Applying data science methodologies with artificial intelligence variant reinterpretation to map and estimate genetic disorder prevalence utilizing clinical data.

Data science methodologies can be utilized to ascertain and analyze clinical genetic data that is often unstructured and rarely used outside of patient encounters. Genetic variants from all genetic testing resulting to a large pediatric healthcare system for a 5-year period were obtained and reinterpreted utilizing the previously validated Franklin© Artificial Intelligence (AI). Using PowerBI©, the data were further matched to patients in the electronic healthcare record to associate with demographic data to generate a variant data table and mapped by ZIP codes. Three thousand and sixty-five variants were identified and 98% were matched to patients with geographic data. Franklin© changed the interpretation for 24% of variants. One hundred and fifty-six clinically actionable variant reinterpretations were made. A total of 739 Mendelian genetic disorders were identified with disorder prevalence estimation. Mapping of variants demonstrated hot-spots for pathogenic genetic variation such as PEX6-associated Zellweger Spectrum Disorder. Seven patients were identified with Bardet-Biedl syndrome and seven patients with Rett syndrome amenable to newly FDA-approved therapeutics. Utilizing readily available software we developed a database and Exploratory Data Analysis (EDA) methodology enabling us to systematically reinterpret variants, estimate variant prevalence, identify conditions amenable to new treatments, and localize geographies enriched for pathogenic variants.

Alpha-mannosidosis: a case with novel ultrastructural and light microscopy findings.

OBJECTIVES: Alpha-mannosidosis is a rare genetic lysosomal storage condition leading to the systemic buildup of oligomannoside. Clinical presentation and associated conditions, as well as the full extent of histopathologic changes associated with this disease process, are not fully understood. CASE PRESENTATION: We present the case of an 8-year-1-month old patient with persistent anemia and who was initially diagnosed with Celiac disease before ultimately being diagnosed with alpha-mannosidosis. As part of his diagnostic work-up, duodenal and bone marrow biopsies were examined by pathology. Duodenal biopsies showed foamy plasma cells expanding the lamina propria which triggered a workup for a genetic storage disease; features suggestive of Celiac disease which resolved on gluten-free diet were also noted by pathology. Bone marrow analysis via electron microscopy showed cytoplasmic granules and inclusions in multiple immune cell lines. CONCLUSIONS: Alpha-mannosidosis can occur with Celiac disease and milder forms may only be suspected from incidental pathology findings. The ultrastructural bone marrow findings from this case, the first to be reported from human, show numerous disease-associated changes in multiple immune cell lines whose contribution to disease-associated immunodeficiency is unclear.

Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD.

Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.

Expression of SRP-9001 dystrophin and stabilization of motor function up to 2 years post-treatment with delandistrogene moxeparvovec gene therapy in individuals with Duchenne muscular dystrophy.

Introduction: Delandistrogene moxeparvovec (SRP-9001) is an investigational gene transfer therapy designed for targeted expression of SRP-9001 dystrophin protein, a shortened dystrophin retaining key functional domains of the wild-type protein. Methods: This Phase 2, double-blind, two-part (48 weeks per part) crossover study (SRP-9001-102 [Study 102]; NCT03769116) evaluated delandistrogene moxeparvovec in patients, aged ≥4 to <8 years with Duchenne muscular dystrophy. Primary endpoints (Part 1) were change from baseline (CFBL) in SRP-9001 dystrophin expression (Week 12), by Western blot, and in North Star Ambulatory Assessment (NSAA) score (Week 48). Safety assessments included treatment-related adverse events (TRAEs). Patients were randomized and stratified by age to placebo (n = 21) or delandistrogene moxeparvovec (n = 20) and crossed over for Part 2. Results: SRP-9001 dystrophin expression was achieved in all patients: mean CFBL to Week 12 was 23.82% and 39.64% normal in Parts 1 and 2, respectively. In Part 1, CFBL to Week 48 in NSAA score (least-squares mean, LSM [standard error]) was +1.7 (0.6) with treatment versus +0.9 (0.6) for placebo; p = 0.37. Disparity in baseline motor function between groups likely confounded these results. In 4- to 5-year-olds with matched baseline motor function, CFBL to Week 48 in NSAA scores was significantly different (+2.5 points; p = 0.0172), but not significantly different in 6-to-7-year-olds with imbalanced baseline motor function (-0.7 points; p = 0.5384). For patients treated with delandistrogene moxeparvovec in Part 2, CFBL to Week 48 in NSAA score was +1.3 (2.7), whereas for those treated in Part 1, NSAA scores were maintained. As all patients in Part 2 were exposed to treatment, results were compared with a propensity-score-weighted external control (EC) cohort. The LSM difference in NSAA score between the Part 2 treated group and EC cohort was statistically significant (+2.0 points; p = 0.0009). The most common TRAEs were vomiting, decreased appetite, and nausea. Most occurred within the first 90 days and all resolved. Discussion: Results indicate robust expression of SRP-9001 dystrophin and overall stabilization in NSAA up to 2 years post-treatment. Differences in NSAA between groups in Part 1 were not significant for the overall population, likely because cohorts were stratified only by age, and other critical prognostic factors were not well matched at baseline.

