Analysis of incidental findings in Qatar genome participants reveals novel functional variants in LMNA and DSP.

In order to report clinically actionable incidental findings in genetic testing, the American College of Medical Genetics and Genomics (ACMG) recommended the evaluation of variants in 59 genes associated with highly penetrant mutations. However, there is a lack of epidemiological data on medically actionable rare variants in these genes in Arab populations. We used whole genome sequencing data from 6045 participants from the Qatar Genome Programme and integrated it with phenotypic data collected by the Qatar Biobank. We identified novel putative pathogenic variants in the 59 ACMG genes by filtering previously unrecorded variants based on computational prediction of pathogenicity, variant rarity and segregation evidence. We assessed the phenotypic associations of candidate variants in genes linked to cardiovascular diseases. Finally, we used a zebrafish knockdown and synthetic human mRNA co-injection assay to functionally characterize two of these novel variants. We assessed the zebrafish cardiac function in terms of heart rate, rhythm and hemodynamics, as well as the heart structure. We identified 52 492 novel variants, which have not been reported in global and disease-specific databases. A total of 74 novel variants were selected with potentially pathogenic effect. We prioritized two novel cardiovascular variants, DSP c.1841A > G (p.Asp614Gly) and LMNA c.326 T > G (p.Val109Gly) for functional characterization. Our results showed that both variants resulted in abnormal zebrafish heart rate, rhythm and structure. This study highlights medically actionable variants that are specific to the Middle Eastern Qatari population.

Functional Characterization of Novel MC4R Variants Identified in Two Unrelated Patients with Morbid Obesity in Qatar.

The leptin-melanocortin pathway is pivotal in appetite and energy homeostasis. Pathogenic variants in genes involved in this pathway lead to severe early-onset monogenic obesity (MO). The MC4R gene plays a central role in leptin-melanocortin signaling, and heterozygous variants in this gene are the most common cause of MO. A targeted gene panel consisting of 52 obesity-related genes was used to screen for variants associated with obesity. Variants were analyzed and filtered to identify potential disease-causing activity and validated using Sanger sequencing. We identified two novel heterozygous variants, c.253A>G p.Ser85Gly and c.802T>C p.Tyr268His, in the MC4R gene in two unrelated patients with morbid obesity and evaluated the functional impact of these variants. The impact of the variants on the MC4R gene was assessed using in silico prediction tools and molecular dynamics simulation. To further study the pathogenicity of the identified variants, GT1-7 cells were transfected with plasmid DNA encoding either wild-type or mutant MC4R variants. The effects of allelic variations in the MC4R gene on cAMP synthesis, MC4R protein level, and activation of PKA, ERB, and CREB signaling pathways in both stimulated and unstimulated ɑ-MSH paradigms were determined for their functional implications. In silico analysis suggested that the variants destabilized the MC4R structure and affected the overall dynamics of the MC4R protein, possibly leading to intracellular receptor retention. In vitro analysis of the functional impact of these variants showed a significant reduction in cell surface receptor expression and impaired extracellular ligand binding activity, leading to reduced cAMP production. Our analysis shows that the variants do not affect total protein expression; however, they are predicted to affect the post-translational localization of the MC4R protein to the cell surface and impair downstream signaling cascades such as PKA, ERK, and CREB signaling pathways. This finding might help our patients to benefit from the novel therapeutic advances for monogenic forms of obesity.

Frequency and management of medically actionable incidental findings from genome and exome sequencing data: a systematic review.

The application of whole genome/exome sequencing technologies in clinical genetics and research has resulted in the discovery of incidental findings unrelated to the primary purpose of genetic testing. The American College of Medical Genetics and Genomics published guidelines for reporting pathogenic and likely pathogenic variants that are deemed to be medically actionable, which allowed us to learn about the epidemiology of incidental findings in different populations. However, consensus guidelines for variant reporting and classification are still lacking. We conducted a systematic literature review of incidental findings in whole genome/exome sequencing studies to obtain a comprehensive understanding of variable reporting and classification methods for variants that are deemed to be medically actionable across different populations. The review highlights the elements that demand further consideration or adjustment.

High Systolic Blood Pressure, Anterior Segment Changes and Visual Impairment Independently Predict Sickle Cell Retinopathy.

