NEW YORK – Bioinformatics company Allelica said on Wednesday that it is collaborating with Taiwanese precision medicine firm SP BioMed on a polygenic risk score (PRS) study of breast cancer.
The goal of the study is to determine the best genotyping technology for genome-wide data generation for future applications such as PRS calculation in the Taiwanese population, Allelica said.
Allelica will use its Predict software to analyze 856 Taiwanese breast cancer samples genotyped by SP BioMed using three different platforms: the Thermo Fisher Axiom Genome-Wide TPM 2.0 Array Plate (Taiwan Precision Medicine V2.0), whole-genome sequencing (WGS) at 30X coverage, and WGS at 2X coverage. The study is expected to wrap up in May of this year.
Predict takes in raw sequencing or genotyping data and performs genome-wide imputation with genetic ancestry assessment. It then calculates and reports Allelica’s breast cancer PRS, comparing it to genetic ancestry-matched reference distributions.
Allelica developed its cross-ancestry breast cancer PRS in collaboration with Invitae last year.
"Generating accurate genetic data at low cost is key to enabling healthcare systems to benefit from the enormous potential of genomic medicine," Allelica CSO George Busby said in a statement. "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."
Allelica plans to add the samples it analyzes in the study to its Federated Learning Initiative (FLI), a program through which the company's collaborators can develop better and more inclusive PRS models without needing to share data.
The company intends to use the FLI as a launchpad for the PRS Alliance, an organization meant to develop accurate PRS that works for any individual, regardless of ancestry or ethnicity.
Allelica is not alone in developing PRS for diverse populations: MyOme and Myriad Genetics have also developed a cross-ancestry breast cancer PRS.