An integrated framework for optimal infrastructure planning for decarbonising heating.

This paper presents the HEGIT (Heat, Electricity and Gas Infrastructure and Technology) model for optimal infrastructure planning for decarbonising heating in buildings. HEGIT is an optimisation model based on Mixed Integer Linear Programming. The model co-optimises the integrated operation and capacity expansion planning of electricity and gas grids as well as heating technologies on the consumer side while maintaining the security of supply and subject to different environmental, operational and system-wide constraints. The three main features of the HEGIT model are:•It incorporates an integrated unit commitment and capacity expansion problem for coordinated operation and long-term investment planning of the electricity and gas grids.•It incorporates the flexible operation of heating technologies in buildings and demand response in operation and long-term investment planning of gas and electricity grids.•It incorporates a multi-scale techno-economic representation of heating technologies design features into the whole energy system modelling and capacity planning.These features enable the model to quantify the impacts of different policies regarding decarbonising heating in buildings on the operation and long-term planning of electricity and gas grids, identify the cost-optimal use of available resources and technologies and identify strategies for maximising synergies between system planning goals and minimising trade-offs. Moreover, the multi-scale feature of the model allows for multi-scale system engineering analysis of decarbonising heating, including system-informed heating technology design, identifying optimal operational setups at the consumer end, and assessing trade-offs between consumer investment in heating technologies and infrastructure requirements in different heat decarbonisation pathways.

A homozygous Gly470Ala variant in PEX6 causes severe Zellweger spectrum disorder.

Zellweger spectrum disorder (ZSD) is a group of autosomal recessive disorders caused by biallelic pathogenic variants in any one of the 13 PEX genes essential for peroxisomal biogenesis. We report a cohort of nine infants who presented at birth with severe neonatal features suggestive of ZSD and found to be homozygous for a variant in PEX6 (NM_000287.4:c.1409G > C[p.Gly470Ala]). All were of Mixtec ancestry and identified by the California Newborn Screening (NBS) Program to have elevated C26:0-lysophosphatidylcholine but no reportable variants in ABCD1. The clinical and biochemical features of this cohort are described within. Gly470Ala may represent a founder variant in the Mixtec population of Central California. ZSD should be considered in patients who present at birth with severe hypotonia and enlarged fontanelles, especially in the setting of an abnormal NBS, Mixtec ancestry, or family history of infant death. There is a need to further characterize the natural history of ZSD, the Gly470Ala variant, and expand upon possible genotype-phenotype correlations.

MT-ATP6 mitochondrial disease identified by newborn screening reveals a distinct biochemical phenotype.

Although decreased citrulline is used as a newborn screening (NBS) marker to identify proximal urea cycle disorders (UCDs), it is also a feature of some mitochondrial diseases, including MT-ATP6 mitochondrial disease. Here we describe biochemical and clinical features of 11 children born to eight mothers from seven separate families who were identified with low citrulline by NBS (range 3-5 µM; screening cutoff >5) and ultimately diagnosed with MT-ATP6 mitochondrial disease. Follow-up testing revealed a pattern of hypocitrullinemia together with elevated propionyl-(C3) and 3-hydroxyisovaleryl-(C5-OH) acylcarnitines, and a homoplasmic pathogenic variant in MT-ATP6 in all cases. Single and multivariate analysis of NBS data from the 11 cases using Collaborative Laboratory Integrated Reports (CLIR; https://clir.mayo.edu) demonstrated citrulline <1st percentile, C3 > 50th percentile, and C5-OH >90th percentile when compared with reference data, as well as unequivocal separation from proximal UCD cases and false-positive low citrulline cases using dual scatter plots. Five of the eight mothers were symptomatic at the time of their child(ren)'s diagnosis, and all mothers and maternal grandmothers evaluated molecularly and biochemically had a homoplasmic pathogenic variant in MT-ATP6, low citrulline, elevated C3, and/or elevated C5-OH. All molecularly confirmed individuals (n = 17) with either no symptoms (n = 12), migraines (n = 1), or a neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) phenotype (n = 3) were found to have an A or U mitochondrial haplogroup, while one child with infantile-lethal Leigh syndrome had a B haplogroup.

