Phillip Dexheimer's research while affiliated with Cincinnati Children's Hospital Medical Center and other places
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Publications (107)
Loss-of-function (LoF) variants in the filaggrin (FLG) gene are the strongest known genetic risk factor for atopic dermatitis (AD), but the impact of these variants on AD outcomes is poorly understood. We comprehensively identified genetic variants through targeted region sequencing of FLG in children participating in the Mechanisms of Progression...
Much of the host antiviral response is mediated through changes to host gene expression levels. Likewise, viruses induce changes to host gene expression levels in order to promote the viral life cycle and evade the host immune system. However, there is no resource that specifically collects human gene expression levels pre- and post- virus infectio...
Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of the viral life cycle has yet to be elucidated. Here, single cell RNA sequencing of HPV16 infect...
As a member of the RUNT domain family core-binding transcription factors, RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). Previous work has established that RUNX1 is involved in the maturation of megakaryocytes and the production of...
Acute B-cell lymphoblastic leukemia (B-ALL) results from oligo-clonal evolution of B-cell progenitors endowed with initiating and propagating leukemia properties. The activation of both the Rac guanine nucleotide exchange factor (Rac GEF) Vav3 and Rac GTPases is required for leukemogenesis mediated by the oncogenic fusion protein BCR-ABL. Vav3 expr...
Background
Children ≤36 months with Diffuse Intrinsic Pontine Glioma (DIPG) have increased long-term survival (LTS, overall survival (OS) ≥24 months). Understanding distinguishing characteristics in this population is critical to improving outcomes.
Methods
Patients ≤36 months at diagnosis enrolled on the International DIPG Registry (IDIPGR) with...
Inflammation of the esophageal epithelium is a hallmark of eosinophilic esophagitis (EoE), an emerging chronic allergic disease. Herein, we probed human esophageal epithelial cells at single-cell resolution during homeostasis and EoE. During allergic inflammation, the epithelial differentiation program was blocked, leading to loss of KRT6high diffe...
To understand the genetic contribution to primary pediatric cardiomyopathy, we performed exome sequencing in a large cohort of 528 children with cardiomyopathy. Using clinical interpretation guidelines and targeting genes implicated in cardiomyopathy, we identified a genetic cause in 32% of affected individuals. Cardiomyopathy sub-phenotypes differ...
BACKGROUND Diffuse intrinsic pontine gliomas (DIPG) generally occur in young school-age children, although can occur in adolescents and young adults. The purpose of this study was to describe clinical, radiological, pathologic, and molecular characteristics in patients ≥10 years of age with DIPG enrolled in the International DIPG Registry (IDIPGR)....
Motivation
Human viruses cause significant mortality, morbidity, and economic disruption worldwide. The human gene expression response to viral infection can yield important insights into the detrimental effects to the host. To date, hundreds of studies have performed genome-scale profiling of the effect of viral infection on human gene expression....
Background
DIPG generally occurs in young school-age children, although can occur in adolescents and young adults. The purpose of this study was to describe clinical, radiological, pathologic, and molecular characteristics in patients ≥10 years of age with DIPG enrolled in the International DIPG Registry (IDIPGR).
Methods
Patients ≥10 years of age...
Background
Crohn disease (CD), environmental enteric dysfunction (EED) and celiac disease are prevalent enteropathies linked to chronic gut inflammation. However, unlike celiac and Crohn that are prevalent in westernized countries, EED is seen in only in low- and middle-income countries of the developing world. Recent work has defined specific EED...
Background
Pediatric cardiomyopathy is a genetically heterogeneous disease with substantial morbidity and mortality. Current guidelines recommend genetic testing in children with hypertrophic, dilated, or restrictive cardiomyopathy, but practice variations exist. Robust data on clinical testing practices and diagnostic yield in children are lacking...
Background & Aims
Environmental enteric dysfunction (EED) limits the Sustainable Development Goals of improved childhood growth and survival. We applied mucosal genomics to advance our understanding of EED.
Methods
The Study of Environmental Enteropathy and Malnutrition (SEEM) followed 416 children from birth to 24 months in a rural district in Pa...
