De novo loss-of-function variant in PTDSS1 is associated with developmental delay.

Heterozygous de novo missense pathogenic variants in PTDSS1 that result in gain-of-function of phosphatidylserine synthase 1 are associated with Lenz-Majewski hyperostotic dwarfism (LMHD). We identified the novel heterozygous de novo variant p.(Leu137Phe) in PTDSS1 in a child with mild-to-moderate developmental delay. Skeletal survey revealed no evidence of LMHD in this patient. Functional assessment of the p.Leu137Phe variant was performed by overexpressing the mutant protein into HEK293 cells. Following C14 -serine labeling and TLC analysis of lipids, we observed that the p.(Leu137Phe) variant displayed no catalytic activity compared to the wild-type enzyme. We conclude that p.(Leu137Phe) variant has decreased enzymatic activity and that is likely to be the etiology of the patient's symptoms given the gene's constraint in the population. This is the first report of the clinical phenotype seen in an individual with a heterozygous loss-of-function variant in PTDSS1. This phenotype is distinct from LMHD, which results from gain-of-function pathogenic variants in the same gene. Evaluation of the neurodevelopmental phenotype of additional individuals with loss-of-function variants in PTDSS1 is indicated to determine the spectrum of associated phenotypes.

Cost Utility of Schlemm's Canal Microstent Injection With Cataract Surgery for Open-angle Glaucoma in the US Medicare System.

PRCIS: Hydrus microstent (HMS) implantation at the time of cataract surgery appears to be cost-effective in mild-to-moderate glaucoma. However, long-term follow-up is essential for a full assessment of device performance, safety and cost-effectiveness. PURPOSE: The aim was to assess the societal cost-utility to the US Medicare system of implanting HMS with cataract surgery versus cataract surgery alone in patients with open-angle glaucoma. PATIENTS: Markov model cohort of patients with mild-to-moderate open-angle glaucoma and visually significant cataract. METHODS: Patients received HMS during cataract surgery versus cataract surgery alone, in a deterministic model over a 2-year horizon using TreeAge software. Both arms received additional ocular hypotensive agents to control intraocular pressure. Treatment effect of HMS was measured as mean number of ocular hypotensive medications and intraocular pressure, which directly impacted transition probabilities. Health states included the Hodapp-Parrish-Anderson glaucoma stages (mild, moderate, advanced, blind) and death. One-way sensitivity and probabilistic sensitivity analyses were conducted on device efficacy and longer time horizons. RESULTS: At 2 years, HMS with cataract surgery in mild glaucoma had an incremental cost-utility ratio of USD 38,346.43 per utility gained, compared with cataract surgery alone. Probabilistic sensitivity analysis was cost-effective in 61.4% of iterations for HMS+cataract surgery. The probability of side-effects with eye drops, utility decrement with side-effects, cost of the HMS and real-world efficacy rate had the greatest impact on model outcomes. HMS must be 85.60% as effective as published data to maintain cost-effectiveness at a willingness-to-pay threshold of USD 50,000. The incremental cost-utility ratio of HMS with cataract surgery in moderate glaucoma was USD 42,895.38. CONCLUSIONS: HMS implantation during cataract surgery appears to be cost-effective for patients with mild-to-moderate glaucoma. Nevertheless, more long-term safety and efficacy data are required.

UBA2 variants underlie a recognizable syndrome with variable aplasia cutis congenita and ectrodactyly.

PURPOSE: The human chromosome 19q13.11 deletion syndrome is associated with a variable phenotype that includes aplasia cutis congenita (ACC) and ectrodactyly as specific features. UBA2 (ubiquitin-like modifier-activating enzyme 2) lies adjacent to the minimal deletion overlap region. We aimed to define the UBA2-related phenotypic spectrum in humans and zebrafish due to sequence variants and to establish the mechanism of disease. METHODS: Exome sequencing was used to detect UBA2 sequence variants in 16 subjects in 7 unrelated families. uba2 loss of function was modeled in zebrafish. Effects of human missense variants were assessed in zebrafish rescue experiments. RESULTS: Seven human UBA2 loss-of-function and missense sequence variants were detected. UBA2-phenotypes included ACC, ectrodactyly, neurodevelopmental abnormalities, ectodermal, skeletal, craniofacial, cardiac, renal, and genital anomalies. uba2 was expressed in zebrafish eye, brain, and pectoral fins; uba2-null fish showed deficient growth, microcephaly, microphthalmia, mandibular hypoplasia, and abnormal fins. uba2-mRNAs with human missense variants failed to rescue nullizygous zebrafish phenotypes. CONCLUSION: UBA2 variants cause a recognizable syndrome with a wide phenotypic spectrum. Our data suggest that loss of UBA2 function underlies the human UBA2 monogenic disorder and highlights the importance of SUMOylation in the development of affected tissues.

Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.

The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3- and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.

Alabama Screening and Intervention for Glaucoma and Eye Health Through Telemedicine (AL-SIGHT): Study Design and Methodology.

PRCIS: This paper presents the methods and protocol of a community-based telemedicine program to identify glaucoma and other eye diseases. PURPOSE: To describe the study rationale and design of the Alabama Screening and Intervention for Glaucoma and eye Health through Telemedicine project. METHODS: The study will implement and evaluate a telemedicine-based detection strategy for glaucoma, diabetic retinopathy, and other eye diseases in at-risk patients seen at federally qualified health centers located in rural Alabama. The study will compare the effectiveness of the remote use of structural and functional ocular imaging devices to an in-person examination. Study participants will receive a remote ocular assessment consisting of visual acuity, intraocular pressure, visual field testing, and imaging of the retina and optic nerve with spectral-domain optical coherence tomography, and the data will be reviewed by an ophthalmologist and optometrist. It will also compare the effectiveness of financial incentives along with a validated patient education program versus a validated patient education program alone in improving follow-up adherence. Finally, cost and cost-effectiveness analyses will be performed on the telemedicine program compared with standard in-person care using effectiveness measured in numbers of detected eye disease cases. CONCLUSIONS: The study aims to develop a model eye health system using telemedicine to prevent vision loss and address eye health among underserved and at-risk populations.

A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity.

Although hundreds of genome-wide association studies-implicated loci have been reported for adult obesity-related traits, less is known about the genetics specific for early-onset obesity and with only a few studies conducted in non-European populations to date. Searching for additional genetic variants associated with childhood obesity, we performed a trans-ancestral meta-analysis of 30 studies consisting of up to 13 005 cases (≥95th percentile of body mass index (BMI) achieved 2-18 years old) and 15 599 controls (consistently <50th percentile of BMI) of European, African, North/South American and East Asian ancestry. Suggestive loci were taken forward for replication in a sample of 1888 cases and 4689 controls from seven cohorts of European and North/South American ancestry. In addition to observing 18 previously implicated BMI or obesity loci, for both early and late onset, we uncovered one completely novel locus in this trans-ancestral analysis (nearest gene, METTL15). The variant was nominally associated with only the European subgroup analysis but had a consistent direction of effect in other ethnicities. We then utilized trans-ancestral Bayesian analysis to narrow down the location of the probable causal variant at each genome-wide significant signal. Of all the fine-mapped loci, we were able to narrow down the causative variant at four known loci to fewer than 10 single nucleotide polymorphisms (SNPs) (FAIM2, GNPDA2, MC4R and SEC16B loci). In conclusion, an ethnically diverse setting has enabled us to both identify an additional pediatric obesity locus and further fine-map existing loci.

Genetics of Obesity in Diverse Populations.

PURPOSE OF REVIEW: The prevalence of obesity continues to rise, fueling a global public health crisis characterized by dramatic increases in type 2 diabetes, cardiovascular disease, and many cancers. In the USA, several minority populations, who bear much of the obesity burden (47% in African Americans and Hispanic/Latinos, compared to 38% in European descent groups), are particularly at risk of downstream chronic disease. Compounding these disparities, most genome-wide association studies (GWAS)-including those of obesity-have largely been conducted in populations of European or East Asian ancestry. In fact, analysis of the GWAS Catalog found that while the proportion of participants of non-European or non-Asian descent had risen from 4% in 2009 to 19% in 2016, African-ancestry participants are still just 3% of GWAS, Hispanic/Latinos are < 0.5%, and other ancestries are < 0.3% or not represented at all. This review summarizes recent developments in obesity genomics in US minority populations, with the goal of reducing obesity health disparities and improving public health programs and access to precision medicine. RECENT FINDINGS: GWAS of populations with the highest burden of obesity are essential to narrow candidate variants for functional follow-up, to identify additional ancestry-specific variants that contribute to individual genetic susceptibility, and to advance both public health and precision medicine approaches to obesity. Given the global public health burden posed by obesity and downstream chronic conditions which disproportionately affect non-European populations, GWAS of obesity-related traits in diverse populations is essential to (1) locate causal variants in GWAS-identified regions through fine mapping, (2) identify variants which influence obesity across ancestries through generalization, and (3) discover novel ancestry-specific variants which may be low frequency in European populations but common in other groups. Recent efforts to expand obesity genomic studies to understudied and underserved populations, including AAAGC, PAGE, and HISLA, are working to reduce obesity health disparities, improve public health, and bring the promise of precision medicine to all.