Sickle cell disease is often complicated by retinopathy, which can be proliferative or non proliferative. Proliferative sickle cell retinopathy potentially leads to blindness. There is a paucity of data on sickle cell disease-related retinopathy from Africa, where the disease is most prevalent. We aimed to determine the clinical, ophthalmic, and laboratory predictors of sickle cell retinopathy in an African population. We conducted a cross-sectional study of 262 participants, aged 13 years and above, with sickle cell disease. Demographic and clinical data were collected using a structured questionnaire and standard physical examinations. Vitreo-retinal specialists performed eye examinations on all the participants. Hematological and biochemical assessments were conducted using standard methods. A multivariate stepwise forward logistic regression was performed to determine the predictors of retinopathy. The median age of the participants was 20 years (interquartile range: 17-25 years). Most of the participants had a homozygous Hb S (HBB: c.20A>T) genotype (96.9%), with 3.1% who carried a Hb S/Hb C (HBB: c.19G>A) genotype. The prevalence of non proliferative sickle cell retinopathy was 24.4%. Only 1.9% had proliferative sickle cell retinopathy (PSCR). Elevated systolic blood pressure (BP) [odds ratio (OR): 6.85, 95% confidence interval (95% CI): 1.05-44.45, p = 0.059], moderate visual impairment (OR: 5.2, 95% CI: 1.39-19.63, p = 0.015), and anterior segment changes (OR: 2.21, 95% CI: 1.19-4.13, p = 0.012) were independently predictive of retinopathy. This study provides new insight into predictors of retinopathy in sickle cell disease, with implications on early screening and prevention.

Maternal Instruction About Jaundice and the Incidence of Acute Bilirubin Encephalopathy in Nigeria.

OBJECTIVE: To evaluate whether teaching mothers about neonatal jaundice will decrease the incidence of acute bilirubin encephalopathy among infants admitted for jaundice. STUDY DESIGN: This was a multicenter, before-after and cross-sectional study. Baseline incidences of encephalopathy were obtained at 4 collaborating medical centers between January 2014 and May 2015 (Phase 1). Structured jaundice instruction was then offered (May to November 2015; Phase 2) in antenatal clinics and postpartum. Descriptive statistics and logistic regression models compared 3 groups: 843 Phase 1 controls, 338 Phase 2 infants whose mothers received both antenatal and postnatal instruction (group A), and 215 Phase 2 infants whose mothers received no instruction (group B) either because the program was not offered to them or by choice. RESULTS: Acute bilirubin encephalopathy occurred in 147 of 843 (17%) Phase 1 and 85 of 659 (13%) Phase 2 admissions, which included 63 of 215 (29%) group B and 5 of 338 (1.5%) group A infants. OR for having acute bilirubin encephalopathy, comparing group A and group B infants adjusted for confounding risk factors, was 0.12 (95% CI 0.03-0.60). Delayed care-seeking (defined as an admission total bilirubin ≥18 mg/dL at age ≥48 hours) was the strongest single predictor of acute bilirubin encephalopathy (OR 11.4; 6.6-19.5). Instruction decreased delay from 49% to 17%. Other major risk factors were home births (OR 2.67; 1.69-4.22) and hemolytic disease (hematocrit ≤35% plus bilirubin ≥20 mg/dL) (OR 3.03; 1.77-5.18). The greater rate of acute bilirubin encephalopathy with home vs hospital birth disappeared if mothers received jaundice instruction. CONCLUSIONS: Providing information about jaundice to mothers was associated with a reduction in the incidence of bilirubin encephalopathy per hospital admission.

Selenium supplementation in patients with peripartum cardiomyopathy: a proof-of-concept trial.

