Consultant, Molecular Haematology & Oncology, Fortis Memorial Research Institute, Gurugram
Part 7 of 9 in Genomics Revolution in Cancer
Inside Next Generation Sequencing: How Genomic Testing Actually Works
January 19, 2025
From Biopsy to Report
Once a suspicious piece of tissue is removed for biopsy, DNA is extracted from that block and put through genome sequencing, also called next generation sequencing. Dr. Nathany's own lab runs this on the Ion Torrent Genexus System, an integrated sequencer with its own robotic arm that prepares the sample and carries out the test, turning raw genetic data into a processed report through dedicated software. The system can process blood, tumour tissue or effectively any other body fluid, and her lab has already completed more than 500 samples on it.
Turnaround Time and Cost
Sequencing itself takes a maximum of 18 hours, which lets Dr. Nathany's lab deliver a report to a patient within three to four days, compared with a typical three-week turnaround internationally. A routine tumour marker panel now covers a minimum of 50 genes. Basic genomic tests cost roughly $300 to $400, rising to about $1,000 for more extensive panels; these costs are not routinely covered by insurers or government health schemes in most countries, so patients often pay out of pocket, though patient access programmes run by drug manufacturers can reduce the cost of the medicines a genomic result points to.
This guide is based on a live Jivo Masterclass: Dr. Shrinidhi Nathany taught doctors across Africa on January 19, 2025.
FROM THE LIVE Q&A
Moderator
Can you clarify more about gene therapy?
Dr. Shrinidhi Nathany
For example, sickle cell anaemia is caused by a point mutation where only one letter in the genome is changing. So what we can do is if A is becoming B, we make the B back to A and edit that gene, and deliver it through an IV cannula in the form of a solution. That is what is going to get integrated into the patient, and the disease can be cured. That is what gene therapy is.
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Frequently Asked Questions
Can we do genomic modifications to prevent cancer?▼
Well, not yet. What we can do is, supposing somebody in my family got cancer, I can get my genes tested so I know whether I am at risk of getting that cancer, and then I can try to catch it early, because once you're at a last stage it becomes difficult to cure. If you catch it early you can still cure the cancer.
What are the common tumour marker genes tested for routinely?▼
The recommendation is to test at least 50 genes. If somebody is interested I can send the list across to the Jivo team and they can share it with everybody.
Is it possible to combine genes from three people to get the desired characteristics of a baby?▼
Yes, that is what is called designer babies, which can be done. You cannot really extract only particular genes, but you can make designer babies now in the lab through clinical embryology.
I didn't understand well the difference between genetics and genomics. Based on which examination or test can we know genetic and genomic compatibility?▼
The difference between genetics and genomics: you are a clinician, you are seeing the patient. What you see in the patient is genetics. What I do in the lab is genomics.
What test is used for [pre-marital] compatibility genomics?▼
It is called genome sequencing.
What sequencing system does Dr. Nathany's lab use for genomic cancer testing?▼
The Ion Torrent Genexus System, an integrated next generation sequencer with a robotic arm that prepares the sample and runs the test.
How long does it take to get a genomic test report?▼
Sequencing itself takes up to 18 hours, and the full report typically reaches the patient within three to four days, compared with about three weeks internationally.
How much does genomic cancer testing typically cost?▼
Roughly $300 to $400 for a basic test, rising to about $1,000 for more extensive panels.
What is the minimum gene panel size recommended for routine tumour marker testing?▼
At least 50 genes, according to Dr. Nathany.
In This Series: Genomics Revolution in Cancer
- 1.Genomics Revolution in Cancer
- 2.Germline Versus Somatic Testing: The Two Pillars of Genomic Testing
- 3.How Genomic Sequencing Changed Precision Medicine in Stage 4 Lung Cancer
- 4.Hereditary Cancer Risk: BRCA, HBOC Syndrome and the Case for Family Testing
- 5.Pharmacogenomics: How Genes Shape Drug Response and Side Effects
- 6.Liquid Biopsy for Cancer Screening: What's Proven and What's Still Under Research
- 7.Inside Next Generation Sequencing: How Genomic Testing Actually Works
- 8.Gene Therapy and Genome Editing: From Sickle Cell Anaemia to CRISPR
- 9.Genomics Beyond Cancer: Cardiology, Neurology and Pre-Marital Screening