Uncertainty in Genomics Impacts Precision Medicine.

As exacting as genetic and genomic testing have become, health professionals continue to encounter uncertainty in their applications to medical practice. As examining the human genome at more refined levels increases, so is the likelihood of encountering uncertainty about the meaning of the information. The history of this concept informs how we might confront and deal with uncertainty, and what the future might hold. Precision medicine holds great promise for establishing more accurate diagnoses, directing specific therapy to patients who will most benefit from it, and avoiding treatments in patients who are most likely to suffer adverse consequences, or at best not benefit. But its application depends importantly on the proper interpretation of a person's genotype.

Microlearning: Evidence-based education that is effective for busy professionals and short attention spans.

Microlearning uses short educational interventions to provide learners with the necessary knowledge and skills to perform specific tasks or solve immediate problems. This approach is increasingly used across digital platforms to engage learners and foster quick comprehension. Microlearning can be used in clinical genetics education to deliver a comprehensive educational intervention that is segmented into smaller discrete but complimentary components. This report discusses one group's approach to using microlearning in clinician education and provides tips that can be applied to other educational efforts. High-quality genetics education has the potential to be disseminated across multiple delivery methods and to multiple audiences, thereby increasing its impact and reach.

A team-based approach to cardiogenomic education.

While many genetic professionals are involved in the education of lay and professional audiences, most do not have formal training in education theory and program design. Partnerships with adult education experts can provide additional resources and improve the level of instruction, thereby increasing the impact of an educational intervention. This report discusses the experience of a multidisciplinary team of educators, clinicians, and researchers partnering to develop evidence-based education for cardiology practitioners. It includes practical advice for how clinicians and educators can develop more effective education through collaboration, needs assessment, instructional design, and iterative content development.

Genomic Epidemiology of Salmonella enterica Circulating in Surface Waters Used in Agriculture and Aquaculture in Central Mexico.

Salmonella enterica can survive in surface waters (SuWa), and the role of nonhost environments in its transmission has acquired increasing relevance. In this study, we conducted comparative genomic analyses of 172 S. enterica isolates collected from SuWa across 3 months in six states of central Mexico during 2019. S. enterica transmission dynamics were assessed using 87 experimental and 112 public isolates from Mexico collected during 2002 through 2019. We also studied genetic relatedness between SuWa isolates and human clinical strains collected in North America during 2005 through 2020. Among experimental isolates, we identified 41 S. enterica serovars and 56 multilocus sequence types (STs). Predominant serovars were Senftenberg (n = 13), Meleagridis, Agona, and Newport (n = 12 each), Give (n = 10), Anatum (n = 8), Adelaide (n = 7), and Infantis, Mbandaka, Ohio, and Typhimurium (n = 6 each). We observed a high genetic diversity in the sample under study, as well as clonal dissemination of strains across distant regions. Some of these strains are epidemiologically important (ST14, ST45, ST118, ST132, ST198, and ST213) and were genotypically close to those involved in clinical cases in North America. Transmission network analysis suggests that SuWa are a relevant source of S. enterica (0.7 source/hub ratio) and contribute to its dissemination as isolates from varied sources and clinical cases have SuWa isolates as common ancestors. Overall, the study shows that SuWa act as reservoirs of various S. enterica serovars of public health significance. Further research is needed to better understand the mechanisms involved in SuWa contamination by S. enterica, as well as to develop interventions to contain its dissemination in food production settings. IMPORTANCE Surface waters are heavily used in food production worldwide. Several human pathogens can survive in these waters for long periods and disseminate to food production environments, contaminating our food supply. One of these pathogens is Salmonella enterica, a leading cause of foodborne infections, hospitalizations, and deaths in many countries. This research demonstrates the role of surface waters as a vehicle for the transmission of Salmonella along food production chains. It also shows that some strains circulating in surface waters are very similar to those implicated in human infections and harbor genes that confer resistance to multiple antibiotics, posing a risk to public health. This study contributes to expand our current knowledge on the ecology and epidemiology of Salmonella in surface waters.

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus.

Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 and 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction includes the two recently diverged species, Sebastes mystinus and S. diaconus, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that S. melanops and S. flavidus were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of Sebastosomus are further supported by morphological, biological, and ecological justifications.

Digital vascular lesions detected by transillumination.

Abnormalities of the capillaries of the digits in hereditary hemorrhagic telangiectasia can be detected by shining through a narrow beam of light through the dorsal side and visualizing the vasculature on the palmar side, a procedure termed transillumination. This study was performed to determine if this method can detect digital vascular abnormalities in aortopathies and arteriopathies. Transillumination was performed in patients with Marfan syndrome (MFS), thoracic aortic aneurysm and dissection (TAAD), vascular Ehlers-Danlos syndrome (vEDS), bicuspid aortic valve with aortopathy, and arteriopathies without aortopathy. Subjects with no known vascular disorders were controls. Digital vascular abnormalities were present in some patients with all of the disorders and were especially frequent in MFS, TAAD, and vEDS. All patients had significantly more digital vascular abnormalities than control subjects. Transillumination can detect vascular abnormalities in digits of patients with a variety of conditions with aortopathy or arteriopathy.

Arachnodactyly represented in art.

Arachnodactyly, a term used since 1902 to describe abnormally long (spider-like) fingers, is a pathologic feature of several heritable conditions, notably the Marfan syndrome and congenital contractural arachnodactyly. A number of prominent artists, dating from the 16th to the 20th centuries, have depicted subjects with unusually long fingers, sometime associated with elongation of the body, neck and head. El Greco incorporated this style in many paintings. Little evidence supports any subject in any of these paintings as having a congenital deformity.

A multi-center study on safety and efficacy of immune checkpoint inhibitors in cancer patients with kidney transplant.

Immune checkpoint inhibitors (ICIs) are widely used for various malignancies. However, their safety and efficacy in patients with a kidney transplant have not been defined. To delineate this, we conducted a multicenter retrospective study of 69 patients with a kidney transplant receiving ICIs between January 2010 and May 2020. For safety, we assessed the incidence, timing, and risk factors of acute graft rejection. For efficacy, objective response rate and overall survival were assessed in cutaneous squamous cell carcinoma and melanoma, the most common cancers in our cohort, and compared with stage-matched 23 patients with squamous cell carcinoma and 14 with melanoma with a kidney transplant not receiving ICIs. Following ICI treatment, 29 out of 69 (42%) patients developed acute rejection, 19 of whom lost their allograft, compared with an acute rejection rate of 5.4% in the non-ICI cohort. Median time from ICI initiation to rejection was 24 days. Factors associated with a lower risk of rejection were mTOR inhibitor use (odds ratio 0.26; 95% confidence interval, 0.09-0.72) and triple-agent immunosuppression (0.67, 0.48-0.92). The objective response ratio was 36.4% and 40% in the squamous cell carcinoma and melanoma subgroups, respectively. In the squamous cell carcinoma subgroup, overall survival was significantly longer in patients treated with ICIs (median overall survival 19.8 months vs. 10.6 months), whereas in the melanoma subgroup, overall survival did not differ between groups. Thus, ICIs were associated with a high risk of rejection in patients with kidney transplants but may lead to improved cancer outcomes. Prospective studies are needed to determine optimal immunosuppression strategies to improve patient outcomes.

Expanding the phenotypic spectrum of Mendelian connective tissue disorders to include prominent kidney phenotypes.

Heritable connective tissue disorders are a group of diseases, each rare, characterized by various combinations of skin, joint, musculoskeletal, organ, and vascular involvement. Although kidney abnormalities have been reported in some connective tissue disorders, they are rarely a presenting feature. Here we present three patients with prominent kidney phenotypes who were found by whole exome sequencing to have variants in established connective tissue genes associated with Loeys-Dietz syndrome and congenital contractural arachnodactyly. These cases highlight the importance of considering connective tissue disease in children presenting with structural kidney disease and also serves to expand the phenotype of Loeys-Dietz syndrome and possibly congenital contractural arachnodactyly to include cystic kidney disease and cystic kidney dysplasia, respectively.

Phase Separation and Histone Epigenetics in Genome Regulation.