BACKGROUND: We studied the efficacy and safety of selenium supplementation in patients who had peripartum cardiomyopathy (PPCM) and selenium deficiency. METHODS: We randomly assigned 100 PPCM patients with left ventricular ejection fraction (LVEF) < 45% and selenium deficiency (< 70 µg/L) to receive either oral Selenium (L-selenomethionine) 200 µg/day for 3 months or nothing, in addition to recommended therapy, in an open-label randomised trial. The primary outcome was a composite of persistence of heart failure (HF) symptoms, unrecovered LV systolic function (LVEF < 55%) or death from any cause. RESULTS: Over a median of 19 months, the primary outcome occurred in 36 of 46 patients (78.3%) in the selenium group and in 43 of 54 patients (79.6%) in the control group (hazard ratio [HR] 0.69; 95% confidence interval [CI] 0.43-1.09; p = 0.113). Persistence of HF symptoms occurred in 18 patients (39.1%) in the selenium group and in 37 patients (68.5%) in the control group (HR 0.53; 95% CI 0.30-0.93; p = 0.006). LVEF < 55% occurred in 33 patients (71.7%) in the selenium group and in 38 patients (70.4%) in the control group (HR 0.91; 95% CI 0.57-1.45; p = 0.944). Death from any cause occurred in 3 patients (6.5%) in the selenium group and in 9 patients (16.7%) in the control group (HR 0.37; 95% CI 0.10-1.37; p = 0.137). CONCLUSIONS: In this study, selenium supplementation did not reduce the risk of the primary outcome, but it significantly reduced HF symptoms, and there was a trend towards a reduction of all-cause mortality. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03081949.

Quantifying the differences in structure and mechanical response of confectionery products resulting from the baking and extrusion processes.

Extrusion has potential advantages over baking in terms of throughput, asset cost and flexibility. However, it is challenging to achieve through extrusion the "light, crispy" texture of a more traditional baked confectionery. This study compares and contrasts for the first time confectionery products produced through these two processes, i.e. baking and extrusion. The microstructural differences are measured using imaging techniques, i.e. Scanning Electron Microscopy (SEM) and X-Ray Tomography (XRT) whereas mechanical characterisation is used to highlight differences in the resulting mechanical properties. Crucial information is presented which shows that the two technologies result in different mechanical properties and microstructures, even if the level of porosity in the two products is kept constant. In addition, confectionery products whether they are produced through baking or extrusion, have irregular geometries. The latter makes mechanical characterisation a real challenge. Therefore this study also presents rigorous methods for measuring true mechanical properties such that meaningful and valid comparisons may be made. The accuracy of the chosen methodologies is verified through experiments using flat and tubular extruded geometries as well as testing the products in various directions. It was concluded that the manufacturing method and, in the case of extrusion, the initial moisture content influences the microstructure and mechanics of confectionery products, both of which have an impact on consumer sensory perception.

Measuring and Increasing Adoption Rates of Cookstoves in a Humanitarian Crisis.

Traditional smoky cooking fires are one of today's greatest environmental threats to human life. These fires, used by 40% of the global population, cause 3.9 million annual premature deaths. "Clean cookstoves" have potential to improve this situation; however, most cookstove programs do not employ objective measurement of adoption to inform design, marketing, subsidies, finance, or dissemination practices. Lack of data prevents insights and may contribute to consistently low adoption rates. In this study, we used sensors and surveys to measure objective versus self-reported adoption of freely-distributed cookstoves in an internally displaced persons camp in Darfur, Sudan. Our data insights demonstrate how to effectively measure and promote adoption, especially in a humanitarian crisis. With sensors, we measured that 71% of participants were cookstove "users" compared to 95% of respondents reporting the improved cookstove was their "primary cookstove." No line of survey questioning, whether direct or indirect, predicted sensor-measured usage. For participants who rarely or never used their cookstoves after initial dissemination ("non-users"), we found significant increases in adoption after a simple followup survey (p = 0.001). The followup converted 83% of prior "non-users" to "users" with average daily adoption of 1.7 cooking hours over 2.2 meals. This increased adoption, which we posit resulted from cookstove familiarization and social conformity, was sustained for a 2-week observation period post intervention.

Severe Growth Hormone Deficiency in an Indian Boy Caused By a Novel 6 kb Homozygous Deletion Spanning the GH1 Gene.

Growth disorders resulting in extreme short stature are often a result of deficiency in growth hormone released from the pituitary gland or defective growth hormone releasing receptor. Genetic defects in the GH1 and GHRHR genes account for around 11.1-20% of extreme short stature cases, resulting in a rare condition called Isolated Growth Hormone Deficiency. We describe the characterization of a GH1 genetic defect discovered in a 3-year-old male patient with extreme short stature, developmental failure and undetectable serum levels of growth hormone. There is a familial history of short stature with both parents being short. Whole genome sequencing of the patient DNA revealed a large novel 6 kb homozygous deletion spanning the entire GH1 gene in the patient. While the deletion was homozygous in the subjects, it was found in a heterozygous state in the parents. Thus we report a novel homozygous deletion including the GH1 gene leading to Isolated Growth Hormone Deficiency- Type 1A associated with extreme short stature.

