Scientific illustration of a migrating breast cancer cell - 3d illustration
Credit: Christoph Burgstedt/Getty Images

Polygenic risk score technology company Allelica announced that it will work with SP BioMED to conduct a study of breast cancer polygenic risk scores (PRS) using data of known breast cancer cases found in Taiwanese biobanks. The goal of the study is to determine the best technology to leverage for developing an accurate, scalable, and cost-effective test for use in downstream applications such as PRS analysis for Taiwan’s population.

“Breast cancer is the most common cause of cancer in Taiwanese women, so understanding the role that genetics plays in this disease risk is critical to identifying women at high risk,” said Allelica CSO, George Busby. “Generating accurate genetic data at low cost is key to enabling healthcare systems to benefit from the enormous potential of genomic medicine. Working together with local providers like SP BioMED to identify the most appropriate technology to drive the development of better medicine across diverse populations is one of Allelica’s top priorities.”

The study will be performed by SP BioMED using Allelica’s PREDICT PRS breast cancer module and will be led by Shih-Feng Tsai of the National Health Research Institutes Taiwan. The research team will analyze 856 Taiwanese breast cancer samples genotyped by SP BioMED and associated laboratories using three different technologies: the Thermo Fisher Axiom Genome-Wide TPM 2.0 (Taiwan Precision Medicine, Version 2.0) Array Plate, whole-genome sequencing (WGS) at 30X coverage, and WGS at 2X coverage.

Raw sequencing data from each method will be analyzed with Allelica’s PREDICT module which performs genome-wide imputation, genetic ancestry assessment, calculation and reporting of Allelica’s breast cancer PRS compared to genetic ancestry matched reference distributions. The breast cancer PRS calculated in the study is Allelica’s proprietary PRS for breast cancer which has been clinically validated in multiple ancestries.

SP BioMED has worked with a network of laboratories in Taiwan focused on offering clinical genetic services to local healthcare providers by providing the necessary genomics technologies and analysis. Their services are targeted to patients with chronic diseases such as cancer and cardiovascular disease, health-conscientious individuals who take an active interest in their personal risk profiles, and participants of biobanks studies for diseases such as chronic kidney disease, coronary artery disease, congestive heart failure, and cancers.

“Predicting genetic risk of chronic diseases, including cancer, is essential for realizing the goal of early detection and precision prevention of common diseases, such as breast cancer,” said Shih-Feng Tsai. “By collaborating with Allelica, we can adopt their PRS technology in Taiwan to implement genomic medicine in clinical practice.”

As part of the project, sample data used for creating PRS will be incorporated with Allelica’s Federated Learning Initiative, which allows Allelica partners and collaborators to help develop improved and more inclusive PRS models without the need to share data. The goal of the initiative is to develop PRS models that can work accurately across diverse ancestries and ethnicities.

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