Next generation gene sequencing

Next Generation Gene Sequencing (NGS) in Cancer

Next generation gene sequencing is a DNA sequencing technology that uses parallel sequencing of multiple fragments of DNA to sequence an individual’s genome. In other words, it is a test that allows us to learn about the sequence of DNA in a person or a cancer and look for changes that could determine its behaviour and inform about potential risks for a cancer or about potential treatment options.

The DNA from a person can be taken from the blood or other areas like the mouth, saliva or hair. In patients with cancer, the DNA can be taken from the biopsy or operated specimen.

There are different types of gene sequencing that can be done. The whole genome of the patient can be sequenced. Alternatively, if the cancer is known and we want to look for specific changes in the DNA, targeted gene panels can be used to get those answers. Multiple such panels are available, and the doctor selects the most appropriate one in that setting.

Potential uses of NGS testing in cancer include

Testing for inherited forms of breast and ovarian cancers. Testing done to look for mutations in BRCA1 and BRCA2 along with PALB2 and TP53

Screening for inherited cancers of gastro-intestinal tract

To look for familial leukaemia syndromes

Looking at tumour DNA to look for potential genetic abnormalities that may be suitable for use of chemotherapy or specific molecular targeted drugs. One such test is to look for microsatellite instability (MSI-H) or mismatch repair deficient (dMMR) in solid tumours that are metastatic.

The decision to go for such a test or not should be thoroughly discussed with the Oncologist or a geneticist as there could be pros and cons for such a test. An informed decision should be taken. It should never be taken without consulting either of these professionals.

Once the sample is sent for testing, it can take 1-2 weeks for the results to come back.

Proper interpretation of NGS results is important. The test may detect many mutations present in the DNA. These will be classified or grouped as pathogenic-able to cause a cancer, likely pathogenic- may be able to cause cancer, benign-does not cause any problems and ‘unknown clinical significance’ which means the importance of it is unknown. It should be realised that not all mutations are harmful and the person or patient having the test should not be unduly alarmed by seeing the result.