Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling.

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel (Urocitellus brunneus) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals.

Rethinking genetic counseling clinical skills training in the time of COVID-19.

The COVID-19 pandemic has had a significant impact on clinical training programs, including genetic counseling graduate programs. The University of Arizona Genetic Counseling Graduate Program responded to limited clinical training opportunities by designing a virtual Clinical Skills Workshop for incoming genetic counseling students. During the workshop, students were introduced to psychosocial and clinical genetics skills through virtual lectures, role-play, and practice sessions, as well as assignments. Program evaluation of the Clinical Skills Workshop demonstrated better preparation of key clinical skills prior to starting clinical rotations and highlighted areas for improvement in future iterations. Although this workshop was developed in response to clinical restrictions due to COVID-19, this approach to providing incoming students with basic clinical skills has been a valuable addition to the UAGCGP curriculum.

Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California.

California's vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California's vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

Complex relationship between TAS2 receptor variations, bitterness perception, and alcohol consumption observed in a population of wine consumers.

Our ability to taste bitterness affects our food choices and alcohol consumption. Alleles in the taste 2 receptor member TAS2R38 have been linked to the ability to perceive bitterness in bitter-tasting compounds and in many foods, and people with these bitterness sensitivity alleles have been shown to be less likely to consume alcohol, presumably because of alcohol's bitter taste. In a survey of 519 participants, almost all of whom regularly consumed alcohol, we observed that genetic variants in TAS2R38 were significantly associated with both increased alcohol consumption and the ability to perceive bitterness in several foods and a bitter chemical. In total, we assayed 39 variants in 25 genes that have been implicated in the genetics of taste perception, and no other variants predicted alcohol consumption. Perception of bitterness in broccoli and a preference for black coffee were also positively associated with alcohol consumption. As the consumption of alcohol is a social activity there may be incentive to appreciate its bitter aspects, and increased perception of bitterness could therefore be associated with consumption of some bitter beverages. As this study's respondents were predominantly frequent consumers of alcohol, these findings may be consistent with previous studies that have seen that increased experience in the consumption of wine is associated with an increased perception of PROP bitterness. Further work elucidating the complex relationship between the genetics of bitter perception and alcohol consumption will better describe these connections.

The Relationship between Temperature and Development in Globodera ellingtonae.

A new cyst nematode species, Globodera ellingtonae, was recently described from populations in Oregon and Idaho. This nematode has been shown to reproduce on potato. Because of this nematode's close relationship to the potato cyst nematodes, G. rostochiensis and G. pallida, an understanding of the risk of its potential spread, including prediction of potential geographical distribution, is required. To determine the development of G. ellingtonae under different temperatures, we conducted growth chamber experiments over a range of temperatures (10.0°C to 26.5°C) and tracked length of time to various developmental stages, including adult females bearing the next generation of eggs. Both the time to peak population densities of G. ellingtonae life stages and their duration in roots generally increased with decreasing temperature. Regression of growth rate to second-stage (J2) and third-stage (J3) juveniles on temperature yielded different base temperatures: 6.3°C and 4.4°C for J2 and J3, respectively. Setting a base temperature of 6°C allowed calculation of the degree-days (DD6) over which different life stages occurred. The largest population densities of J2 were found in roots between 50 and 200 DD6. Population densities of J3 peaked between 200 and 300 DD6. Adult males were detected in soil starting at 300 to 400 DD6 and remained detectable for approximately 500 DD6. By 784 to 884 DD6, half of the eggs in adult females contained vermiform juveniles. Given the similarity in temperature ranges for successful development between G. ellingtonae and G. rostochiensis, G. ellingtonae populations likely could survive in the same geographic range in which G. rostochiensis now occurs.

Genetic counseling for personal genomic testing: optimizing client uptake of post-test telephonic counseling services.

The field of genetic counseling faces a broad challenge: many potential clients may not be aware of the value and benefit of genetic counseling services, and therefore may not utilize those services. Navigenics is a personal genomic testing company that provides telephonic genetic counseling services for multifactorial diseases and pharmacogenetics. When first offered in 2008, utilization of the Navigenics genetic counseling service was less than expected. To explore the basis for under-utilization and potential mechanisms for increasing uptake, Navigenics initiated a quality improvement study, in which three different methods of engaging clients in the uptake of genetic counseling services were assessed over the course of 1 year. Outcomes showed significant differences in uptake rates between methodologies (7.5%, 24.6%, and 60.1%), yielding an 8-fold increase in service utilization when post-test telephonic outreach to all clients was performed. Further, utilization spanned all risk levels based on client results, evidence that not only clients with high-risk results were motivated to engage in the genetic counseling service. This research indicates that implementing strategies to educate clients about genetic counseling can positively impact client engagement and utilization of available services.

Personal genomic testing as part of the complete breast cancer risk assessment: a case report.

Patient access and utilization of personal genomic testing is becoming increasingly common. We present a case of a patient's personal genomic screening results leading to early detection of infiltrating breast ductal cell carcinoma via MRI scan. This case exemplifies the successful integration of personal genomic testing into the primary care setting, with the guidance and support of genetic counseling services. We discuss the scientific basis of the patient's genome scan results and risk assessment, and how this informed her decision-making and subsequent screening. We also expound upon the role of personal genomic testing as compared to other screening tests in the complete breast cancer risk assessment.

The role of financial factors in acceptance of clinical BRCA genetic testing.

Many women who are offered BRCA genetic testing by genetics professionals do not have the test, possibly for financial reasons. We explored financial factors implicated in non-uptake of BRCA testing in women who had received genetic counseling in a clinical setting. Specifically, we described financial factors (affordability, health insurance, other) involved with BRCA testing; compared nonfinancial factors (disease, sociodemographic, risk assessment) in women who did not have BRCA testing (nontesters) with women who had the test (testers); showed associations of financial and nonfinancial factors with BRCA testing; and identified predictors of non-uptake of BRCA testing. The sample of 100 women (64 nontesters and 36 testers) completed an anonymous mailed survey on financial factors; 52 of the nontesters answered questions about nonfinancial factors. Testers had significantly better affordability and insurance coverage (p < 0.001), more diagnoses of breast or ovarian cancer (p < 0.05) and higher rates of receiving post-counseling risk estimates (p < 0.05), than nontesters. Non-uptake was 5.5-fold more likely in women that could not afford full or partial payment for the test and was 15.5-fold more likely in women that did not recall receiving risk estimates post-counseling. For many women having risk factors for breast/ovarian cancer, affordability of BRCA testing and insurance coverage for the test remain problematic. Post-counseling reminders of risk estimates may contribute to uptake of testing.