Fidelity Biosciences (United States)

Molecular testing in non-small cell lung cancer (NSCLC) identifies patients likely to respond to targeted therapeutics. Panel-based testing often employs next-generation sequencing, but challenges include high sample failure rates, quality control issues, high tissue requirements and long turnaround times. Significant proportions of patients do not receive appropriate targeted therapy, with inferior clinical outcomes. Aspyre Lung is a targeted genomic profiling assay for 114 actionable or prognostic genomic variants across 11 genes with a two-day turnaround time of specimen to result. We profiled 198 NSCLC patient tissue samples using Aspyre Lung and a next-generation sequencing- (NGS)-based assay. Cohort A comprised 107 samples that failed to inform due to NGS quality checks, and Cohort B 91 samples that underwent successful NGS testing. Results were compared, and discrepancies resolved by orthogonal methods. For Cohort A (NGS fails), 103 (96 %) passed Aspyre Lung quality control, successfully yielding genomic results, including 48 (47 %) samples with ≥ one variant. In Cohort B (NGS pass), all samples passed Aspyre quality control with 97 % concordance to NGS-based testing. Notably, 80 % EGFR variant-positive samples were stages I and II. Aspyre Lung profiled 96 % of samples where NGS-based methods failed, and uncovered variants in samples successfully tested by NGS and deemed negative. Aspyre Lung detected ALK and EGFR variants from patients with early-stage disease, demonstrating utility as a rapid screening assay prior to neoadjuvant immuno-chemotherapy consideration.

Abstract Cytosine and adenosine base editors show great potential in research and clinical applications. Current iterations of the deaminase—the enzyme used to create precise single-nucleotide changes via base editing—exhibit various off-target effects, including Cas-independent off-targeting, off-base editing, and bystander editing. Engineered deaminases are typically derived from eukaryotic deaminases, which are larger and exhibit high levels of Cas-independent DNA editing, or from evolved variants of the E. coli TadA protein (ecTadA), which are smaller but frequently cause off-base editing. To overcome the limitations inherent to using a single protein sequence as the basis for engineering, we diversified 95 newly identified TadA orthologs by introducing literature-derived mutations and DNA shuffling to yield millions of training sequences for measuring base editor efficiency. Rather than pursuing multiple rounds of random mutagenesis and selection, we trained generative models on the performance data from the diversified pools of variants and drew on information-theoretic insights to efficiently explore the deaminase sequence space to generate diverse and high-performing deaminases. From a single round of diversification, we created a small set of novel and specific cytosine and adenosine deaminases that were markedly distinct in sequence from published base editor deaminases. We additionally found that the deaminases created by our model generally outperform those which we identified through typical directed evolution. The novel adenosine and cytosine deaminases identified in this work showed high on-base activity, comparable to the leading published base editors, but with demonstrably lower off-base activity. The cytosine deaminases were particularly compact compared to known sequences due to a truncation in their final α-helix.

Disease resistance genes in livestock provide health benefits to animals and opportunities for farmers to meet the growing demand for affordable, high-quality protein. Previously, researchers used gene editing to modify the porcine CD163 gene and demonstrated resistance to a harmful virus that causes porcine reproductive and respiratory syndrome (PRRS). To maximize potential benefits, this disease resistance trait needs to be present in commercially relevant breeding populations for multiplication and distribution of pigs. Toward this goal, a first-of-its-kind, scaled gene editing program was established to introduce a single modified CD163 allele into four genetically diverse, elite porcine lines. This effort produced healthy pigs that resisted PRRS virus infection as determined by macrophage and animal challenges. This founder population will be used for additional disease and trait testing, multiplication, and commercial distribution upon regulatory approval. Applying CRISPR-Cas to eliminate a viral disease represents a major step toward improving animal health.

Annals of the New York Academy of SciencesVolume 473, Issue 1 p. 535-536 Decreased Striatal Levels of Ascorbic Acid in High Pressure Exposed Ratsa T. P. OBRENOVITCH, T. P. OBRENOVITCH Centre d'Etudes et de Recherches Biophysiologiques Appliquees a la Marine, Toulon-Naval, F-83800, FranceSearch for more papers by this authorJ. L. GILLARD, J. L. GILLARD Centre d'Etudes et de Recherches Biophysiologiques Appliquees a la Marine, Toulon-Naval, F-83800, FranceSearch for more papers by this author T. P. OBRENOVITCH, T. P. OBRENOVITCH Centre d'Etudes et de Recherches Biophysiologiques Appliquees a la Marine, Toulon-Naval, F-83800, FranceSearch for more papers by this authorJ. L. GILLARD, J. L. GILLARD Centre d'Etudes et de Recherches Biophysiologiques Appliquees a la Marine, Toulon-Naval, F-83800, FranceSearch for more papers by this author First published: December 1986 https://doi.org/10.1111/j.1749-6632.1986.tb23652.x a Supported by D.R.E.T. grant no. 82–11–44. AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume473, Issue1Neurochemical Analysis of the Conscious Brain: Voltammetry and Push-Pull PerfusionDecember 1986Pages 535-536 RelatedInformation