A Report on Foundation Medicine's Tumor-Focused Sequencing Technology BMEG 101 Module 1 Project Abstract: Biotechnologies are needed to accurately identify mutations in patients that cause diseases such as cancer and use that molecular information to prescribe better treatments, potentially saving lives. Otherwise, patients will continue to be given treatments that are ineffective towards the mutations that cause their medical condition. One of those companies involved in producing these technologies is Foundation Medicine, a bioinformatics company that develops genomic profiling tests to identify mutations that cause cancer, created the Foundation One(F1) CDx test. This product sequences clinical tumor samples to categorize and introns from cancer-associated genes, leading to more personalized treatments for cancer patients. This report explores how the Foundation One(F1) CDx test is utilized to address the diagnosis of genetic mutations and how the product can benefit patients. Moreover, the report also goes into detail about Foundation
One's patents and how competitors are competing with Foundation One with similar products. Furthermore, we also delve into how the company utilizes genomics and bioinformatics to design and use the product for patients, possible improvements to the test, and the social and ethical implications of the test and similar products. Introduction: Genetics testing on biopsy samples is a method used in cancer diagnosis which helps practitioners administer drugs that target known mutated genes of a tumor. However, tumor cells tend to develop new molecular aberrations through resistance to applied cancer therapies which limits the efficiency of cancer-targeted therapies (Janku, 2014). In response to the challenges caused by tumor heterogeneity, Roche (previously Foundation Medicine), a company specialized in tumor genomic profiling, introduced DNA sequencing technologies in clinical testing for cancer (Sheridan, 2018). Foundation Medicine's F1CDx and Guardant Health's G360 are FDA approved liquid biopsies that use biomarkers found in blood samples to profile a patient's tumor and provide them with more personalized therapies. This non-invasive procedure presents fewer risks than tissue biopsies
and is more easily obtainable. It also allows for a real time monitoring of the tumor genetic changes. However, discrepancies are found between the two liquid biopsy methods and this cell free testing remains not fully accurate. Roche is working on increasing the number and variety of detectable potential causative driver genes as well as collecting more data on patients' real outcome in order to improve treatment algorithms and rationale for molecule-guided therapies (Sheridan, 2018). The lack of information on the tumor's histology from liquid biopsies and the clinical risks associated with therapies suggested by the genomic analysis are other limitations faced by sequencing testing and personalized cancer therapies that are yet to be addressed. Company's Solution: The solution implemented by F1 is rooted in precision oncology and next-generation sequencing (NGS). Tests take samples from a tumour or blood and sequence the DNA to locate mutations by comparison against a database of over 300 cancer-related genes (Roche Foundation Medicine, n.d.). Physicians receive results with suggested therapies and drugs. Furthermore, with more tests completed, it expands the network of mapped cancer