Summary of Federal Cooperative Agreement Award

The University of California Santa Cruz received a $450,000 Cooperative Agreement award from the National Cancer Institute (NCI) under the Cancer Biology Research program (CFDA 93.396) for the period May 1, 2026 through April 30, 2029. The project, titled "Pangenome-Aware Methods for Accurate Somatic Variant Discovery in Cancer Genomics," delivers three primary products and services: (1) expansion of the Cancer Standards Long-Read Evaluation (CASTLE) collection to twelve tumor-normal cell line pairs sequenced with multiple technologies (Illumina, Oxford Nanopore, and PacBio HiFi), complete with telomere-to-telomere germline genome assemblies and comprehensive benchmark variant sets released without access restrictions; (2) development of new versions of the DeepSomatic variant caller incorporating pangenome information through pangenome-based read mapping, haplotype integration, and personalized reference approaches to reduce reference bias; and (3) extension of the Severus structural variant caller to work with complete germline assemblies and pangenome references using multiple mapping approaches including diploid assemblies and personalized pangenome references.

These deliverables directly advance the Cancer Biology Research program's objective to provide fundamental information on cancer mechanisms and improve methods for cancer detection and diagnosis by addressing key technical challenges in somatic variant detection, including tumor heterogeneity, reference bias, and the limitations of linear reference genome approaches. The openly released benchmark datasets and enhanced computational tools will support the broader research community in developing more accurate cancer genomics methodologies.