Liquid-liquid phase separation is increasingly recognized as a phenomenon that affects cell behavior. For example, phase separation of transcription factors and coactivators has been shown to drive efficient transcription. For many years, phase separation of intracellular components has been observed; however, only recently have researchers been able to garner functional significance from such events. Inspired from recent literature that describes phase separation of chromatin in a histone-dependent manner, we review the role and effect of phase separation and histone epigenetics in regulating the genome and discuss how these phenomena can be leveraged to control cell behavior.

Gridlock and beltways: the genetic context of urban invasions.

The rapid expansion of urban land across the globe presents new and numerous opportunities for invasive species to spread and flourish. Ecologists historically rejected urban ecosystems as important environments for ecology and evolution research but are beginning to recognize the importance of these systems in shaping the biology of invasion. Urbanization can aid the introduction, establishment, and spread of invaders, and these processes have substantial consequences on native species and ecosystems. Therefore, it is valuable to understand how urban areas influence populations at all stages in the invasion process. Population genetic tools are essential to explore the driving forces of invasive species dispersal, connectivity, and adaptation within cities. In this review, we synthesize current research about the influence of urban landscapes on invasion genetics dynamics. We conclude that urban areas are not only points of entry for many invasive species, they also facilitate population establishment, are pools for genetic diversity, and provide corridors for further spread both within and out of cities. We recommend the continued use of genetic studies to inform invasive species management and to understand the underlying ecological and evolutionary processes governing successful invasion.

Rapid data-driven model reduction of nonlinear dynamical systems including chemical reaction networks using ℓ1-regularization.

Large-scale nonlinear dynamical systems, such as models of atmospheric hydrodynamics, chemical reaction networks, and electronic circuits, often involve thousands or more interacting components. In order to identify key components in the complex dynamical system as well as to accelerate simulations, model reduction is often desirable. In this work, we develop a new data-driven method utilizing ℓ1-regularization for model reduction of nonlinear dynamical systems, which involves minimal parameterization and has polynomial-time complexity, allowing it to easily handle large-scale systems with as many as thousands of components in a matter of minutes. A primary objective of our model reduction method is interpretability, that is to identify key components of the dynamical system that contribute to behaviors of interest, rather than just finding an efficient projection of the dynamical system onto lower dimensions. Our method produces a family of reduced models that exhibit a trade-off between model complexity and estimation error. We find empirically that our method chooses reduced models with good extrapolation properties, an important consideration in practical applications. The reduction and extrapolation performance of our method are illustrated by applications to the Lorenz model and chemical reaction rate equations, where performance is found to be competitive with or better than state-of-the-art approaches.

Molecular Mechanisms of Macular Degeneration Associated with the Complement Factor H Y402H Mutation.

A single nucleotide polymorphism, tyrosine at position 402 to histidine (Y402H), within the gene encoding complement factor H (FH) predisposes individuals to acquiring age-related macular degeneration (AMD) after aging. This polymorphism occurs in short consensus repeat (SCR) 7 of FH and results in decreased binding affinity of SCR6-8 for heparin. As FH is responsible for regulating the complement system, decreased affinity for heparin results in decreased regulation on surfaces of self. To understand the involvement of the Y402H polymorphism in AMD, we leverage methods from bioinformatics and computational biophysics to quantify structural and dynamical differences between SCR7 isoforms that contribute to decreased pattern recognition in SCR7H402. Our data from molecular and Brownian dynamics simulations suggest a revised mechanism for decreased heparin binding. In this model, transient contacts not observed in structures for SCR7 are predicted to occur in molecular dynamics simulations between coevolved residues Y402 and I412, stabilizing SCR7Y402 in a conformation that promotes association with heparin. H402 in the risk isoform is less likely to form a contact with I412 and samples a larger conformational space than Y402. We observe energy minima for sidechains of Y402 and R404 from SCR7Y402 that are predicted to associate with heparin at a rate constant faster than energy minima for sidechains of H402 and R404 from SCR7H402. As both carbohydrate density and degree of sulfation decrease with age in Bruch's membrane of the macula, the decreased heparin recognition of SCR7H402 may contribute to the pathogenesis of AMD.