An adequate understanding of the relationships between radiographic and genomic features in diffuse intrinsic pontine glioma (DIPG) is essential, especially in the absence of universal biopsy, to further characterize the molecular heterogeneity of this disease and determine which patients are most likely to respond to biologically-driven therapies....
Background and aims:
Ileal strictures are the major indication for resective surgery in Crohn's disease (CD). We aimed to define ileal gene programs present at diagnosis linked with future stricturing behavior during five year follow-up, and to identify potential small molecules to reverse these gene signatures.
Methods:
Antimicrobial serologies...
Antibiotic-resistant superbug bacteria represent a global health problem with no imminent solutions. Here we demonstrate that the combination (termed AB569) of acidified nitrite (A-NO 2⁻ ) and Na 2 -EDTA (disodium ethylenediaminetetraacetic acid) inhibited all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing th...
Background
Stricturing complications account for substantial morbidity in Crohn’s disease (CD). We aimed to define ileal gene programmes present at diagnosis in paediatric CD associated with future stricturing behaviour (B2), and to identify potential small molecules to reverse these gene signatures.
Methods
Antimicrobial serologies and ileal gene...
In Neurofibromatosis type 1, NF1 gene mutations in Schwann cells (SC) drive benign plexiform neurofibroma (PNF), and no additional SC changes explain patient-to-patient variability in tumor number. Evidence from twin studies suggests that variable expressivity might be caused by unidentified modifier genes. Whole exome sequencing of SC and fibrobla...
To understand the molecular pathogenesis of human disease, precision analyses to define alterations within and between disease-associated cell populations are desperately needed. Single-cell genomics represents an ideal platform to enable the identification and comparison of normal and diseased transcriptional cell populations. We created cellHarmo...
CCR1, a BIM cell class associated protein, is not detected in hepatobiliary Linneg mononuclear cells.
Mice were treated with either PBS or IL-33 for 4 days, after which mononuclear cells were isolated from liver as described in Methods, stained with fluorescent antibodies, and analyzed by flow cytometry. Cells were gated as shown in Fig 7 to identi...
IL-33 promotes type 2 immunity, epithelial repair, and tissue fibrosis by activating group 2 innate lymphoid cells (ILC2). ILC2 lack all known surface markers of mature T, B, NK, and myeloid cell lineages (Linneg), express the IL-33 receptor ST2, and release type 2 cytokines which contribute to cholangiocyte proliferation and activation of hepatic...
Single cell RNA sequencing reveals 17 unique cell classes of CD45+Linneg mononuclear cells in the liver and extrahepatic bile duct.
Cluster analysis of the top 200 genes identifies 17 total CD45+Linneg cell classes in the liver and/or EHBD in PBS- or IL-33 treated Balb/c mice. Gene expression is shown as a color gradient from yellow (high expressio...
BD-ILC1 associated proteins are not detected in hepatobiliary Linneg mononuclear cells.
Mice were treated with either PBS or IL-33 for 4 days, after which mononuclear cells were isolated from liver and EHBD as described in Methods, stained with fluorescent antibodies, and analyzed by flow cytometry. Cells were gated as shown in Fig 6 to identify CD...
PBS and IL33 treated whole Liver and BD gene expression matrix TPM value.
(ZIP)
Total cell yield of liver and EHBD mononuclear cells for single-cell RNA sequencing.
(DOCX)
PBS and IL33 treated single cell gene expression matrix TPM value.
(ZIP)
Background
Molecular mechanisms driving disease course and response to initial therapy in ulcerative colitis (UC) are poorly understood. In the full PROTECT cohort, the strongest predictor of corticosteroids (CS)-free remission by Weeks 12 or 52 was Week 4 (WK4) remission. We used pre-treatment rectal biopsies in new-onset UC, and defined key pathw...
Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408...
Age-of-diagnosis associated variation in disease location and antimicrobial sero-reactivity has suggested fundamental differences in pediatric Crohn Disease (CD) pathogenesis. This variation may be related to pubertal peak incidence of ileal involvement and Peyer’s patches maturation, represented by IFNγ-expressing Th1 cells. However, direct mucosa...
