personalizedmedicine – Sapien Biosciences

Genetic Counselling an Personalized Medicine conference in Hyderabad

July 25, 2023/0 Comments/in Blog/by admin

Delighted to be a part of 8th Annual BGCI #conference held at the #University of Hyderabad from July 7th to 9th, 2023 where Rakesh Sharma, PhD and Madhuri R presented posters titled “Molecular landscape of #lung adenocarcinoma in India for personalizing therapy” and “Driver gene alterations in EGFR and IDH1 are mutually exclusive in Indian Gliomas”.

Jugnu Jain and Kalpana Kannabiran were invited by Dr Q. Annie Hasan to chair the session on “Psychosocial #ethical and legal issues in #genetics and #genomics ” including panelists Dhavendra kumar Mahati Chittem Saveetha Meganathan, Kelly Ormond and Peter Abad.
Reena Trivedi Vaishnavi Suresh helped put the panel together.

It was an enriching experience, filled with insightful presentations and discussions.

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

April 8, 2023/0 Comments/in Blog/by admin

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.

Digital library of whole slide Images Built at Sapien

February 28, 2023/0 Comments/in Blog/by admin

Sapien is focusing on the emerging area of Digital Pathology combined with Machine Learning (ML) and Artificial Intelligence (AI), to improve the diagnoses, to sub-classify patients into more clinically-relevant phenotypes and predict outcomes. Sophisticated image analysis tools combined with computational advances allow whole slide images (WSI) to be analysed using ML / AI to develop algorithms to aid pathologists and clinicians to personalize treatment.

For this purpose, Sapien is creating a high-resolution library of WSI from hundreds of cancer specimens’ FFPE blocks for which demographic and diagnostic data has already been curated and structured by the biobank.
In breast cancer for example, matched sets of H&E, ER, PR, HER2, Ki67/MIB images from the same case have been scanned at 40X magnification from 750+ cases, spanning all stages, grades and histotypes in pathology. Even benign breast tumors as well as normal breast tissues have been scanned as controls. Multiple scanners (Philips, Morphle, Motic) are being used to also allow normalization across different platforms for solutions.

ImageNet, IBM, TCGA have large image datasets in oncology; Sapien’s digital library is the largest such database for Indian cancer patients. Sapien is adding treatment and outcomes data, as well as genetic variant data, to these cancer cases, in the hope of deep learning approaches making it possible for the inexpensive, more widely available HE images to replace the need for IHC-, FISH- and gene-based biomarker analysis.
https://www.ibm.com/blogs/research/2020/03/benefits-ai-for-breast-cancer-detection/
https://www.sciencedirect.com/science/article/pii/S2153353922003510
**https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9037318/**

Landscape of Kinase gene fusions in cancers

December 30, 2021/0 Comments/in Blog/by admin

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

November 27, 2021/0 Comments/in Blog/by admin

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

KRAS mutations in Breast cancer may be treatable

October 13, 2021/0 Comments/in Blog/by admin

For decades, mutations in #KRAS have been known to cause cancers in multiple organs and the gene KRAS itself was considered ‘undruggable’. Of the many mutations, KRAS-G12C is known to occur in nearly 13% of #NSCLC cases. There were no known treatments that can target KRAS-G12C mutation until recently. May 2021 heralded the #fdaapproval of Sotorasib, granted to #amgen, for treatment of #lungcancer with the G12C mutation in KRAS. Exciting results showed a reduction in tumour burden in more than 37% of the trial participants. This paves the way for testing the efficacy of the drug in multiple other cancers harbouring this driver mutation.
Our data identified nearly 7.8% of breast cancer #FFPE samples bearing the KRAS-G12C mutation, bringing hope of this #drug to people with #breastcancer.

Sapien’s samples and real world data enables validation of a new Indian breast cancer test with high concordance to OncotypeDx test

November 4, 2020/0 Comments/in Blog/by admin

In 2014, Sapien partnered with Oncostem Diagnostics to provide our curated breast cancer FFPE blocks and RWE 5 years treatment and recurrence outcome data to enable the validation of a new test to accurately determine the risk of recurrence in early stage breast ca patients. A key goal of the test was to identify patients at low risk that could avoid chemotherapy and its side-effects, a major benefit to #cancerpatients (see Sapien referenced in this & previous papers).

https://onlinelibrary.wiley.com/doi/full/10.1002/cam4.3495

It’s gratifying to see their first test, canAssist Breast for hormone positive breast cancer patients, perform equivalent to the gold standard Oncotype Dx test, a more expensive and higher TAT for Indian patients.

Our deep collection of matched FFPE blocks and longitudinal RWE data to enable precision medicine tests has continued to grow, both in breast cancer (>10,000 cases), and in #colorectalcancer, #lungcancer, #oralcancer, #kidneycancer, #ovariancancer #glioma #liver cancers. Contact us at queries@sapienbio.com