Critical values notification: A nationwide survey of practices among clinical laboratories across Nigeria.

Background: Critical value notification (CVN) entails notifying doctors or other laboratory users of aberrant laboratory results that threaten the patient's life and of any values for which reporting delays could negatively impact the patient's health. Critical value notification practices in clinical laboratories in Nigeria and sub-Saharan Africa are largely unknown. Objective: We conducted a nationwide survey to obtain baseline information on CVN practice by Nigeria's laboratories. Methods: This cross-sectional study was conducted among purposively selected secondary- and tertiary-tier, public and private clinical laboratories across northern and southern Nigeria between October 2015 and December 2015. Consenting senior laboratory staff completed and returned a structured questionnaire, that gathered data on respondents' demographics, designations, and institutional characteristics and practices regarding CVN. Results: One hundred and thirty-four laboratories responded to the questionnaires. Only 69 (51.5 %) laboratories practised CVN; only 23 (33.3%) had existing written policies guiding the practice. Most (43; 62.3%) laboratories use similar critical values (CVs) for adult and paediatric populations. Most laboratories (27; 39.1%) obtained their CVs by combining published literature and local opinions from stakeholders. Physical dispatch (42; 60.9%) followed by telephone calls (38; 55.1%) were the most common means of notification. Private laboratories, compared with public hospital laboratories, were likelier to have separate paediatric CV lists (p = 0.019) and practise telephone notifications (p < 0.001). Conclusion: Critical value notification practices vary and are often suboptimal in many clinical laboratories in Nigeria, which is exacerbated by the absence of guiding policies and national recommendations for post-analytical procedures. What this study adds: This study provides baseline information on CVN practice by Nigeria's laboratories. The study explores the causes of practice variations that can serve as a foundation for enhancing critical reporting and post-analytical services, particularly in clinical laboratories in sub-Saharan Africa.

Understanding the Genetics of Early-Onset Obesity in a Cohort of Children From Qatar.

CONTEXT: Monogenic obesity is a rare form of obesity due to pathogenic variants in genes implicated in the leptin-melanocortin signaling pathway and accounts for around 5% of severe early-onset obesity. Mutations in the genes encoding the MC4R, leptin, and leptin receptor are commonly reported in various populations to cause monogenic obesity. Determining the genetic cause has important clinical benefits as novel therapeutic interventions are now available for some forms of monogenic obesity. OBJECTIVE: To unravel the genetic causes of early-onset obesity in the population of Qatar. METHODS: In total, 243 patients with early-onset obesity (above the 95% percentile) and age of onset below 10 years were screened for monogenic obesity variants using a targeted gene panel, consisting of 52 obesity-related genes. RESULTS: Thirty rare variants potentially associated with obesity were identified in 36 of 243 (14.8%) probands in 15 candidate genes (LEP, LEPR, POMC, MC3R, MC4R, MRAP2, SH2B1, BDNF, NTRK2, DYRK1B, SIM1, GNAS, ADCY3, RAI1, and BBS2). Twenty-three of the variants identified were novel to this study and the rest, 7 variants, were previously reported in literature. Variants in MC4R were the most common cause of obesity in our cohort (19%) and the c.485C>T p.T162I variant was the most frequent MC4R variant seen in 5 patients. CONCLUSION: We identified likely pathogenic/pathogenic variants that seem to explain the phenotype of around 14.8% of our cases. Variants in the MC4R gene are the commonest cause of early-onset obesity in our population. Our study represents the largest monogenic obesity cohort in the Middle East and revealed novel obesity variants in this understudied population. Functional studies will be required to elucidate the molecular mechanism of their pathogenicity.

A ferromagnetic Eu-Pt surface compound grown below hexagonal boron nitride.