Direct and indirect genetic effects on triglycerides through omics and correlated phenotypes.

Even though there has been great success in identifying lipid-associated single-nucleotide polymorphisms (SNPs), the mechanisms through which the SNPs act on each trait are poorly understood. The emergence of large, complex biological data sets in well-characterized cohort studies offers an opportunity to investigate the genetic effects on trait variability as a way of informing the causal genes and biochemical pathways that are involved in lipoprotein metabolism. However, methods for simultaneously analyzing multiple omics, environmental exposures, and longitudinally measured, correlated phenotypes are lacking. The purpose of our study was to demonstrate the utility of the structural equation modeling (SEM) approach to inform our understanding of the pathways by which genetic variants lead to disease risk. With the SEM method, we examine multiple pathways directly and indirectly through previously identified triglyceride (TG)-associated SNPs, methylation, and high-density lipoprotein (HDL), including sex, age, and smoking behavior, while adding in biologically plausible direct and indirect pathways. We observed significant SNP effects (P < 0.05 and directionally consistent) on TGs at visit 4 (TG4) for five loci, including rs645040 (DOCK7), rs964184 (ZPR1/ZNF259), rs4765127 (ZNF664), rs1121980 (FTO), and rs10401969 (SUGP1). Across these loci, we identify three with strong evidence of an indirect genetic effect on TG4 through HDL, one with evidence of pleiotropic effect on HDL and TG4, and one variant that acts on TG4 indirectly through a nearby methylation site. Such information can be used to prioritize candidate genes in regions of interest, inform mechanisms of action of methylation effects, and highlight possible genes with pleiotropic effects.

Compliance With Primary Open-angle Glaucoma and Primary Open-angle Glaucoma Suspect Preferred Practice Patterns in a Retail-based Eye Clinic.

PURPOSE: To determine the level of adherence to the American Academy of Ophthalmology preferred practice pattern (PPP) guidelines for quality primary open-angle glaucoma (POAG) and POAG suspect (POAGS) care among retail-based optometrists. METHODS: Patients with a diagnosis of POAG or POAGS who participated in a telemedicine pilot project were included. Patients' charts were evaluated for 15 elements of PPP guidelines for glaucoma care. Results were further stratified by number of follow-up visits and diagnosis. RESULTS: Of 360 identified patients, 10 elements were documented in over 98%. Documentation of the remaining 5 components was as follows: dilated fundus examination 91.1%, central corneal thickness (CCT) 88.6%, visual field 78.9%, gonioscopy 47.5%, and target intraocular pressure (IOP) 15.6%. in total, 32.8% of patients were seen once, whereas the remaining 67.2% had multiple visits. In patients with multiple visits, providers were more likely to document systemic history (100.0% vs. 97.5%; P=0.0346), review of systems (100.0% vs. 97.5%; P=0.0346), gonioscopy (60.0% vs. 22.0%; P<0.001), CCT (94.2% vs. 77.1%; P<0.001), visual field (97.5% vs. 40.7%; P<0.001), and target IOP (22.4% vs. 1.7%; P<0.001) compared with single visit patients. In stratifying results by diagnosis, POAG patients more often received visual field testing (92.7% vs. 68.9%; P<0.001) and had an established target IOP (35.1% vs. 1.4%; P<0.001) compared with POAGS patients. CONCLUSIONS: Compliance with PPP guidelines for glaucoma care was very high for most elements but lower for performing dilated fundus examination, CCT, visual field, gonioscopy, and target IOP. This study highlights deficiencies in care likely to hamper the detection of glaucoma progression.

Association Between Immigration History and Inflammatory Marker Profiles Among Older Adult Mexican Americans.

