Novel EGFR mutations in diffuse midline gliomas using cost-effective strategies: A report of 2 cases.

Background: Diffuse midline gliomas (DMGs) are malignant tumors predominantly affecting children, often leading to poor outcomes. The 2021 World Health Organization classification identifies 3 subtypes of DMGs, all characterized by the loss of H3K27 trimethylation. Here, we report 2 cases of DMG with Epidermal Growth Factor Receptor (EGFR) mutations within exon 20, contributing to the understanding of the molecular complexity of these pediatric brain tumors. Methods: An economical immunohistochemical panel was designed to aid in the diagnosis of most DMGs in resource-constrained regions. Sanger sequencing was employed to identify rare EGFR mutations in exon 20 of 2 cases. Results: Molecular analyses of 2 cases of DMG revealed novel EGFR mutations within exon 20. These mutations were identified using cost-effective diagnostic approaches. The presence of EGFR mutations expands the molecular landscape of DMGs and highlights the genetic heterogeneity within this tumor entity. Conclusions: These findings underscore the molecular heterogeneity of DMGs and the significance of identifying novel mutations, such as EGFR mutations in exon 20. Further research into the molecular mechanisms underlying DMGs is warranted to advance therapeutic strategies and improve outcomes for pediatric patients.

Beware of little expenses: Low-value endocrinological blood tests in geriatric medical inpatients.

OBJECTIVES: Blood tests for endocrinological derangements are frequently requested in general medical inpatients, in particular those in the older age group. Interrogation of these tests may present opportunities for healthcare savings. METHODS: This multicentre retrospective study over a 2.5-year period examined the frequency with which three common endocrinological investigations [thyroid stimulating hormone (TSH), HbA1c, 25-hydroxy Vitamin D3] were performed in this population, including the frequency of duplicate tests within a given admission, and the frequency of abnormal test results. The Medicare Benefits Schedule was used to calculate the cost associated with these tests. RESULTS: There were 28,564 individual admissions included in the study. Individuals ≥65 years old were the majority of inpatients in whom the selected tests were performed (80% of tests). TSH was performed in 6730 admissions, HbA1c was performed in 2259 admissions, and vitamin D levels were performed in 5632 admissions. There were 6114 vitamin D tests performed during the study period, of which 2911 (48%) returned outside the normal range. The cost associated with vitamin D level testing was $183,726. Over the study period, 8% of tests for TSH, HbA1c, and Vitamin D were duplicates (where a second test was performed within a single admission), which was associated with a cost of $32,134. CONCLUSIONS: Tests for common endocrinological abnormalities are associated with significant healthcare costs. Avenues by which future savings may be pursued include the investigation of strategies to reduce duplicate ordering and examining the rationale and guidelines associated with ordering tests such as vitamin D levels.

Cost-effective genotyping for classical congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD) in resource-poor settings: multiplex ligation probe amplification (MLPA) with/without sequential next-generation sequencing (NGS).

PURPOSE: Genotyping of classic congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD) is becoming increasingly significant beyond prenatal counseling in the current era of emerging gene therapy/editing technologies. While the knowledge of common variants helps in designing cost-effective genotyping strategies, limited data are currently available from the Indian subcontinent, especially South India, mainly due to financial constraints. The aim of this study is to assess the genotype of individuals with classic CAH from a South Indian cohort in a cost-effective manner. METHODS: The genotypes of 46 unrelated subjects with classic CAH were studied through initial multiplex ligation-dependent probe amplification (MLPA) using the SALSA MLPA Probe-mix P050 CAH (MRC Holland). Next-generation sequencing (NGS) was done in 10 subjects, as their MLPA was either negative or showed heterozygous variants. RESULTS: The common variants observed in our study population of 46 subjects were large deletions (35.8%), intron 2 variant [c.293-13A/C > G] (35.8%), 8 bp del [c.332_339del p.(Gly111Valfs*21)] (7.7%), and R356W [c.1069 C > T p.(Arg357Trp)] (6.6%). MLPA alone detected pathogenic variants in 78.2% of the initial study samples (36/46). Sequential NGS resulted in a 100% detection rate in our study population. CONCLUSION: MLPA appears to be an effective first genotyping modality for this South Indian cohort due to the high prevalence of large deletions and common variants. MLPA as a first initial screening genotyping test with sequential NGS when required may be a cost-effective and highly sensitive approach to CYP21A2 genotyping in our part of the world and in resource-poor settings.