One of the fundamental applications for monolayer-thick 2D materials is their use as protective layers of metal surfaces and in situ intercalated reactive materials in ambient conditions. Here we investigate the structural, electronic, and magnetic properties, as well as the chemical stability in air of a very reactive metal, Europium, after intercalation between a hexagonal boron nitride (hBN) layer and a Pt substrate. We demonstrate that Eu intercalation leads to a hBN-covered ferromagnetic EuPt2 surface alloy with divalent Eu2+ atoms at the interface. We expose the system to ambient conditions and find a partial conservation of the di-valent signal and hence the Eu-Pt interface. The use of a curved Pt substrate allows us to explore the changes in the Eu valence state and the ambient pressure protection at different substrate planes. The interfacial EuPt2 surface alloy formation remains the same, but the resistance of the protecting hBN layer to ambient conditions is reduced, likely due to a rougher surface and a more discontinuous hBN coating.

A Novel Homozygous MC2R Variant Leading to Type-1 Familial Glucocorticoid Deficiency.

Context: Type 1 familial glucocorticoid deficiency (FGD) (OMIM #607397) is a rare autosomal recessive disorder due to mutations in melanocortin-2-receptor (MC2R) gene encoding the G protein-coupled adrenocorticotropic (ACTH) transmembrane receptor. Objective: The aim of the study is to describe 2 siblings born to a healthy consanguineous family presenting with clinical and biochemical features of FGD, harboring a novel homozygous MC2R variant. Methods: Both patients are siblings born at term via normal delivery with normal birth weights. The first sibling presented with symptoms of hypoglycemia, repeated episodes of infections starting from 2 days of age. At 18 months of age, low serum cortisol was found, and he was started on hydrocortisone replacement therapy. The second sibling developed hypoglycemia on day 1 after birth, investigations revealed low serum sodium and cortisol levels and was also commenced on hydrocortisone treatment. Whole exome sequencing (WES) and in vitro functional studies on cell line transfected with wild-type and mutant plasmid clones were undertaken. Results: WES revealed a novel homozygous missense mutation c.326T>A, p.Leu109Gln in the MC2R gene. In-silico prediction tools predicted the effect of this mutation to be deleterious. In vitro study using HEK293 cells transfected with MC2R wild-type and mutant clones showed a defect in protein expression and cAMP generation when stimulated with ACTH. Conclusion: Homozygous semiconserved p.Leu109Gln mutation disrupts cAMP production and MC2R protein expression leading to ACTH resistance. This study provides additional evidence that this novel pathogenic variant in MC2R results in FGD phenotypes.

Homozygous Insulin Promotor Gene Mutation Causing Permanent Neonatal Diabetes Mellitus and Childhood Onset Autoantibody Negative Diabetes in the Same Family.

PURPOSE: To report a family with a homozygous INS promotor gene mutation causing permanent neonatal diabetes mellitus (PNDM) in one sibling and autoantibody negative childhood onset diabetes in another sibling. CASE PRESENTATION: Patient 1 is a 12-year-old girl born at term with low birth weight to a consanguineous family, diagnosed with PNDM at 26 days of life. She presented with ketoacidosis and has a severe course of disease with high insulin requirement. Patient 2 is a 9-year-old girl born at term with normal weight, who presented with ketoacidosis at 2 years of age. Both subjects have negative type 1 autoantibodies. On genetic testing, a mutation in the promoter region of INS gene c.-331 C>G was found in homozygous state in both subjects and in a heterozygous state in parents. CONCLUSION: Homozygous INS gene promotor mutations may present with either PNDM or later onset autoantibody negative diabetes in childhood. This suggests that homozygous INS gene promotor mutations show marked heterogeneity in clinical presentation within individuals in the same family. The pathophysiology of this is not well known but could be related to a number of factors, including the position of the variant, penetrance, other associated genetic defects, HLA etc. Premarital screening and genetic counselling is recommended for highly consanguineous families to reduce occurrence of such conditions.

Understanding the Mechanism of Dysglycemia in a Fanconi-Bickel Syndrome Patient.