BACKGROUND
Children <3 years with DIPG are reported to have a higher rate of long-term survival (LTS, overall survival (OS) ≥24 months). In patients <3 years with centrally confirmed DIPG, we compared clinical, radiological, histological and molecular characteristics between LTS versus short-term survivors (STS <24 months).
METHODS
Data from child...
INTRODUCTION
Patients ≥10 years of age with a DIPG are reported to have a higher rate of long-term survival (≥24 months). The purpose of this study was to compare clinical, radiological, pathological and molecular characteristics between patients ≥10 years old with DIPG who were long-term survivors (LTS) vs short-term survivors (STS) and assess bio...
Eosinophilic esophagitis (EoE) is an allergic inflammatory esophageal disorder with a complex underlying genetic etiology often associated with other comorbidities. Using whole-exome sequencing (WES) of 63 patients with EoE and 60 unaffected family members and family-based trio analysis, we sought to uncover rare coding variants. WES analysis ident...
Background
Long noncoding RNAs (lncRNA) are key regulators of gene transcription and many show tissue-specific expression. We previously defined a novel inflammatory and metabolic ileal gene signature in treatment-naive pediatric Crohn disease (CD). We now extend our analyses to include potential regulatory lncRNA.
Methods
Using RNAseq, we systema...
Background
Long non-coding RNAs (lncRNA) are key regulators of gene transcription and many show tissue-specific expression. We previously defined a novel inflammatory and metabolic ileal gene signature in treatment naïve paediatric Crohn disease (CD). We now extend our analyses to include potential regulatory lncRNA.
Methods
Using RNAseq of the Cr...
Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in “enhancerless” self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vecto...
Congenital heart disease (CHD) affects up to 1% of live births. Although a genetic etiology is indicated by an increased recurrence risk, sporadic occurrence suggests that CHD genetics is complex. Here, we show that hypoplastic left heart syndrome (HLHS), a severe CHD, is multigenic and genetically heterogeneous. Using mouse forward genetics, we re...
11514
Background: Contemporary chemotherapy-based regimens provide cures for most pediatric & AYA cancers. However, for patients with relapsed/refractory malignancies, outcomes are poor & imply a distinct and aggressive biology. Identifying common themes in the molecular architecture & oncogenic mechanisms in these patients is a critical priority f...
The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-rene...
‘LungGENS’, our previously developed web tool for mapping single-cell gene expression in the developing lung, has been well received by the pulmonary research community. With continued support from the ‘LungMAP’ consortium, we extended the scope of the LungGENS database to accommodate transcriptomics data from pulmonary tissues and cells from human...
To the editor:
Fanconi anemia (FA) results from defects in genes involved in the DNA repair pathway and is characterized by progressive bone marrow failure (BMF) and a high incidence of cancer.[1][1] Currently, hematopoietic stem cell transplant (HSCT) is the only curative option for the BMF. Due
The widespread availability of next-generation sequencing (NGS) has transformed our understanding of human genetic variation and its impact on human health. This chapter describes the most common DNA sequencing technologies available to research and clinical laboratories today, and resources for interpreting the functional impact of genetic variant...
The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genom...
Document S1. Supplemental Experimental Procedures, Supplemental Results, Figures S1–S6, and Tables S1–S9
The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genom...
Through inadvertent oversight of the authors, the paper [1] failed to acknowledge funding support from Genome Canada. The Acknowledgement section should include the text:
“This work was supported by the Canadian Centre for Computational Genomics (C3G), part of the Genome Innovation Network (GIN), funded by Genome Canada through Genome Quebec and O...
Introduction: Diffuse intrinsic pontine glioma (DIPG) and midline high-grade glioma (mHGG) are lethal childhood brain tumors. Spatial genomic heterogeneity has been well-described in adult HGG but has not been comprehensively characterized in pediatric HGG. We performed whole exome sequencing on 38-matched primary, contiguous, and metastatic tumor...