The Cost of Raising Individuals with Fragile X or Chromosome 15 Imprinting Disorders in Australia.

The study characterised differences in costs associated with raising a child between four rare disorders and examined the associations between these costs with clinical severity. Caregivers of 108 individuals with Prader-Willi, Angelman (AS), Chromosome 15q Duplication and fragile X (FXS) syndromes completed a modified Client Services Receipt Inventory and participants completed intellectual/developmental functioning and autism assessments. AS incurred the highest yearly costs per individual ($AUD96,994), while FXS had the lowest costs ($AUD33,221). Intellectual functioning negatively predicted total costs, after controlling for diagnosis. The effect of intellectual functioning on total costs for those with AS was significantly different to the other syndromes. The study highlights the significant costs associated with these syndromes, particularly AS, linked with severity of intellectual functioning.

Genomic Resources to Guide Improvement of the Shea Tree.

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.

Phenotypic features in MECP2 duplication syndrome: Effects of age.

BACKGROUND: MECP2 Duplication syndrome (MDS) is a rare X-linked genomic disorder that is caused by interstitial chromosomal duplications at Xq28 encompassing the MECP2 gene. Although phenotypic features in MDS have been described, there is a limited understanding of the range of severity of these features, and how they evolve with age. METHODS: The cross-sectional results of N = 69 participants (ages 6 months-33 years) enrolled in a natural history study of MDS are presented. Clinical severity was assessed using a clinician-report measure as well as a parent-report measure. Data was also gathered related to the top 3 concerns of parents as selected from the most salient symptoms related to MDS. The Child Health Questionnaire was also utilized to obtain parental reports of each child's quality of life to establish disease burden. RESULTS: The results of linear regression from the clinician-reported measure show that overall clinical severity scores, motor dysfunction, and functional skills are significantly worse with increasing age. Top concerns rated by parents included lack of effective communication, abnormal walking/balance issues, constipation, and seizures. Higher levels of clinical severity were also related to lower physical health quality of life scores as reported by parents. CONCLUSIONS: The data suggest that increasing levels of clinical severity are noted with older age, and this is primarily attributable to motor dysfunction, and functional skills. The results provide an important foundation for creating an MDS-specific severity scale highlighting the most important domains to target for treatment trials and will help clinicians and researchers define clinically meaningful changes.

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.

BACKGROUND: Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. RESULTS: Our results showed 1.3-21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. CONCLUSIONS: These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.

Exact median-tree inference for unrooted reconciliation costs.

BACKGROUND: Solving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from collections of discordant gene trees. These problems are NP-hard, and therefore are, in practice, typically addressed by local search heuristics. So far, however, such heuristics lack any provable correctness or precision. Further, even for small phylogenetic studies, it has been demonstrated that local search heuristics may only provide sub-optimal solutions. Obviating such heuristic uncertainties are exact dynamic programming solutions that allow solving tree reconciliation problems for smaller phylogenetic studies. Despite these promises, such exact solutions are only suitable for credibly rooted input gene trees, which constitute only a tiny fraction of the readily available gene trees. Standard gene tree inference approaches provide only unrooted gene trees and accurately rooting such trees is often difficult, if not impossible. RESULTS: Here, we describe complex dynamic programming solutions that represent the first nonnaïve exact solutions for solving the tree reconciliation problems for unrooted input gene trees. Further, we show that the asymptotic runtime of the proposed solutions does not increase when compared to the most time-efficient dynamic programming solutions for rooted input trees. CONCLUSIONS: In an experimental evaluation, we demonstrate that the described solutions for unrooted gene trees are, like the solutions for rooted input gene trees, suitable for smaller phylogenetic studies. Finally, for the first time, we study the accuracy of classic local search heuristics for unrooted tree reconciliation problems.

Strategic management in local hospital markets: service duplication or service differentiation.

