Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is.

Von Hippel-Lindau (VHL) disease is a rare, autosomal dominant disorder that predisposes individuals to developing tumors in many organs. There is significant phenotypic variability and genetic variants encountered within this syndrome, posing a considerable challenge to patient care. The lack of VHL variant data sharing paired with the absence of aggregated genotype-phenotype information results in an arduous process, when characterizing genetic variants and predicting patient prognosis. To address these gaps in knowledge, the Clinical Genome Resource (ClinGen) VHL Variant Curation Expert Panel (VCEP) has been resolving a list of variants of uncertain significance within the VHL gene. Through community curation, we crowdsourced the laborious task of variant annotation by modifying the ClinGen Community Curation (C3)-developed Baseline Annotation protocol and annotating all published VHL cases with the reported genotype-phenotype information in Hypothes.is, an open-access web annotation tool. This process, incorporated into the ClinGen VCEP's workflow, will aid in their curation efforts. To facilitate the curation at all levels of genetics expertise, our team developed a 4-day biocuration training protocol and resource guide. To date, 91.3% of annotations have been completed by undergraduate and high-school students without formal academic genetics specialization. Here, we present our VHL-specific annotation protocol utilizing Hypothes.is, which offers a standardized method to present case-resolution data, and our biocuration training protocol, which can be adapted for other rare disease platforms. By facilitating training for community curation of VHL disease, we increased student engagement with clinical genetics while enhancing knowledge translation in the field of hereditary cancer. Database URL: https://hypothes.is/groups/dKymJJpZ/vhl-hypothesis-annotation.

Large scale genotype- and phenotype-driven machine learning in Von Hippel-Lindau disease.

Von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome where individuals are predisposed to tumor development in the brain, adrenal gland, kidney, and other organs. It is caused by pathogenic variants in the VHL tumor suppressor gene. Standardized disease information has been difficult to collect due to the rarity and diversity of VHL patients. Over 4100 unique articles published until October 2019 were screened for germline genotype-phenotype data. Patient data were translated into standardized descriptions using Human Genome Variation Society gene variant nomenclature and Human Phenotype Ontology terms and has been manually curated into an open-access knowledgebase called Clinical Interpretation of Variants in Cancer. In total, 634 unique VHL variants, 2882 patients, and 1991 families from 427 papers were captured. We identified relationship trends between phenotype and genotype data using classic statistical methods and spectral clustering unsupervised learning. Our analyses reveal earlier onset of pheochromocytoma/paraganglioma and retinal angiomas, phenotype co-occurrences and genotype-phenotype correlations including hotspots. It confirms existing VHL associations and can be used to identify new patterns and associations in VHL disease. Our database serves as an aggregate knowledge translation tool to facilitate sharing information about the pathogenicity of VHL variants.

Chemosensory and Behavioural Responses of Ixodes scapularis to Natural Products: Role of Chemosensory Organs in Volatile Detection.

Blacklegged ticks, Ixodes scapularis, represent a significant public health concern due to their vectoring of tick-borne disease. Despite their medical importance, there is still limited knowledge of the chemosensory system of this species, and thus a poor understanding of host-seeking behaviour and chemical ecology. We investigated the electrophysiological sensitivity of adult female blacklegged ticks to attractants and plant-derived compounds via an electrode inserted into the scutum. The response of female ticks to binary mixtures with a constant concentration of a selected attractant (butyric acid) and increasing concentration of volatile organic compounds (VOCs) (geraniol, phenethyl alcohol, ß-citronellol, and citral) was recorded. A strict relationship between increasing volatile concentration and a decreasing response was observed for each VOC. Y-tube bioassays confirmed that tick attraction towards butyric acid decreased with the presence of a VOC, which exerted a deterrent effect. To determine the specific role of sensory appendages involved in the detection of attractant chemical stimuli, we tested tick electrophysiological response after removing appendages that house chemosensory sensilla (foretarsi, pedipalps, or both). The chemosensory response was related to the molecular structure of attractant odorant, and the lack of pedipalps significantly reduced olfactory responses, suggesting they play an important role in detecting attractants. This study provides new insight into the neurophysiological mechanisms underlying tick olfaction and the potential for interactions between attractant and deterrent chemical detection.

Behavioral responses of Ixodes scapularis tick to natural products: development of novel repellents.

The spread of blacklegged ticks (Ixodes scapularis) and growing threat of Lyme disease transmission has increased demand for effective, safe and environmentally friendly repellent products. Plant-derived essential oils are natural products that exhibit insecticidal and repellant activities and represent a promising alternative to synthetic repellants. However, mechanisms by which ticks detect odor stimuli and how such stimuli may function as repellents are not well understood. We examined the repellent activity of selected essential oil components towards I. scapularis in short- and long-term dose-response trials. To determine the specific olfactory organs involved in detection of chemical stimuli, we tested tick behavioral response in repellency bioassays after removing appendages that house chemosensory sensilla (e.g., foretarsi or pedipalps). New prototype formulae were tested in longevity trials repelling up to 95% of tested ticks after 1 h post-application. This study provides new insight regarding tick olfaction and behavior, and innovative methods for selecting appropriate chemicals for development of novel plant-based repellent products for protection from ticks.