Next generation phenotyping with quantitative narration for DEGCAGS syndrome.

The diagnosis of rare Mendelian disorders usually relies upon the interpretation of prose and is complicated by a lack of objective, reproducible phenotypic data. To address this limitation, we developed a next generation phenotyping workflow to phenotypically characterize developmental delay with gastrointestinal, cardiovascular, genitourinary, and skeletal abnormalities (DEGCAGS). We identified 15 people affected with DEGCAGS, including one novel patient identified at our hospital and 14 patients previously reported in the literature. Human Phenotype Ontology (HPO) terms were extracted from the patient chart and literature review. The HPO terms were sorted by count according to HPO hierarchy of terms. Phenotypes that cosegregate were identified utilizing a co-occurrence matrix. A quantitative narrative illustrated by violin plots was created for our patient from phenotypic data per each day of hospital admission. A total of 252 unique HPO terms were extracted from the patient record and literature review. The highest count of systemically sorted and unsorted terms and the most commonly co-occurring terms were described. A violin plot of phenotype occurrences demonstrated a progression of phenotypes over time. NGP offers a quantitative approach to phenotyping to generate phenotypic data in an objective and reproducible manner akin to NGS.

Accompanying effects of sewage sludge and pine needle biochar with selected organic additives on the soil and plant variables.

The effects of synthetic fertilizer and nutrient leaching are causing serious problems impacting soil function and its fertility. Mitigation of nutrient leaching and use of chemical fertilizer is crucial as fertile land adds up sustainability to climate changes. Biochar produced from agricultural bio-waste and municipal solid waste has been used for crop production and when applied in combination with organic nutrients may support mitigation of nutrient loss and adverse effects of chemical fertilizers. Different types of biochar and their application for soil enhancement have been observed, pine needle and sewage sludge derived low-temperature biochar along with compost, organic fertilizer in the form of manure and microalgal biomass may interact with soil chemistry and plant growth to impact nutrient loss and compensate the hazardous effect of chemical fertilizer, but it has not been investigated yet. This present study elaborates application of sewage sludge and pine needle biochar produced at 400 °C in an application rate of 5 % w/w and 10 t h-1 in combination with compost, manure and microalgal biomasses of Closteriopsis acicularis (BM1) and Tetradesmus nygaardi (BM2) on the growth of Chickpea (Cicer arietinum) and Fenugreek (Trigonella foenum-graecum) crop assessed in a pot experiment over a two crop (Chickpea - Fenugreek) cycle in Pakistan. Results depict that the pine needle biochar with additives has increased plant height by 104.1 ± 2.76 cm and fresh biomass by 49.9 ± 1.02 g, buffered the soil pH to 6.5 for optimum growth of crops and enhance carbon retention by 36 %. This study highlights the valorization of sewage sludge and pine needle into biochar and the effect of biochar augmentation, its impact on soil nutrients and plant biomass enhancement. The greener approach also mitigates and helps in the sustainable management of solid wastes.

The use of system dynamics for energy and environmental education.

The use of system dynamics as a learning tool for developing sustainable energy strategies and environmental education has advanced in recent years with the availability of new modelling software and webtools. Among the existing models, we highlight the online 2050 Calculators, which aim at simulating scenarios for greenhouse gas emissions, energy planning, sustainable land use, and food consumption. The objective of this study is to assess the available calculators and their contribution to an interdisciplinary education via systems thinking. We carried out a review of the existing models worldwide and ran some of the tools with students from three different postgraduate programmes at master's level at Imperial College London (United Kingdom) and IFP School (France), whilst also assessing their individual views afterwards. The assessments were conducted once a year during three subsequent years: 2019, 2020, and 2021. The results are discussed under the epistemology of critical pedagogy, showing that the use of webtools, such as the 2050 Calculators, can significantly contribute to the students' environmental awareness and political engagement, providing important lessons about the use of system dynamics for policy and science education.