Foreign-born Hispanics have better cardiometabolic health upon arrival in the US than their US-born counterparts, yet this advantage diminishes as duration of residence in the US increases. Underlying mechanisms explaining this paradox have been understudied. Using data from the Sacramento Area Latino Study on Aging (SALSA), this study examined immigration history (immigrant generation and duration of US residence) in relation to biomarkers of inflammation (interleukin-6 (IL-6), soluble forms of type 1 and 2 receptors of tumor necrosis factor-alpha (sTNF-R1 and sTNF-R2), C-reactive protein (CRP), leptin, adiponectin) in a sample of 1,290 predominantly Mexican-origin immigrants. Second and ≥3rd generation immigrants had higher IL-6 and leptin levels than 1st generation immigrants living in the US for less than 15 years (2nd generation percent difference = 45.9; 95% CI: 24.7, 70.7 and 3rd generation percent difference = 41.8; 95% CI: 17.7, 70.4). CRP and sTNF-R1 levels were higher among ≥3rd generation immigrants than 1st generation immigrants with less than 15 years of US residency. Worse inflammatory profiles were observed among Mexican-origin immigrants with longer US immigration histories, independent of health, and behavioral factors. Additional research is warranted to understand the factors that shape trajectories of biological risk across generations of Hispanics.

Reaching the Unreachable: Novel Approaches to Telemedicine Screening of Underserved Populations for Vitreoretinal Disease.

Telemedicine involves electronic communication between a physician in one location and a patient in another location to provide remote medical care. Ophthalmologists are increasingly employing telemedicine, particularly in retinal disease screening and monitoring. Telemedicine has been utilized to decrease barriers to care and yield greater patient satisfaction and lower costs, while maintaining high sensitivity and specificity. This review discusses common patient barriers to eye care, innovative approaches to retinal disease screening and monitoring using telemedicine, and eye care policy initiatives needed to enact large-scale telemedicine eye disease screening programs.

Genome-wide association of trajectories of systolic blood pressure change.

BACKGROUND: There is great interindividual variation in systolic blood pressure (SBP) as a result of the influences of several factors, including sex, ancestry, smoking status, medication use, and, especially, age. The majority of genetic studies have examined SBP measured cross-sectionally; however, SBP changes over time, and not necessarily in a linear fashion. Therefore, this study conducted a genome-wide association (GWA) study of SBP change trajectories using data available through the Genetic Analysis Workshop 19 (GAW19) of 959 individuals from 20 extended Mexican American families from the San Antonio Family Studies with up to 4 measures of SBP. We performed structural equation modeling (SEM) while taking into account potential genetic effects to identify how, if at all, to include covariates in estimating the SBP change trajectories using a mixture model based latent class growth modeling (LCGM) approach for use in the GWA analyses. RESULTS: The semiparametric LCGM approach identified 5 trajectory classes that captured SBP changes across age. Each LCGM identified trajectory group was ranked based on the average number of cumulative years as hypertensive. Using a pairwise comparison of these classes the heritability estimates range from 12 to 94 % (SE = 17 to 40 %). CONCLUSION: These identified trajectories are significantly heritable, and we identified a total of 8 promising loci that influence one's trajectory in SBP change across age. Our results demonstrate the potential utility of capitalizing on extant genetic data and longitudinal SBP assessments available through GAW19 to explore novel analytical methods with promising results.

Von Hippel-Lindau Disease: Genetics and Role of Genetic Counseling in a Multiple Neoplasia Syndrome.

Von Hippel-Lindau disease (VHL) is one of the most common inherited neoplasia syndromes and is characterized by highly vascular tumors of the eyes, brain, and spine, as well as benign and malignant tumors and/or cysts of the kidneys, adrenal medullae and sympathetic paraganglia, endolymphatic sac, epididymis, and broad ligament. Since the discovery of the VHL gene in 1993, more than 900 families with VHL have been identified and examined. Genetic testing for VHL is widely available and will detect a disease-causing mutation in rate 95% to 100% of individuals who have a clinical diagnosis of VHL, making it the standard of care for diagnosis of VHL. Furthermore, genetic testing for VHL is indicated in some individuals with seemingly sporadic VHL-related tumor types, as ≤ 10% of pheochromocytoma or early-onset renal cell carcinoma and ≤ 40% of CNS hemangioblastoma harbor germline VHL mutations without a family history or additional features of VHL disease. The majority of VHL mutations are private, but there are also well-characterized founder mutations. VHL is a complex, multiorgan disease that spans the breadth of oncology subspecialties, and, as such, providers in these subspecialties should be aware of when to consider a diagnosis of VHL, when to refer a patient to a genetics specialist for consideration of gene testing, and, perhaps most importantly, how to communicate this sensitive information in an age-appropriate manner to at-risk families. This review will provide state-of-the-art information regarding the genetics of VHL and will serve as a key reference for nongenetics professionals who encounter patients with VHL.

