquired or somatic mutations in multiple genes, diagnostic tests for cancer must be able to detect somatic mutations from clinical samples.
  • Driver versus passenger mutations – although the number of accumulated mutations in a tumor tissue is relatively high we can distinguish between the mutations that fuel the growth of the tumor i.e. driver mutations versus the mutations that are a mere side effect of the higher mutation rate of cancer cells i.e. passenger mutations. Such distinction allows us to select and sequence the most relevant genes responsible for driving tumor growth.
  • Prognostic mutations – for the same tumor type from two individuals (e.g. lung cancer from two different patients), mutations in certain combinations of genes render the tumor more aggressive and metastatic. Inclusion of such genes in the diagnostic test empowers the clinician to provide more precise information to the patient.
  • Pharmacogenomic/theranostic mutations – in the context of cancer (and other diseases) we understand that mutations in certain genes (germline and/or somatic) directly affect an individual’s susceptibility to certain drugs. Moreover, in the last decade, we have witnessed the development of more and more molecular targeted therapies for cancer. For targeted drugs to be effective, the tumor type under treatment should be expressing the target molecule in cancer cells. Overall, assessment of mutations in genes that dictate response to general chemotherapy and those in specific cellular targets can guide the physician to choose the most appropriate drug regimens and can greatly increase the clinical outcome of therapy.

CGI_kovar_IMG_4797-300x200This level of diagnostic, prognostic, theranostic, and molecular typing approach is the center piece of the emerging field of precision medicine and NGS plays a vital role in empowering doctors to use actionable genetic information for most effective clinical management of cancer. NGS has already been instrumental in the discovery phase of cancer diagnostics and continues to fuel clinically relevant research that will increase personalization of diagnosis and treatment of cancer. Its biggest impact has been in the area of offering NGS based diagnostic panels. Several companies now offer NGS testing for a selection/panel of genes involved in hereditary cancers, genes that are most commonly mutated in solid tumors, and a few panels representing the most frequently mutated genes in specific cancers e.g. myeloid malignancies and breast cancer.

A cross-section of the global NGS market (valued at approximately $4B) and the cancer diagnostics market (worth $7.1B) represents the true market relevant to NGS-based oncology precision medicine. The major trend that will drive growth of this market is the increasing awareness and demand from patients to have access to sophisticated testing. We have developed several novel therapies and made great progress to mitigate cancer related mortality however, late and less comprehensive diagnosis invariably confines it to the realm of a terminal diseases.

The continued reduction in the cost of DNA sequencing is expected to make early and comprehensive testing more affordable.As precision medicine takes a center stage in the 21st century there are a few key challenges that lie ahead of us. Arguably, the overall goal of precision medicine would be to have the analyzed entire gnome of an individual available at the physician’s fingertips to guide the best available and most cost effective therapeutic path for the patient. Cancer Genetics has already engaged in making this a reality for the treatment of renal cancer patients. The annual cost of treatment with brand name drug, Sunitinib can cost tens of thousandths of dollars and treatment for even a trial period can be significant. The use of NGS to sequence a few genes can help confirm that the patient will respond favorably to the drug and make the therapy more efficient. Such innovation lies at the heart of improving cancer care and disrupting the march of cancer. We know that different populations have different genetic markers that affect incidence, progression and response to therapy. Building a local knowledge base that allows effective use of such differences to guide our decision making in the clinical context will increase the efficacy and accuracy of precision oncology.

Cancer Genetics India offers one such panel of 50 genes that are generally mutated in solid tumors such as breast, colon, lung, gastrointestinal, and ovarian. DNA extracted from clinical samples is tested for mutations in genes that are targeted for therapy (e.g. Her2 targeted by trastuzumab or lapatinib, EGFR targeted by cetuximab or erlotinib,   KIT, RET, PDGF-Rs, VEGF-Rs targeted by sunitinib). The presence and levels of proteins encoded by these genes in tumor tissue is indicative of their susceptibility to specific drugs. Mutations in other genes included in the panel maybe indicative of the invasiveness of the tumor. Such information is useful for the physician to set the patient’s expectations about therapeutic management and outcome. At CG-India we plan on continuing to build on this offering and bring state-of-the-art NGS-based cancer diagnostic capabilities from the western world to the Indian community. Conducting studies that focus on re-validating a few NGS-based diagnostic panels for the Indian population and developing novel panels relevant to the Indian market are on our priority list.

The Indian market for NGS-based diagnostics in general remains unregulated by the government. We should be mindful of quality compromised service providers and ensure that the highest standards of cancer care are delivered to our community in a timely manner. The demand for NGS-based oncology testing is increasing and there is significant investment in augmenting the industry. In the face of meeting high demand in unregulated markets the onus of delivering the best quality innovative products is on the industry.