BACKGROUND: The purpose of this study is to assess the influences of market structure on hospitals' strategic decision to duplicate or differentiate services and to assess the relationship of duplication and differentiation to hospital performance. This study is different from previous research because it examines how a hospital decides which services to be duplicated or differentiated in a dyadic relationship embedded in a complex competitive network. METHODS: We use Linear Structural Equations (LISREL) to simultaneously estimate the relationships among market structure, duplicated and differentiated services, and performance. All non-federal, general acute hospitals in urban counties in the United States with more than one hospital are included in the sample (n = 1726). Forty-two high-tech services are selected for the study. Data are compiled from the American Hospital Association Annual Survey of Hospitals, Area Resource File, and CMS cost report files. State data from HealthLeaders-InterStudy for 2015 are also used. RESULTS: The findings provide support that hospitals duplicate and differentiate services relative to rivals in a local market. Size asymmetry between hospitals is related to both service duplication (negatively) and service differentiation (positively). With greater size asymmetry, a hospital utilizes its valuable resources for its own advantage to thwart competition from rivals by differentiating more high-tech services and reducing service duplication. Geographic distance is positively related to service duplication, with duplication increasing as distance between hospitals increases. Market competition is associated with lower service duplication. Both service differentiation and service duplication are associated with lower market share, higher costs, and lower profits. CONCLUSIONS: The findings underscore the role of market structure as a check and balance on the provision of high-tech services. Hospital management should consider cutting back some services that are oversupplied and/or unprofitable and analyze the supply and demand in the market to avoid overdoing both service duplication and service differentiation.

CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice.

Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.

Model-Based Detection of Whole-Genome Duplications in a Phylogeny.

Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the "background" gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set of a priori selected WGD hypotheses and cannot be used to discover WGDs in a phylogeny. In this study, we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth-death model that includes WGD in a flexible hierarchical Bayesian approach and use reversible-jump Markov chain Monte Carlo to perform Bayesian inference of branch-specific duplication, loss, and WGD retention rates across the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants, and discuss the statistical intricacies of model-based WGD inference.

Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing.

Transposable elements can be highly mutagenic because when they transpose they can insert into genes and disrupt their function, a propensity which has been exploited in many organisms to generate tagged mutant alleles. The Mutator (Mu) family transposon is a family of DNA-type transposons in maize with a particularly high duplication frequency, which results in large numbers of new mutations in lineages that carry active Mu elements. Here we describe a rapid and cost-effective Miseq-based Mu transposon profiling pipeline. This method can also be used for identifying flanking sequences of other types of long insertions such as T-DNAs.

Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model.

BACKGROUND: Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which can be difficult to estimate. Prior work has explored the relationship between event costs and maximum parsimony reconciliations in the duplication-loss and duplication-transfer-loss models, but no studies have addressed this relationship in the more complicated duplication-loss-coalescence model. RESULTS: We provide a fixed-parameter tractable algorithm for computing Pareto-optimal reconciliations and recording all events that arise in those reconciliations, along with their frequencies. We apply this method to a case study of 16 fungi to systematically characterize the complexity of MPR space across event costs and identify events supported across this space. CONCLUSION: This work provides a new framework for studying the relationship between event costs and reconciliations that incorporates both macro-evolutionary events and population effects and is thus broadly applicable across eukaryotic species.

Regulatory effect of decreasing therapeutic duplication of respiratory drugs using a prescription database between 2012 and 2015.

Duplicative drug use increases the risk of adverse drug reactions and expends healthcare resources unnecessarily. No epidemiological evidence of the prevalence of therapeutic duplication (TD) involving respiratory system drugs exists. Therefore, we describe the prescription patterns of these drugs and estimate changes in TD rates following implementation of a new regulation in 2013. A time-series analysis using national healthcare data was conducted, involving eight classes, and patients prescribed any of these drugs between 2012 and 2015. We used two definitions of TD; duplicative prescriptions overlapped for more than 30 days by the same prescriber and for more than 1 day by different prescribers. We calculated relative and absolute difference in TD rates after the regulation. TD by the same prescriber decreased for respiratory drugs of six classes, but increased more than 10% for antihistamines (+10.28, +0.05). TD by a different prescriber decreased only for xanthine bronchodilators, but increased more than 10% for beta-receptor agonists (+27.07, +1.42), leukotriene receptor antagonists (+16.10, +0.44), cough suppressants (+15.64, +0.52), mucolytic agents (+11.16, +0.67). The 2013 regulation regarding respiratory drugs did not have the anticipated effect of reducing TD prevalence; more effective interventions are needed.

Estimation of duplication history under a stochastic model for tandem repeats.