A Review of Fanconi Anemia for the Practicing Pediatrician.

Early recognition of a patient who might have Fancomi anemia by the general pediatrician and referral to a tertiary care center with a dedicated cancer risk program is critical for early diagnosis. Genetic testing and close multidisciplinary surveillance is required for patients with this syndrome and their families because of its multisystem involvement and propensity for early-onset bone marrow failure and leukemic transformation. This article reviews the clinical symptoms and signs, radiologic findings, and screening guidelines of FA for the general pediatrician.

Integrated genomic analysis suggests MLL3 is a novel candidate susceptibility gene for familial nasopharyngeal carcinoma.

BACKGROUND: Little is known about genetic factors associated with nasopharyngeal carcinoma (NPC). To gain insight into NPC etiology, we performed whole exome sequencing on germline and tumor DNA from three closely related family members with NPC. METHODS: The family was ascertained through the Pediatric Familial Cancer Clinic at The University of Chicago (Chicago, IL). The diagnosis of NPC was confirmed pathologically for each individual. For each sample sequenced, 97.3% of the exome was covered at 5×, with an average depth of 44×. Candidate germline and somatic variants associated with NPC were identified and prioritized using a custom pipeline. RESULTS: We discovered 72 rare deleterious germline variants in 56 genes shared by all three individuals. Of these, only three are in previously identified NPC-associated genes, all of which are located within MLL3, a gene known to be somatically altered in NPC. One variant introduces an early stop codon in MLL3, which predicts complete loss-of-function. Tumor DNA analysis revealed somatic mutations and Epstein-Barr virus (EBV) integration events; none, however, were shared among all three individuals. CONCLUSIONS: These data suggest that inherited mutations in MLL3 may have predisposed these three individuals from a single family to develop NPC, and may cooperate with individually acquired somatic mutations or EBV integration events in NPC etiology. IMPACT: Our finding is the first instance of a plausible candidate high penetrance inherited mutation predisposing to NPC.

Establishing a translational genomics infrastructure in pediatric cancer: the GREAT KIDS experience.

We have recently established a biobanking and sequencing pipeline at the University of Chicago dubbed Genomics for Risk Evaluation and Anticancer Therapy in Kids. We plan to intersect family and personal history of cancer and other diseases with multidimensional genomic profiling in order to: understand how genetics may have contributed to the development of cancer for each child, and investigate the spectrum of genomic alterations within a tumor spatially (e.g., primary site vs distant metastasis) and over time (e.g., diagnosis vs relapse). This review highlights some of the practical considerations involved in creating such a program including the capacity to use our platform for multi-institutional collaborations.

Genetic risk factors for BMI and obesity in an ethnically diverse population: results from the population architecture using genomics and epidemiology (PAGE) study.

OBJECTIVE: Several genome-wide association studies (GWAS) have demonstrated that common genetic variants contribute to obesity. However, studies of this complex trait have focused on ancestrally European populations, despite the high prevalence of obesity in some minority groups. DESIGN AND METHODS: As part of the "Population Architecture using Genomics and Epidemiology (PAGE)" Consortium, we investigated the association between 13 GWAS-identified single-nucleotide polymorphisms (SNPs) and BMI and obesity in 69,775 subjects, including 6,149 American Indians, 15,415 African-Americans, 2,438 East Asians, 7,346 Hispanics, 604 Pacific Islanders, and 37,823 European Americans. For the BMI-increasing allele of each SNP, we calculated ß coefficients using linear regression (for BMI) and risk estimates using logistic regression (for obesity defined as BMI ≥ 30) followed by fixed-effects meta-analysis to combine results across PAGE sites. Analyses stratified by racial/ethnic group assumed an additive genetic model and were adjusted for age, sex, and current smoking. We defined "replicating SNPs" (in European Americans) and "generalizing SNPs" (in other racial/ethnic groups) as those associated with an allele frequency-specific increase in BMI. RESULTS: By this definition, we replicated 9/13 SNP associations (5 out of 8 loci) in European Americans. We also generalized 8/13 SNP associations (5/8 loci) in East Asians, 7/13 (5/8 loci) in African Americans, 6/13 (4/8 loci) in Hispanics, 5/8 in Pacific Islanders (5/8 loci), and 5/9 (4/8 loci) in American Indians. CONCLUSION: Linkage disequilibrium patterns suggest that tagSNPs selected for European Americans may not adequately tag causal variants in other ancestry groups. Accordingly, fine-mapping in large samples is needed to comprehensively explore these loci in diverse populations.