Marfan syndrome: improved clinical history results in expanded natural history.

Life expectancy for a person with Marfan syndrome has essentially doubled over the past four decades. During this period, the clinical histories of the organs managed routinely have improved, and will continue to be. Prominent examples are the eyes, the heart and aorta, and some features of the skeletal system. Meanwhile, the natural histories of organ systems that have not been subjected to treatment need to be described. This is particularly important as due to the improved life span many symptoms and organ systems are only recently being recognized as being intrinsic to Marfan syndrome. Examples are the distal aorta and peripheral arteries, ventricular function, the central nervous system, sleep apnea, and adiposity. As a result, each person with Marfan syndrome will need to be evaluated and followed by more specialists than previously. Moreover, the coordinator of diagnostic testing and clinical referral must be aware of the expanded phenotype as people with Marfan syndrome age and the importance of life-long management of classical and novel features. The benefits of increased longevity and its consequences need to be addressed by investigators, health-care providers, and patients alike.

Health-Related Quality of Life in Children and Young Adults with Marfan Syndrome.

OBJECTIVE: To assess health-related quality of life (HRQOL) in a large multicenter cohort of children and young adults with Marfan syndrome participating in the Pediatric Heart Network Marfan Trial. STUDY DESIGN: The Pediatric Quality of Life Inventory (PedsQL) 4.0 Generic Core Scales were administered to 321 subjects with Marfan syndrome (5-25 years). PedsQL scores were compared with healthy population norms. The impact of treatment arm (atenolol vs losartan), severity of clinical features, and number of patient-reported symptoms on HRQOL was assessed by general linear models. RESULTS: Mean PedsQL scores in children (5-18 years) with Marfan syndrome were lower than healthy population norms for physical (P ≤ .003) and psychosocial (P < .001) domains; mean psychosocial scores for adults (19-25 years) were greater than healthy norms (P < .001). HRQOL across multiple domains correlated inversely with frequency of patient-reported symptoms (r = 0.30-0.38, P < .0001). Those <18 years of age with neurodevelopmental disorders (mainly learning disability, attention-deficit/hyperactivity disorder) had lower mean PedsQL scores (5.5-7.4 lower, P < .04). A multivariable model found age, sex, patient-reported symptoms, and neurodevelopmental disorder to be independent predictors of HRQOL. There were no differences in HRQOL scores by treatment arm, aortic root z score, number of skeletal features, or presence of ectopia lentis. CONCLUSIONS: Children and adolescents with Marfan syndrome were at high risk for impaired HRQOL. Patient-reported symptoms and neurodevelopmental disorder, but not treatment arm or severity of Marfan syndrome-related physical findings, were associated with lower HRQOL.

Multi-level Determinants of Clinic Attendance and Antiretroviral Treatment Adherence Among Fishermen Living with HIV/AIDS in Communities on Lake Victoria, Uganda.

This cross-sectional study assessed determinants of HIV clinic appointment attendance and antiretroviral treatment (ART) adherence among 300 male fisherfolk on ART in Wakiso District, Uganda. Multi-level factors associated with missed HIV clinic visits included those at the individual (age, AOR = 0.98, 95% CI 0.97-0.99), interpersonal (being single/separated from partner, AOR: 1.25, 95% CI 1.01-1.54), normative (anticipated HIV stigma, AOR: 1.55, 95% CI 1.05-2.29) and physical/built environment-level (travel time to the HIV clinic, AOR: 1.11, 95% CI 1.02-1.20; structural-barriers to ART adherence, AOR: 1.27, 95% CI 1.04-1.56; accessing care on a landing site vs. an island, AOR: 1.35, 95% CI 1.08-1.67). Factors associated with ART non-adherence included those at the individual (age, ß: - 0.01, η2 = 0.03; monthly income, ß: - 0.01, η2 = 0.02) and normative levels (anticipated HIV stigma, ß: 0.10, η2 = 0.02; enacted HIV stigma, ß: 0.11, η2 = 0.02). Differentiated models of HIV care that integrate stigma reduction and social support, and reduce the number of clinic visits needed, should be explored in this setting to reduce multi-level barriers to accessing HIV care and ART adherence.

Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia.

INTRODUCTION: Hereditary haemorrhagic telangiectasia (HHT) is a genetically heterogeneous disorder caused by mutations in the genes ENG, ACVRL1, and SMAD4. Yet the genetic cause remains unknown for some families even after exhaustive exome analysis. We hypothesised that non-coding regions of the known HHT genes may harbour variants that disrupt splicing in these cases. METHODS: DNA from 35 individuals with clinical findings of HHT and 2 healthy controls from 13 families underwent whole genome sequencing. Additionally, 87 unrelated cases suspected to have HHT were evaluated using a custom designed next-generation sequencing panel to capture the coding and non-coding regions of ENG, ACVRL1 and SMAD4. Individuals from both groups had tested negative previously for a mutation in the coding region of known HHT genes. Samples were sequenced on a HiSeq2500 instrument and data were analysed to identify novel and rare variants. RESULTS: Eight cases had a novel non-coding ACVRL1 variant that disrupted splicing. One family had an ACVRL1intron 9:chromosome 3 translocation, the first reported case of a translocation causing HHT. The other seven cases had a variant located within a ~300 bp CT-rich 'hotspot' region of ACVRL1intron 9 that disrupted splicing. CONCLUSIONS: Despite the difficulty of interpreting deep intronic variants, our study highlights the importance of non-coding regions in the disease mechanism of HHT, particularly the CT-rich hotspot region of ACVRL1intron 9. The addition of this region to HHT molecular diagnostic testing algorithms will improve clinical sensitivity.

Germline Loss-of-Function Mutations in EPHB4 Cause a Second Form of Capillary Malformation-Arteriovenous Malformation (CM-AVM2) Deregulating RAS-MAPK Signaling.

BACKGROUND: Most arteriovenous malformations (AVMs) are localized and occur sporadically. However, they also can be multifocal in autosomal-dominant disorders, such as hereditary hemorrhagic telangiectasia and capillary malformation (CM)-AVM. Previously, we identified RASA1 mutations in 50% of patients with CM-AVM. Herein we studied non-RASA1 patients to further elucidate the pathogenicity of CMs and AVMs. METHODS: We conducted a genome-wide linkage study on a CM-AVM family. Whole-exome sequencing was also performed on 9 unrelated CM-AVM families. We identified a candidate gene and screened it in a large series of patients. The influence of several missense variants on protein function was also studied in vitro. RESULTS: We found evidence for linkage in 2 loci. Whole-exome sequencing data unraveled 4 distinct damaging variants in EPHB4 in 5 families that cosegregated with CM-AVM. Overall, screening of EPHB4 detected 47 distinct mutations in 54 index patients: 27 led to a premature stop codon or splice-site alteration, suggesting loss of function. The other 20 are nonsynonymous variants that result in amino acid substitutions. In vitro expression of several mutations confirmed loss of function of EPHB4. The clinical features included multifocal CMs, telangiectasias, and AVMs. CONCLUSIONS: We found EPHB4 mutations in patients with multifocal CMs associated with AVMs. The phenotype, CM-AVM2, mimics RASA1-related CM-AVM1 and also hereditary hemorrhagic telangiectasia. RASA1-encoded p120RASGAP is a direct effector of EPHB4. Our data highlight the pathogenetic importance of this interaction and indicts EPHB4-RAS-ERK signaling pathway as a major cause for AVMs.

Covered Stents in the Treatment of Pulmonary Arteriovenous Malformations.

Seven patients with pulmonary arteriovenous malformations (PAVMs) not well suited to coil and/or plug treatment were treated with expanded polytetrafluoroethylene-covered stents. Mean diameter of treated arteries was 6 mm. Complete technical success was achieved in 7 of 8 PAVMs, 6 using only covered stents and 1 using both a covered and a bare stent owing to endoleak. In 1 patient, the parent vessel was sacrificed after identification of additional feeding vessels following stent graft placement. In 6 patients with median imaging follow-up of 8 months (range, 1-121 months), all stent grafts were patent, and all treated PAVMs were completely excluded without persistence.