On this World Cancer Day, we get the experts to throw light on the advent of next-generation sequencing (NGS) for cancer diagnosis.

 

NGS has provided a powerful weapon to various scientific investigators to discover and unveil hundreds of genes which are involved in various cancers. These advances will inevitably reveal novel ways of not only diagnosing the cancer but also assist in tailoring the right therapy to cancer patients.

In fact, over the last few years, this promising technology has been transferred to clinical diagnostics in oncology with the aim to better define which therapy should be given in each patient. No doubt the application of NGS has created a paradigm shift when it comes to patient care, but it will certainly require close collaboration between drug development companies, medical oncologists, and health authorities.

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Background

Cancer begins when genes in a cell become abnormal and the cell starts to grow and divide out of control. The milestone elucidation of the first human genome sequence in 2001 was the first step in understanding how the instructions coded in DNA lead to a functioning human being.

This led us to derive meaningful knowledge from the DNA sequence, and now we can confidently say that virtually every cancer has some basis in our genes. The rapid development of DNA sequencing technologies has driven a revolution in our understanding of this highly complex and diverse group of diseases.

Next generation sequencing or massive parallel sequencing are rapidly becoming the standard for molecular assays and represent huge potential value to the practice of oncology.

The basic principle involves rapid sequencing of thousands to millions of DNA and RNA molecules simultaneously, and thus represents an effective way to capture a large amount of genomic information about a cancer in a very short period of time.

Let us understand the role of this technology in the diagnosis and treatment of cancer leading to paradigm shift in the overall management of the disease.

Genetic Screening of Cancer

The study of cancer genomes has revealed abnormalities in genes that drive the development and growth of many types of cancer.

About 5-10% of cancers are hereditary in nature and certain genetic variants that are often inherited from a parent increase the risk of developing a particular type of cancer. These genetic changes contribute to the development of a disease but do not directly cause it.

Some people with a predisposing genetic variation will never get the disease while others will, even within the same family. Clinical genetic testing for cancer-risk assessment has become widespread over the last few years, with evidence-based testing guidelines for hereditary breast and ovarian cancer. For example, presence of BRCA1 and BRCA2 mutation in individuals with a strong family history of cancer, there is a 50-80% increased risk of developing breast cancer and or 40-60% of ovarian cancer by the age of 70.

Similarly, mutation in APC gene increases the risk for developing colon cancer, CDH1 mutation increases risk of hereditary diffuse gastric cancer, SMAD4 mutation for prostate cancer so on and so forth. These genomic variations can be easily screened by single gene or multiple genes testing simultaneously by the help of NGS technology.

Many labs across India and other parts of the world are offering single or multiple genes testing for hereditary cancer. Infact, American Society of Clinical Oncology recognizes that concurrent multigene testing (ie, panel testing) may be efficient in circumstances that require evaluation of multiple high-penetrance genes of established clinical utility as possible explanations for a patient’s personal or family history of cancer. Assessment of multiple genes associated with hereditary cancers can be useful in determining personal or familial risks and also enables timely intervention to prevent the disease occurrence.

Genetic diagnosis and clinical assessment of cancer

Currently, NGS-based gene mutation panels are slowly used for cancer diagnostics. In 2015, National Comprehensive Cancer Network guideline recommended NGS gene panels for patients with hereditary and ovarian cancer who have tested negative for high-penetrance genes such as BRCA. Interestingly, in a recent study from US, around 141 patients who tested negative for BRCA1/2, evaluation by an NGS panel of 40 genes identified 16 patients who have pathogenic variants in 9 non-BRCA genes thereby assisting in genetic diagnosis.

There could be three different ways by which NGS can be used for clinical diagnostics, ie- gene panels, whole genome sequencing (WGS) and whole exome sequencing (WES).

These approaches are being used not only for cancer, but also for diagnosis of rare genetic diseases and patients with intellectual disability with a diagnostics yield between 25 and 30%. Though genome-based diagnostics are comparatively newer and there are only fewer studies that evaluate their use at this moment.

Advance personalized cancer treatment

Personalised medicine involves using information about a person’s cancer to help diagnose, treat and find out about how well treatment is working. So basically it allows selection of the “right treatment” to the “right patient” at the “right time”. The whole objective of the personalized treatment is achieving maximum drug efficacy with a minimum side effect.

Over the last one decade, numerous genetic alterations have been identified across different cancers which can be used as potential target for treating the cancer. For example, presence of EGFR gene mutation is an indication for treating the patient with anti-EGFR therapy such as Gefitinib. Thus the drug gefitinib will be effective only in those lung cancer patients whose tumor harbor EGFR gene mutation. Similarly, a doctor can check for KRAS gene mutation testing in colon cancer before deciding personalized cetuximab treatment to colon cancer patients.

Thus, Identification of driver alterations can guide the way to treatment with matched targeted therapies in various cancers. Likewise, several recurrent driver mutations have been or are currently being clinically validated (i.e., associated with benefit to specific targeted agents), including BRAF V600E, KIT, EGFR, ERBB2, FGFR3, PIK3CA, AKT1, TSC1, and ROS1 mutations, ERBB2 amplifications, and ALK translocations in different cancer types.

All these years, oncologists were looking for single gene testing related to specific cancer type before deciding personalized treatment, which was often time consuming, costly and wastage of precious tumor samples.

Thanks to NGS based testing, we now have the capacity to measure multiple genetic mutations across different genes in the same assay. This approach seems to be the latest trend in today’s clinical practice which is highly sensitive, cost effective and saves precious tumor samples.

Infact, globally there is general agreement that NGS should be the standard method when several genes must be tested in the same patient for deciding the personalized treatment. For example, based on the various scientific evidence it has been concluded that patients with non-small cell lung cancers (NSCLC) should be tested for mutations in EGFR, BRAF, ERBB2, ROS1, and ALK using NGS methods. Similarly, ER +ve breast cancer patients should be tested for mutations in PIK3CA, ESR1, AKT1, ERBB2, and again, it seems likely that NGS will become the standard method for diagnosis of genomic alterations in breast cancer as well.

Currently, there are various tumor hotspot mutation panels (10 genes, 50 genes, 52 genes etc) which are available in many advanced genomic labs across different parts of the globe. However, one of the major questions related to the use of the NGS in routine practice concerns the number of genes that should be tested.

Thus, it is justified to look for those genetic alterations in a broader holistic way. Thus the comprehensive nature of NGS has the potential to replace a multitude of single gene tests that are currently performed on multiple discrete specimens with a single test on one specimen.

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Contributed by Dr Firoz Ahmad, PhD, Research Scientist & Senior Manager, R&D, SRL Limited and Dr B R Das, PhD Advisor & Mentor-R&D, Molecular Pathology & Clinical Research Services, SRL Limited.

Disclaimer-The information and views set out in this article are those of the author(s) and do not necessarily reflect the official opinion of M3 India. Neither M3 India nor any person acting on their behalf may be held responsible for the use which may be made of the information contained therein.