Comprehensive Genomic Profiling (CGP): Modern standard for personalized cancer care

BY: Dr Ashutosh Upadhyay - 14 Jun-2021

Cancer, a diverse group of diseases is driven by results of genetic alterations that facilitates to aberrant and uncontrolled cellular proliferation. Cancer treatments in 21st century is becoming more and more personalized, so there is focus on developing medicine and therapies for the patients that are tailored towards individual aspects instead of trying to treat everybody the same way. One shoe size, doesn’t fit All!

By Decoding DNA sequences, scientists now have the ability to reach powerful insights into cancer biology. The genomic classification of cancer is leading to the identification and use of better diagnostic, prognostic and predictive biomarkers with an effective management than earlier.

 

Why early diagnosis is important? 

To put things into perspective; let me ask you a couple of questions:

1) Who do you think have higher chance of experiencing in life? being diagnosed by cancer or having a motor vehicle accident 

2) Who do you think have higher fatality rate; Cancer patients or a person facing a vehicular accident?

If you are a part of the majority, a vehicular accident would have been your answer for both these questions.

Interestingly, chances of a person getting into a motor vehicle accident is 1/366 while them getting cancer in their life time is 1/4th. According to National Safety Council List, the chances of a person dying from cancer (1/7 ratio) are phenomenally higher than them dying from vehicular accident (1/103 ratio)

As you can see contrary to popular belief cancer is not only a more probable but also a more fatal threat than vehicular accident. Yet many of us would take our cars for servicing rather than getting our bodies regularly checked-up. 

 

Early diagnosis: Early advantage

An early diagnosis is very significant as it leads to better management by providing early treatment hence, an improved chance of survival and decreased morbidity rate. The diagnosis of cancer demands detection of changes at the molecular level, particularly at the initiation. Thus, attempts have been made to develop molecular techniques to detect changes in genetics, epigenetics, and identification of molecular markers; all of which have improved the diagnosis of cancers. 

 

Traditional technologies for Cancer detection

Traditionally techniques like variants of PCRs, FISH (variants of FISH), DNA, and protein microarray etc have been utilized and are still in use for cancer detection. Therapies based on variations in the gene are becoming significant to treat patient with tumours. Sequencing the genome to detect genetic divergence or variants for theragnostic purposes is the main agenda of targeted therapy or designing precise medicine for a disorder. Initially, techniques like Sanger sequencing and pyrosequencing were extensively used for genetic study.

 

Next Best in Cancer: Evolution of Tumour genomic assessment

Over time, the invention of Next-generation sequencing (NGS), has eased sequencing in a way to revolutionize the diagnosis of cancer further. For personalizing many cancers and finally determining the optimal treatment of these tumours, high-throughput gene sequencing has reputed itself as an indispensable technology within the last 15 years. NGS essentially brought lime light to precision medicine. Mostly when the proportion of cancer cells in a tissue sample is low or when there is genetic heterogeneity. NGS having a low limit of detection gives greater flexibility with the testing. It is rapid and economical for sequencing multiple targets than other standard methods like PCR. NGS permits more comprehensive coverage of genes and increases diagnostic yield as samples can be multiplexed.

Detection of cancer-specific molecular markers, an intensive ongoing field of research is expected to assist tremendously in the early diagnosis and treatment of cancers.

There is growing number of gene-based therapies accompanied with rising demand for solutions that enable the development of accurate biomarkers. The studies are advancing to the adoption of ANOTHER NGS BASED TEST- comprehensive genomic profiling (CGP), which helps and guide treatment decisions based on the molecular drivers of disease. CGP supports putting these findings into practice to simultaneously test for all types of genomic alterations. These may include mutations, copy number variations, and gene-fusions, for a panel of cancer-associated genes. It intends to revolutionize current testing, drug and tumor-type specific companion diagnostic tests that are designed to detect a small subset of the potentially actionable variations. CGP offers simultaneous detection of all classes of genomic alterations across hundreds of genes with a single test from each single sample. 

 

Cancer:  From Uncertainty to focus with CGP!

TruSight Oncology 500 (TSO500) gene panel from Illumina is currently on the market as RUO product that analyses hundreds of current and emerging cancer-related biomarkers. These include:

1) The assay targets 523 genes to also assess small variants, splice variants, and fusions, with hybrid-capture chemistry that ensures high sensitivity and fewer sample dropouts

2) Key immunotherapy markers like TMB and MSI as well as site agnostic markers such as NTRK fusions with known and other unknown partners, using 1.94 MB of genomic content.

3) The workflow is complemented with sophisticated software algorithms to yield results similar to whole-exome sequencing. 

To personalize diagnosis and management of cancers, it has become vital to unravel genetic abnormalities with targeted therapies directed against specific gene mutations. 

“CGP is the seat belt that safeguards you against the unknown bumps in the road of life.”

References: 
https://thepathologist.com/app-notes/comprehensive-genomic-profiling
https://valientemott.com/blog/chances-of-dying-in-a-car-crash/
https://thepathologist.com/fileadmin/pdf/Karger-FF-CGP_ePDF.pdf

 

About the Author

 

 

Dr Ashutosh Upadhyay 
Product Manager, Clinical Genomics
Premas Life Sciences
ashutosh@premaslifesciences.com

Ashutosh is doctorate from University of Delhi South Campus, New Delhi, where he worked on microbial genetics studying the Pseudomonas fluorescence for its biocontrol properties. He did his post- doctoral training at Colorado State University, Colorado – USA in Drug discovery and target developments in Mycobacteria. Currently, he is employed in the capacity of Product Manager, Clinical Genomics in Premas Lifesciences, based in Bangalore. His role is clinical marketing and enabling clinical labs in doing Next Generation Sequencing mainly in oncology testing, reproductive genetics health and related areas.
 

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