Background: Fanconi anemia (FA) is the most common cause of inherited bone marrow failure (BMF). Currently, the only curative option for the BMF in FA is an allogenic hematopoietic stem cell transplant (HSCT). However, due to the underlying DNA repair defect, FA patients poorly tolerate alkylating chemotherapy or irradiation based conditioning, whi...
The chromatin-binding DEK protein was recently reported to promote the growth of HPV+ and HPV- head and neck squamous cell carcinomas (HNSCCs). Relevant cellular and molecular mechanism(s) controlled by DEK in HNSCC remain poorly understood. While DEK is known to regulate specific transcriptional targets, global DEK-dependent gene networks in HNSCC...
During fetal development, nephrons of the metanephric kidney form from a mesenchynnal progenitor population that differentiates en masse before or shortly after birth. We explored intrinsic and extrinsic mechanisms controlling progenitor lifespan in a transplantation assay that allowed us to compare engraftment of old and young progenitors into the...
RhoA GTPase has been shown in vitro in cell lines and in vivo in non-mammalian organisms to regulate cell division, particularly during cytokinesis and abscission, when two daughter cells partition through coordinated actomyosin and microtubule machineries. In order to investigate the role of this GTPase in the rapidly proliferating mammalian eryth...
Single-gene mutations cause syndromes of intrahepatic cholestasis, but previous multi-gene mutation screening in children with idiopathic cholestasis failed to fulfill diagnostic criteria in about two-thirds of children. In adults with fibrosing cholestatic disease, heterozygous ABCB4 mutations were present in 34% of patients. Here, we hypothesized...
Safely achieving long-term engraftment of genetically modified hematopoietic stem cells (HSCs) that maintain therapeutic transgene expression is the benchmark for successful application of gene therapy for hemoglobinopathies. We used the pigtailed macaque HSC transplantation model to ascertain the long-term safety and stability of a γ-globin lentiv...
Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder associated with allergic hypersensitivity to food. We interrogated >1.5 million genetic variants in EoE cases of European ancestry and subsequently in a multi-site cohort with local and out-of-study control subjects. In addition to replicating association of the 5q22 locus (meta-anal...
Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, pa...
Eosinophilic esophagitis (EoE) is an allergic inflammatory disorder of the esophagus that is compounded by genetic predisposition and hypersensitivity to environmental antigens. Using high-density oligonucleotide expression chips, a disease-specific esophageal transcript signature was identified and was shown to be largely reversible with therapy....
We present a gene expression atlas of early mouse craniofacial development. Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin...
Objective
Our objective was to investigate the role of bile acids in hepatic steatosis reduction after vertical sleeve gastrectomy (VSG).
Design and Methods
High fat diet (HFD) induced obese C57Bl/6 mice were randomized to: VSG, Sham operation (Sham), Sham operation with pair feeding to VSG (Sham-PF), or non-surgical controls (Naïve). All mice wer...
111
Growth Factor Independence 1 (Gfi1) is a regulator of HSC maintenance, and lack of Gfi1 leads to myeloid progenitor accumulation and neutropenia. The Gfi1 transcription factor contains both a SNAG repressor domain, and a zinc-finger DNA-binding domain. A proline to alanine substitution at position 2 in the SNAG domain (P2A) blocks RCoR/Lysine S...
976
Introduction
Erythrocyte cytoskeleton disorders, a common cause of hereditary hemolytic anemia, consist of a genetically and phenotypically variable group of diseases that include hereditary spherocytosis (HS), elliptocytosis (HE), pyropoikilocytosis (HPP), and stomatocytosis (HSt) syndromes. The diagnosis is most commonly based on the morphol...
Preeclampsia occurs more frequently in women of African ancestry. The cause of this hypertensive complication is unclear, but placental oxidative stress may play a role. Because mitochondria are the major sites of oxidative phosphorylation, we hypothesized that placentas of preeclamptic pregnancies harbor mitochondrial DNA (mtDNA) mutations. Next-g...
13
Mutations in ELANE, GFI1, G6PC3, and HAX1 account for the genetic defects in many patients with severe congenital neutropenia (SCN). Here we utilized next generation sequencing technology to characterize genome-wide transcriptome activity and chromatin structure states associated with normal and SCN–affected hematopoietic precursor cells. We pro...