Life cycle assessment (LCA): informing the development of a sustainable circular bioeconomy?

The role of life cycle assessment (LCA) in informing the development of a sustainable and circular bioeconomy is discussed. We analyse the critical challenges remaining in using LCA and propose improvements needed to resolve future development challenges. Biobased systems are often complex combinations of technologies and practices that are geographically dispersed over long distances and with heterogeneous and uncertain sets of indicators and impacts. Recent studies have provided methodological suggestions on how LCA can be improved for evaluating the sustainability of biobased systems with a new focus on emerging systems, helping to identify environmental and social opportunities prior to large R&D investments. However, accessing economies of scale and improved conversion efficiencies while maintaining compatibility across broad ranges of sustainability indicators and public acceptability remain key challenges for the bioeconomy. LCA can inform, but not by itself resolve this complex dimension of sustainability. Future policy interventions that aim to promote the bioeconomy and support strategic value chains will benefit from the systematic use of LCA. However, the LCA community needs to develop the mechanisms and tools needed to generate agreement and coordinate the standards and incentives that will underpin a successful biobased transition. Systematic stakeholder engagement and the use of multidisciplinary analysis in combination with LCA are essential components of emergent LCA methods. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.

A hybrid approach to identifying and assessing interactions between climate action (SDG13) policies and a range of SDGs in a UK context.

In 2015 the United Nations drafted the Paris Agreement and established the Sustainable Development Goals (SDGs) for all nations. A question of increasing relevance is the extent to which the pursuit of climate action (SDG 13) interacts both positively and negatively with other SDGs. We tackle this question through a two-pronged approach: a novel, automated keyword search to identify linkages between SDGs and UK climate-relevant policies; and a detailed expert survey to evaluate these linkages through specific examples. We consider a particular subset of SDGs relating to health, economic growth, affordable and clean energy and sustainable cities and communities. Overall, we find that of the 89 UK climate-relevant policies assessed, most are particularly interlinked with the delivery of SDG 7 (Affordable and Clean Energy) and SDG 11 (Sustainable Cities and Communities) and that certain UK policies, like the Industrial Strategy and 25-Year Environment Plan, interlink with a wide range of SDGs. Focusing on these climate-relevant policies is therefore likely to deliver a wide range of synergies across SDGs 3 (Good Health and Well-being), 7, 8 (Decent Work and Economic Growth), 9 (Industry, Innovation and Infrastructure), 11, 14 (Life Below Water) and 15 (Life on Land). The expert survey demonstrates that in addition to the range of mostly synergistic interlinkages identified in the keyword search, there are also important potential trade-offs to consider. Our analysis provides an important new toolkit for the research and policy communities to consider interactions between SDGs, which can be employed across a range of national and international contexts. Supplementary Information: The online version contains supplementary material available at 10.1007/s43621-021-00051-w.

A well-tolerated core needle muscle biopsy process suitable for children and adults.

Serial muscle biopsies within clinical trials for Duchenne muscular dystrophy (DMD) are critical to document therapeutic responses. Less invasive means of sampling muscle are needed. We analyzed a retrospective consecutive case-series cohort of vacuum-assisted core needle muscle biopsy procedures performed on healthy and dystrophic individuals at a single institution assessing for safety and reliability of obtaining sufficient high-quality biopsy tissue for histologic assessment in adult and pediatric subjects. Of 471 muscle cores from 128 biopsy procedures, 377-550 mg of total muscle tissue was obtained per procedure with mean core weight of 129 mg (SD, 25.1 mg). All biopsies were adequate for histological assessment. There were no significant adverse events. This core needle biopsy approach, when combined with improved sample processing, provides a safe means to consistently obtain muscle samples for diagnostic and clinical trial applications.

Myopathy associated with homozygous PYROXD1 pathogenic variants detected by genome sequencing.

Biallelic pathogenic variants in the gene PYROXD1 have recently been described to cause early-onset autosomal recessive myopathy. Myopathy associated with PYROXD1 pathogenic variants is rare and reported in only 17 individuals. Known pathogenic variants in PYROXD1 include missense, insertion and essential splice-site variants. Here we describe a consanguineous family of individuals affected with late-onset myopathy and homozygous PYROXD1 missense variants (NM_024854.5:c.464A>G [p.Asn155Ser]) expanding our understanding of the possible disease phenotypes of PYROXD1-associated myopathy.

