Tag Archive for: genomicmedicine

Some driver RET mutations are not observed in Indian cancers

The impact of two driver mutations of RET gene, V804M/L and S891A, on Thyroid cancer was described recently by Pichardo et al in JAMA Otolaryngology, 2023. In a population screening, 75 people were identified to have 2 Pathogenic or Likely Pathogenic (P/LP) germline variants of the RET gene. 20 out of these 75 patients chose to undergo prophylactic thyroidectomy even though they did not have any symptoms of cancer. After surgery, pathological analysis of their tissue detected the growth of medullary or papillary thyroid cancer (PTC) in 12 and 2 patients respectively, i.e., 70% of patients with these 2 mutations had been harboring cancer unknowingly!
We examined the presence of these 2 RET variants in Sapien’s 61 Indian thyroid cancer samples profiled in the OncoMineDx panel by ThermoFisher. P/LP mutations were seen in 4 cases, all below the age of 40. Three cases were PTCs and 1 Follicular, with an overall percentage of 6%. The variants detected were V804M/L (3 cases) and C618Y (1 case, Follicular). No case of S891A mutation was detected.
We also checked for RET mutations in our genetically profiled lung cancers (103 cases) where 28 cases had SNVs with 5 cases of V804M, and 1 case had a fusion. No case of S891A was observed. Similarly, among 449 breast cancers, 280 CRCs, 47 gliomas and few cases each of endometrium, urinary bladder and prostate cancers that have been genetically profiled, many cases of V804M/L and other P/LP RET mutations were observed but none of S891A.

HER2 Oncogenic mutations and amplifications are common across many Indian solid tumors

Until recently, HER2 (or ErbB2) targeting drugs were only approved for HER2-amplified breast & gastric cancers. FDA has now granted accelerated approval for trastuzumab or Enhertu to treat lung cancer patients bearing activating HER2 mutations. We analyzed our data of ~1000 solid cancer cases generated using the OncomineTM Dx NGS panel to determine the pattern of ERBB2 amplification vs. mutations. We see that in some cancers, amplifications are more common (breast, gastric, endometrial cancers) but in others, activating mutations are more common (colorectal, lung, thyroid and gliomas) with the most common mutation being V842I in Indian samples. Molecular insights gained from such NGS analysis can hopefully improve precision medicine by expanding the use of approved HER2-targeting drugs for colorectal, endometrial, gliomas, thyroid and other cancer patients that are likely to benefit from them.

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Landscape of Kinase gene fusions in cancers

Tyrosine kinases such as ALK, RET and ROS1 are often activated by translocations or chromosomal rearrangements that result in increased oncogenic activity and are attractive candidates for targeted therapy. In our #biobank, we have identified many patient samples harbouring ALK, RET and ROS1 rearrangements by NGS.

FDA approved drugs such as Crizotinib (Xalkori, #Pfizer), Ceritinib (Zykadia, #Novartis), and Alectinib (Alecensa, #Roche) that target the kinase activity of ALK; Pralsetinib (Gavreto, Roche) targeting RET fusions in NSCLC; Entrectinib (Rozlytrek, Roche) for ROS1+ metastatic NSCLCs, and novel drugs in #clinicaltrials offer promising therapeutic approaches for not just lung but also breast, colorectal and other solid tumours.

ALK targeted therapy for lung cancer: Integration of NGS genome profiling in management of ALK-mutated NSCLCs in India

The NGS genotyping of our NSCLC cases using ThermoFisher’s Oncomine panel identified 8 genetic variants in the ALK gene in 9 cases (16.67%), some of which, such as G1202R and S1206Y surprisingly confer resistance to #Crizotinib treatment, but demonstrate sensitivity to second-generation ALK inhibitors such as #Brigatinib and #Ceritinib, which are currently approved for the treatment of metastatic lung cancers (Sullivan I et al., Ther Adv Med Oncol 2016).

Integration of NGS genetic profiling of tumour samples could play a beneficial role in the management of ALK mutated NSCLCs in India by helping identify the best targeted therapy among Brigatinib, Ceritinib and Crizotinib upfront, based on the mutational profile.

https://www.alkpositive.org/

https://www.cancer.org/cancer/lung-cancer/treating-non-small-cell/targeted-therapies.html

https://www.lung.org/lung-health-diseases/lung-disease-lookup/lung-cancer/symptoms-diagnosis/biomarker-testing/alk-lung-cancer

Building Genotype-Phenotype Correlation Data for Lung Cancer in India

Sapien is curating real world data for the lung cancer cases in the biobank. While 90-95% of our NSCLC samples are biopsies which are mostly exhausted in patient diagnosis and subsequent clinical #biomarker evaluation, the resection samples are being characterized genomically in Oncomine panel to correlate the demographic, diagnostic, treatment and outcomes data with genetic mutations.
The first of such 48 cases showed a very high number of SNVs (479), CNVs (5), Fusions (6) and indels (14). Highest number of mutations were observed in KEAP1 (43.2% of all mutations), followed by STK11 (31.5% of all mutations).