Fanconi-Bickel Syndrome (FBS) is a rare disorder of carbohydrate metabolism that is characterized mainly by the accumulation of glycogen in the liver and kidney. It is inherited as an autosomal recessive disorder caused by mutations in the SLC2A2 gene, which encodes for GLUT2. Patients with FBS have dysglycemia but the molecular mechanisms of dysglycemia are still not clearly understood. Therefore, we aimed to understand the underlying molecular mechanisms of dysglycemia in a patient with FBS. Genomic DNA was isolated from a peripheral blood sample and analyzed by whole genome and Sanger sequencing. CRISPR-Cas9 was used to introduce a mutation that mimics the patient's mutation in a human kidney cell line expressing GLUT2 (HEK293T). Mutant cells were used for molecular analysis to investigate the effects of the mutation on the expression and function of GLUT2, as well as the expression of other genes implicated in dysglycemia. The patient was found to have a homozygous nonsense mutation (c.901C>T, R301X) in the SLC2A2 gene. CRISPR-Cas9 successfully mimicked the patient's mutation in HEK293T cells. The mutant cells showed overexpression of a dysfunctional GLUT2 protein, resulting in reduced glucose release activity and enhanced intracellular glucose accumulation. In addition, other glucose transporters (SGLT1 and SGLT2 in the kidney) were found to be induced in the mutant cells. These findings suggest the last loops (loops 9-12) of GLUT2 are essential for glucose transport activity and indicate that GLUT2 dysfunction is associated with dysglycemia in FBS.

Understanding the Role of GLUT2 in Dysglycemia Associated with Fanconi-Bickel Syndrome.

Fanconi−Bickel Syndrome (FBS) is a rare disorder of carbohydrate metabolism that is characterized by the accumulation of glycogen mainly in the liver. It is inherited in an autosomal recessive manner due to mutations in the SLC2A2 gene. SLC2A2 encodes for the glucose transporter GLUT2 and is expressed in tissues that are involved in glucose homeostasis. The molecular mechanisms of dysglycemia in FBS are still not clearly understood. In this study, we report two cases of FBS with classical phenotypes of FBS associated with dysglycemia. Genomic DNA was extracted and analyzed by whole-genome and Sanger sequencing, and patient PBMCs were used for molecular analysis. One patient had an exonic SLC2A2 mutation (c.1093C>T in exon 9, R365X), while the other patient had a novel intronic SLC2A2 mutation (c.613-7T>G). Surprisingly, the exonic mutation resulted in the overexpression of dysfunctional GLUT2, resulting in the dysregulated expression of other glucose transporters. The intronic mutation did not affect the coding sequence of GLUT2, its expression, or glucose transport activity. However, it was associated with the expression of miRNAs correlated with type 1 diabetes mellitus, with a particular significant overexpression of hsa-miR-29a-3p implicated in insulin production and secretion. Our findings suggest that SLC2A2 mutations cause dysglycemia in FBS either by a direct effect on GLUT2 expression and/or activity or, indirectly, by the dysregulated expression of miRNAs implicated in glucose homeostasis.

Common coronary artery occlusions in patients with myocardial infarction.

Introduction: coronary artery disease (CAD) is a significant cardiovascular disease (CVD) that affects people worldwide. This study aimed to determine the main occluded coronary arteries in patients with myocardial infarction in Najran, Kingdom of Saudi Arabia (KSA). Methods: a retrospective cross-sectional study conducted between March 2020 and March 2021 and involving 661 myocardial infarction patients recruited from two hospitals (King Khalid Hospital and Prince Sultan Centre for Healthcare in Najran) used sampling for enrolled patients. Patients over the age of 15 years, current residents of KSA, and diagnosed with coronary artery occlusion based on at least one identifiable coronary lesion on a coronary angiography were considered eligible. We created generalized linear mixed models to investigate patients´ clinical and coronary angiographic features and identify statistically relevant components. Results: there were 661 CAD cases in this study: 548 (82.9%) males and 113 (17.1%) females, with a mean and standard deviation (SD) age of 4.03 ± 1.370 years. Ages of the 661 participants ranged from 15 to 85, who had been diagnosed with myocardial infarction were evaluated. It was found that most of the patients were in the 55-64 age range. The majority of cases (366 (55.4%) had ST-segment elevation myocardial infarction (STEMI), 187 (28.3%) had non-ST-segment elevation (NSTEMI), 101 (15.3%) had acute coronary syndrome-non-ST-segment elevation (ACS-NSTEMI), and 7 (1.1%) had acute coronary syndrome-ST-segment elevation (ACS-STEMI). Conclusion: the left anterior descending artery (LAD) is the commonest lesion found in both ST-segment elevation and non-ST-segment elevation myocardial infarction patients.