Diagnostic utility of transcriptome sequencing for rare Mendelian diseases.

PURPOSE: We investigated the value of transcriptome sequencing (RNAseq) in ascertaining the consequence of DNA variants on RNA transcripts to improve the diagnostic rate from exome or genome sequencing for undiagnosed Mendelian diseases spanning a wide spectrum of clinical indications. METHODS: From 234 subjects referred to the Undiagnosed Diseases Network, University of California-Los Angeles clinical site between July 2014 and August 2018, 113 were enrolled for high likelihood of having rare undiagnosed, suspected genetic conditions despite thorough prior clinical evaluation. Exome or genome sequencing and RNAseq were performed, and RNAseq data was integrated with genome sequencing data for DNA variant interpretation genome-wide. RESULTS: The molecular diagnostic rate by exome or genome sequencing was 31%. Integration of RNAseq with genome sequencing resulted in an additional seven cases with clear diagnosis of a known genetic disease. Thus, the overall molecular diagnostic rate was 38%, and 18% of all genetic diagnoses returned required RNAseq to determine variant causality. CONCLUSION: In this rare disease cohort with a wide spectrum of undiagnosed, suspected genetic conditions, RNAseq analysis increased the molecular diagnostic rate above that possible with genome sequencing analysis alone even without availability of the most appropriate tissue type to assess.

Technoeconomic and life-cycle analysis of single-step catalytic conversion of wet ethanol into fungible fuel blendstocks.

Technoeconomic and life-cycle analyses are presented for catalytic conversion of ethanol to fungible hydrocarbon fuel blendstocks, informed by advances in catalyst and process development. Whereas prior work toward this end focused on 3-step processes featuring dehydration, oligomerization, and hydrogenation, the consolidated alcohol dehydration and oligomerization (CADO) approach described here results in 1-step conversion of wet ethanol vapor (40 wt% in water) to hydrocarbons and water over a metal-modified zeolite catalyst. A development project increased liquid hydrocarbon yields from 36% of theoretical to >80%, reduced catalyst cost by an order of magnitude, scaled up the process by 300-fold, and reduced projected costs of ethanol conversion 12-fold. Current CADO products conform most closely to gasoline blendstocks, but can be blended with jet fuel at low levels today, and could potentially be blended at higher levels in the future. Operating plus annualized capital costs for conversion of wet ethanol to fungible blendstocks are estimated at $2.00/GJ for CADO today and $1.44/GJ in the future, similar to the unit energy cost of producing anhydrous ethanol from wet ethanol ($1.46/GJ). Including the cost of ethanol from either corn or future cellulosic biomass but not production incentives, projected minimum selling prices for fungible blendstocks produced via CADO are competitive with conventional jet fuel when oil is $100 per barrel but not at $60 per barrel. However, with existing production incentives, the projected minimum blendstock selling price is competitive with oil at $60 per barrel. Life-cycle greenhouse gas emission reductions for CADO-derived hydrocarbon blendstocks closely follow those for the ethanol feedstock.

Myopathy, lactic acidosis and sideroblastic anemia 1 (MLASA1): A 25-year follow-up.

Mitochondrial myopathy, lactic acidosis and sideroblastic anemia 1 (MLASA1) is a rare disease caused by biallelic pathogenic variants in the PUS1 gene. There are eleven MLASA1 patients reported worldwide with the majority of the patients originating from the Shiraz region of Iran. The rarity of this disease poses challenges to counseling patients due to a lack of natural history data. This report reviews what is known regarding MLASA1 and describes two brothers with MLASA1 who were cared for over the course of 10 years at the University of California Los Angeles. The brothers suffered from chronic anemia, transfusion dependency and muscle wasting that lead to respiratory insufficiency and death in one of the brothers.

Non-Cystic Fibrosis-Related Meconium Ileus: GUCY2C-Associated Disease Discovered through Rapid Neonatal Whole-Exome Sequencing.

Meconium ileus is caused by cystic fibrosis; however, mutations in the GUCY2C gene also cause this disease. We report non-cystic fibrosis meconium ileus in an infant of non-Middle Eastern origin with compound heterozygous mutations in GUCY2C.