Current regimens for the detection and surveillance of bladder cancer are invasive and have suboptimal sensitivity. Here, we present a novel high-throughput sequencing (HTS) method for detection of urine tumor DNA (utDNA) called utDNA CAPP-Seq (uCAPP-Seq) and apply it to 67 healthy adults and 118 patients with early-stage bladder cancer who had urine collected either prior to treatment or during surveillance. Using this targeted sequencing approach, we detected a median of 6 mutations per patient with bladder cancer and observed surprisingly frequent mutations of the PLEKHS1 promoter (46%), suggesting these mutations represent a useful biomarker for detection of bladder cancer. We detected utDNA pretreatment in 93% of cases using a tumor mutationinformed approach and in 84% when blinded to tumor mutation status, with 96% to 100% specifi city. In the surveillance setting, we detected utDNA in 91% of patients who ultimately recurred, with utDNA detection preceding clinical progression in 92% of cases. uCAPP-Seq outperformed a commonly used ancillary test (UroVysion, P = 0.02) and cytology and cystoscopy combined (P ≤ 0.006), detecting 100% of bladder cancer cases detected by cytology and 82% that cytology missed. Our results indicate that uCAPP-Seq is a promising approach for early detection and surveillance of bladder cancer. SIGNIFICANCE: This study shows that utDNA can be detected using HTS with high sensitivity and specifi city in patients with early-stage bladder cancer and during post-treatment surveillance, signifi cantly outperforming standard diagnostic modalities and facilitating noninvasive detection, genotyping, and monitoring.

Artificial intelligence (AI) algorithms continue to rival human performance on a variety of clinical tasks, while their actual impact on human diagnosticians, when incorporated into clinical workflows, remains relatively unexplored. In this study, we developed a deep learning-based assistant to help pathologists differentiate between two subtypes of primary liver cancer, hepatocellular carcinoma and cholangiocarcinoma, on hematoxylin and eosin-stained whole-slide images (WSI), and evaluated its effect on the diagnostic performance of 11 pathologists with varying levels of expertise. Our model achieved accuracies of 0.885 on a validation set of 26 WSI, and 0.842 on an independent test set of 80 WSI. Although use of the assistant did not change the mean accuracy of the 11 pathologists (p = 0.184, OR = 1.281), it significantly improved the accuracy (p = 0.045, OR = 1.499) of a subset of nine pathologists who fell within well-defined experience levels (GI subspecialists, non-GI subspecialists, and trainees). In the assisted state, model accuracy significantly impacted the diagnostic decisions of all 11 pathologists. As expected, when the model's prediction was correct, assistance significantly improved accuracy (p = 0.000, OR = 4.289), whereas when the model's prediction was incorrect, assistance significantly decreased accuracy (p = 0.000, OR = 0.253), with both effects holding across all pathologist experience levels and case difficulty levels. Our results highlight the challenges of translating AI models into the clinical setting, and emphasize the importance of taking into account potential unintended negative consequences of model assistance when designing and testing medical AI-assistance tools.npj Digital Medicine (2020) 3:23 ; https://doi.

Photoswitchable distance constraints in the form of photoisomerizable chemical cross-links offer a general approach to the design of reversibly photocontrolled proteins. To apply these effectively, however, one must have guidelines for the choice of cross-linker structure and cross-linker attachment sites. Here we investigate the effects of varying cross-linker structure on the photocontrol of folding of the Fyn SH3 domain, a well-studied model protein. We develop a theoretical framework based on an explicit-chain model of protein folding, modified to include detailed model linkers, that allows prediction of the effect of a given linker on the free energy of folding of a protein. Using this framework, we were able to quantitatively explain the experimental result that a longer, but somewhat flexible, cross-linker is less destabilizing to the folded state than a shorter more rigid cross-linker. The models also suggest how misfolded states may be generated by cross-linking, providing a rationale for altered dynamics seen in nuclear magnetic resonance analyses of these proteins. The theoretical framework is readily portable to any protein of known folded state structure and thus can be used to guide the design of photoswitchable proteins generally.

Objective Controversy persists regarding appropriate radiographic surveillance strategies following lung cancer resection. We compared the impact of surveillance CT scan (CT) vs. chest radiograph (CXR) in patients who underwent resection for stage I lung cancer. Methods A retrospective analysis was performed of all patients undergoing resection for pathologic stage I lung cancer from January 2000–April 2013. After resection, follow-up included routine history and physical exam in conjunction with CXR or CT at the discretion of the treating physician. Identification of successive lung malignancy (i.e. recurrence at any new site or new primary) and survival were recorded. Results There were 554 evaluable patients with 232 undergoing routine postoperative CT and 322 receiving routine CXR. Postoperative five-year survival was 67.8% in the CT group vs. 74.8% in the CXR group (p = 0.603). Successive lung malignancy was found in 27% (63/232) of patients undergoing CT vs. 22% (72/322) receiving CXR (p = 0.19). The mean time from surgery to diagnosis of successive malignancy was 1.93 years for CT vs. 2.56 years for CXR (p = 0.046). For the CT group, 41% (26/63) of successive malignancies were treated with curative intent vs. 40% (29/72) in the CXR group (p = 0.639). Cox-proportional hazard analysis indicated imaging modality (CT vs. CXR) was not associated with survival (p = 0.958). Conclusion Surveillance CT may result in earlier diagnosis of successive malignancy vs. CXR in stage I lung cancer, although no difference in survival was demonstrated. A randomized trial would help determine the impact of postoperative surveillance strategies on survival.

No abstract