String sequence analysis revealed that silk spinning behavior of adult female Embioptera varies from species-specific to individualistic. This analysis included 26 species from ten taxonomic families with a total of 115 individuals. Spin-steps, 28 possible positions of the front feet during spinning, were scored from hour-long DVD recordings produced in the laboratory. Entire transcripts of hundreds to thousands of spin-steps per individual were compared by computing Levenshtein edit distances between all possible pairs of subsequences, with lengths ranging from 5 to 25—intraspecific similarity scores were then computed. Silk gallery characteristics and architecture, body size, climatic variables, and phylogenetic relationships were tested as possible drivers of intraspecific similarity in spinning behavior. Significant differences in intraspecific similarity aligned most strongly with climatic variables such that those species living in regions with high temperature seasonality, low annual precipitation, and high annual temperatures displayed more species-stereotypical spinning sequences than those from other regions, such as tropical forests. Phylogenetic signal was significant but weakly so, suggesting that environmental drivers play a stronger role in shaping the evolution of silk spinning. Body size also appears to play a role in that those of similar size are more like each other, even if not related.

Non-Small Cell Lung Cancer (NSCLC) is the most common type of lung cancer with 236,740 new cases diagnosed in 2022 in the United States. In this study, we demonstrate the performance of a digital PCR (dPCR) based assay that reports 15 (NCCN) biomarkers using only 1 slide of FFPE tissue. ChromaCode’s High Definition PCR (HDPCR™) NSCLC Tumor Profiling Panel (Research Use Only) detects guideline biomarkers including variants for EGFR, BRAF, KRAS, ERBB2, ALK, ROS1, RET, MET, and NTRK1-3 with a 24 hour turnaround time and a simple PCR workflow. A total of 34 NSCLC FFPE specimens were evaluated using the HDPCR NSCLC Panel. DNA and RNA were extracted from a single 10 µm section of specimen, with a sister section previously characterized with the Oncomine Precision Assay GX. The DNA/RNA eluates (20ng DNA per well, 20ng RNA) were run with the HDPCR NSCLC Panel on the Qiagen QIAcuity dPCR instrument. Data analysis was conducted using ChromaCloud™, which includes a proprietary algorithm that can detect and quantify 6 targets (5 targets and 1 internal control) for each of the 3 wells. DNA samples discordant with the comparator assay were evaluated using the Archer DNA VariantPlex panel, while RNA discordant samples were analyzed using the Archer RNA fusion plex panel. Of the 34 specimens evaluated, 16 SNV, 13 Insertion/Deletion, and 7 fusion positive specimens were identified using NGS. On the dPCR assay, the results show a high-level of agreement, after discordant resolution, of 95.8% across the panel. The minor allele fraction (MAF), also calculated using ChromaCode Cloud, ranged from 5% to 90%. With 20 ng input (Qubit), the average copy number of amplifiable DNA ranged from 791 copies (~2.3 ng) to 6583 copies (~19.9 ng) with a mean of 2410 copies (~7.43 ng). Here we demonstrate that the HDPCR NSCLC Tumor Profiling Panel provides comparable performance to validated NGS assays with a turnaround that enables adherence to guideline-recommended treatment, and a low sample requirement that maximizes the number of patients for molecular testing. The standard protocols used by the assay and the use of a cloud based analysis pipeline enables easy deployment of this assay in any lab. Citation Format: Kerri Cabrera, Jeff Gole, Bryan Leatham, Isabel Regoli, Tiffany Martinez, Andrew Richards, Leah Herdt, Juan Enciso, Paige Berroteran, Heather Carolan, Brad Brown. Performance of a 24-hour turnaround, guideline-complete NSCLC assay, optimized for sparse samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2194.

Background The SARS-CoV-2 pandemic has demonstrated the need for streamlined workflows in high-throughput testing. In extraction-based testing, limited extraction reagents and required proprietary instrumentation may pose a bottleneck for labs. As a solution, ChromaCode developed a Direct Extraction protocol for the HDPCR™ SARS-CoV-2 Assay, distributed in accordance with the guidance on Policy for Coronavirus Disease-2019 Tests During the Public Health Emergency, Section IV.C., which allows for the processing of specimens without an extraction system. In lieu of an extraction system, the Direct Extraction protocol uses a thermal cycler to lyse and inactivate specimens which are directly added to the Polymerase Chain Reaction (PCR). Methods The Limit of Detection (LoD), Clinical Performance, and effect of Interfering Substances was determined for the Direct Extraction protocol. The LoD was established on 6 PCR platforms with dilutions of inactivated SARS-CoV-2 virus spiked into residual, negative nasopharyngeal swab (NPS) matrix. Clinical performance was assessed with 48 positive and 50 negative frozen retrospective samples using the Direct Extraction protocol compared to an external Emergency Use Authorized (EUA) comparator assays (cobas® Liat® SARS-CoV-2 & Influenza A/B assay and the Hologic Panther Fusion® SARS-CoV-2 Assay respectively) on three PCR platforms. The Direct Extraction protocol was evaluated for performance in the presence of 13 potentially interfering substances that can be present in a respiratory specimen. Results The LoD of the Direct Extraction protocol ranges from 1000 – 3000 genomic equivalents (GE)/mL. The clinical performance of the assay was 95.8% positive agreement (95% CI of 84.6% - 99.3%) and 100% negative agreement (95% CI of 90.9% - 100% or 91.1% – 100%) across all three PCR platforms tested. The viral target was detected at 3X LoD for all interferents tested. Conclusion The Direct Extraction protocol of ChromaCode’s SARS-CoV-2 Assay is a sensitive test that eliminates the need for sample extraction and performs very well against traditional extraction-based workflows. The inclusion of this protocol can reduce costs, reliance on extraction systems, and time associated with extraction-based protocols. Disclosures Meghna Yadav, Ph.D. Molecular Biology, ChromaCode Inc. (Employee, Shareholder) Tiffany Martinez, n/a, ChromaCode (Employee, Shareholder) Isabel Regoli, MS, Bioinformatics, ChromaCode (Employee, Shareholder) Osvaldo Hernandez, B.S., Molecular Biology, ChromaCode (Employee, Shareholder) Phuong Le, B.S., Biochemistry, ChromaCode (Employee, Shareholder) Heather Carolan, Masters, Computational Molecular Biology, ChromaCode (Employee, Shareholder) Brad Brown, Ph.D Biomedical Sciences, ChromaCode (Employee, Shareholder) Karen Menge, Ph.D. Biochemistry, ChromaCode (Employee, Shareholder)ChromaCode (Employee, Shareholder)