BACKGROUND: Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of the same pattern in tandem repeats and their high variability, they contain a wealth of information about the mutations that have led to their formation. The ability to extract this information can enhance our understanding of evolutionary mechanisms. RESULTS: We present a stochastic model for the formation of tandem repeats via tandem duplication and substitution mutations. Based on the analysis of this model, we develop a method for estimating the relative mutation rates of duplications and substitutions, as well as the total number of mutations, in the history of a tandem repeat sequence. We validate our estimation method via Monte Carlo simulation and show that it outperforms the state-of-the-art algorithm for discovering the duplication history. We also apply our method to tandem repeat sequences in the human genome, where it demonstrates the different behaviors of micro- and mini-satellites and can be used to compare mutation rates across chromosomes. It is observed that chromosomes that exhibit the highest mutation activity in tandem repeat regions are the same as those thought to have the highest overall mutation rates. However, unlike previous works that rely on comparing human and chimpanzee genomes to measure mutation rates, the proposed method allows us to find chromosomes with the highest mutation activity based on a single genome, in essence by comparing (approximate) copies of the pattern in tandem repeats. CONCLUSION: The prevalence of tandem repeats in most organisms and the efficiency of the proposed method enable studying various aspects of the formation of tandem repeats and the surrounding sequences in a wide range of settings. AVAILABILITY: The implementation of the estimation method is available at http://ips.lab.virginia.edu/smtr .

The impact of a medication record sharing program among diabetes patients under a single-payer system: The role of inquiry rate.

OBJECTIVE: Taiwan's single health insurer introduced a medication record exchange platform, the PharmaCloud program, in 2013. This study aimed to evaluate the effects of the medication record inquiry rate on medication duplication among patients with diabetes. MATERIALS AND METHODS: A retrospective pre-post design with a comparison group was conducted using nationwide health insurance claim data of diabetic patients from 2013 to 2014. Patients whose medication record inquiry rate fell within the upper 25th percentile were classified as the high-inquiry group, and the others as the low-inquiry group. The dependent variables were the likelihood of receiving duplicated medication and the overlapped medication days of the study subjects. Generalized estimation equations with difference-in-difference analysis were calculated to examine the net effect of the PharmaCloud inquiry rate for a matched sub-sample. RESULTS: In total, 106,508 patients with diabetes were randomly selected. From 2013 to 2014, the medication duplication rate was reduced 7.76 percentile (54.12%-46.36%) for the high-inquiry group and 9.58 percentile (63.72%-54.14%) for the low-inquiry group; the average medication overlap periods were shortened 4.36 days (8.49-4.13) and 6.29 days (11.28-4.99), respectively. The regression models showed patients in the high-inquiry group were more likely to receive duplicated medication (OR = 1.11, 95% C.I. = 1.07-1.16) and with longer overlapped days (7.53%, P = 0.0081) after the program. CONCLUSION: The medication record sharing program has reduced medication duplication among diabetes patients. However, higher inquiry rate did not lead to greater reduction in medication duplication; the overall effect might be due to enhanced internal control via prescription alert system in hospitals rather physician's review of the records.

Quadratic transformation inequalities for Gaussian hypergeometric function.

In the article, we present several quadratic transformation inequalities for Gaussian hypergeometric function and find the analogs of duplication inequalities for the generalized Grötzsch ring function.

Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization.

BACKGROUND: Gene duplication has been identified as a key process driving functional change in many genomes. Several biological models exist for the evolution of a pair of duplicates after a duplication event, and it is believed that gene duplicates can evolve in different ways, according to one process, or a mix of processes. Subfunctionalization is one such process, under which the two duplicates can be preserved by dividing up the function of the original gene between them. Analysis of genomic data using subfunctionalization and related processes has thus far been relatively coarse-grained, with mathematical treatments usually focusing on the phenomenological features of gene duplicate evolution. RESULTS: Here, we develop and analyze a mathematical model using the mechanics of subfunctionalization and the assumption of Poisson rates of mutation. By making use of the results from the literature on the Phase-Type distribution, we are able to derive exact analytical results for the model. The main advantage of the mechanistic model is that it leads to testable predictions of the phenomenological behavior (instead of building this behavior into the model a priori), and allows for the estimation of biologically meaningful parameters. We fit the survival function implied by this model to real genome data (Homo sapiens, Mus musculus, Rattus norvegicus and Canis familiaris), and compare the fit against commonly used phenomenological survival functions. We estimate the number of regulatory regions, and rates of mutation (relative to silent site mutation) in the coding and regulatory regions. We find that for the four genomes tested the subfunctionalization model predicts that duplicates most-likely have just a few regulatory regions, and the rate of mutation in the coding region is around 5-10 times greater than the rate in the regulatory regions. This is the first model-based estimate of the number of regulatory regions in duplicates. CONCLUSIONS: Strong agreement between empirical results and the predictions of our model suggest that subfunctionalization provides a consistent explanation for the evolution of many gene duplicates.