Comparison and Optimization of Simple DNA Extraction Methods for LAMP-Based Point-of-Care Applications Employing Submillimeter Skin Biopsies.

Loop-mediated isothermal amplification (LAMP) has gained particular attention for point-of-care (POC) applications due to its advantages over traditional nucleic acid testing approaches. However, a prevailing limitation of LAMP in POC applications is nucleic acid extraction from the sample prior to analysis. This is particularly true for complex samples such as submillimeter skin biopsies where lysis and digestion involve intricate and lengthy procedures.

Automated detection of Kaposi sarcoma-associated herpesvirus infected cells in immunohistochemical images of skin biopsies.

Immunohistochemical (IHC) staining for the antigen of Kaposi sarcoma-associated herpesvirus (KSHV), latency-associated nuclear antigen (LANA), is helpful in diagnosing Kaposi sarcoma (KS). A challenge, however, lies in distinguishing anti-LANA-positive cells from morphologically similar brown counterparts. In this work, we demonstrate a framework for automated localization and quantification of LANA positivity in whole slide images (WSI) of skin biopsies, leveraging weakly supervised multiple instance learning (MIL) while reducing false positive predictions by introducing a novel morphology-based slide aggregation method.

Rapid, equipment-free extraction of DNA from skin biopsies for point-of-care diagnostics.

Kaposi's sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi's sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process.

Evaluation of a field deployable, high-throughput RT-LAMP device as an early warning system for COVID-19 through SARS-CoV-2 measurements in wastewater.

Quantification of SARS-CoV-2 RNA copies in wastewater can be used to estimate COVID-19 prevalence in communities. While such results are important for mitigating disease spread, SARS-CoV-2 measurements require sophisticated equipment and trained personnel, for which a centralized laboratory is necessary. This significantly impacts the time to result, defeating its purpose as an early warning detection tool.