Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.

Image-guided radiation therapy (IGRT) involves two main procedures, performed in different rooms on different days: (1) treatment planning in the simulator room on the first day, and (2) radiotherapy in the linear accelerator room over multiple subsequent days. Both the simulator and the linear accelerator include CT imaging capabilities, which enables both treatment planning and reproducible patient setup, but does not provide good soft tissue contrast or allow monitoring of the target during treatment. We propose a cooperatively-controlled robot to reproducibly position an ultrasound (US) probe on the patient during simulation and treatment, thereby improving soft tissue visualization and allowing real-time monitoring of the target. A key goal of the robotic system is to produce consistent tissue deformations for both CT and US imaging, which simplifies registration of these two modalities. This paper presents the robotic system design and describes a novel control algorithm that employs virtual springs to implement guidance virtual fixtures during "hands on" cooperative control.

The Small Animal Radiation Research Platform (SARRP) is a novel and complete system capable of delivering multidirectional (focal), kilo-voltage radiation fields to targets in small animals under robotic control using cone-beam CT (CBCT) image guidance. The capability of the SARRP to deliver highly focused beams to multiple animal models provides new research opportunities that more realistically bridge laboratory research and clinical translation. This paper describes the design and operation of the SARRP for precise radiation delivery. Different delivery procedures are presented which enable the system to radiate through a series of points, representative of a complex shape. A particularly interesting case is shell dose irradiation, where the goal is to deliver a high dose of radiation to the shape surface, with minimal dose to the shape interior. The ability to deliver a dose shell allows mechanistic research of how a tumor interacts with its microenvironment to sustain its growth and lead to its resistance or recurrence.