Despite its high heritability, a large fraction of individuals with schizophrenia do not have a family history of the disease (sporadic cases). Here we examined the possibility that rare de novo protein-altering mutations contribute to the genetic component of schizophrenia by sequencing the exomes of 53 sporadic cases, 22 unaffected controls and t...
Comparative retinal gene expression analysis in two rodent models of oxygen-induced retinopathy (OIR) was performed to identify the genes and pathways involved in retinal neovascularization.
Three independent experimental runs were conducted for each species, according to standard protocols for induction of OIR. Total retinal RNA was isolated at tw...
IVT pan-neural enriched genes. These worksheets contain pan-neural enriched data sets previously published in our lab [8]. This data has been updated from WS140 to WS170 to reflect changes in C. elegans annotation.
Full list of GFP reporter lines generated for figure 8. List strain names and full expression patterns of GFP reporter lines built for this analysis.
WT-Pico pan-neural enriched and depleted genes. These worksheets list the pan-neural enriched genes from WT-Pico and also genes depleted in the WT-Pico data set relative to reference samples.
A comparison of transcripts enriched in IVT and WT-Pico pan-neural data sets. The three worksheets contained in this file list genes found in the IVT-only data set, the WT-Pico-only data set, or genes enriched in both the IVT and WT-Pico data sets.
Citations
... To visualize genomic regions of interest we used Bacterial Artificial Chromosome (BAC) clones RP11-990E14 (hg38 -chr3:169,692,858-169,870,368 mapping to Telomerase RNA Component TERC), and RP11-662P23 (hg38 -chr5:56,420,151-56,608,998 mapping to the specific region of HPV16 integration on chromosome 5 in Tumor 4). In addition to human BAC clones we also used a plasmid containing the entire genomic sequence of HPV16 as reported in 100,101 . BAC DNA and HPV16 plasmid DNA was isolated and labeled by nick translation as we previously described 102,103 using the following dUTPs from Dyomics (Jena, GE, USA): DY-495-dUTP (within the green spectrum to visualize RP11-662P23); DY-530-aadUTP (within the gold spectrum to visualize RP11-990E14); and DY-590-dUTP (within the red spectrum to visualize HPV16). ...
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... In module 2, the expressions of genes involved in ribosome biogenesis (such as RPL5, RPL14, RPL21, RPL10 and NPM1, etc.) were lower in MDS/ sAML (supplemental Fig. S2F). In module 3, the results indicated that RUNX1 [25,26], ZBTB16 [27], GATA2 [28,29] and MEIS1 [30] which involved in the myeloid cell differentiation and the pathogenesis of acute leukemia showed higher levels of expression in cells from the MDS across differentiation (Fig. 2F). Moreover, the expression of genes involved in macrophage and granulocyte differentiation (PRKX [31], RELB [32] and CSF3R [33]), cell proliferation (PIP4K2A [34]) and anti-apoptotic regulator B cell lymphoma 2 (BCL2 [35]) were also higher in MDS/ sAML (Fig. 2F). ...
... Estudos recentes têm destacado a existência de subtipos moleculares distintos dentro dos GPID, cada um com perfis genéticos e biológicos únicos que influenciam a progressão do tumor e a resposta aos tratamentos. A caracterização desses subtipos moleculares é essencial para a identificação de biomarcadores preditivos e o desenvolvimento de estratégias terapêuticas mais direcionadas e eficazes para cada perfil tumoral específico (Erker et al., 2022). ...
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... uen et al (14) reported that VAV3 knockdown could regulate the cell cycle and metastasis-related molecules via inhibition of the PI3K-AKT signaling pathway in colorectal cancer cells. Recently, Nayak (26) reported that nuclear VAV3 served an important role in B-cell lymphoblastic leukemogenesis through regulation of nuclear Bmi1 phosphorylation and polycomb repression complex-1 (PRC1) activity. the role of BMI 1 in the regulation of glioblastoma migration, invasion and stem cell renewal has been reported by numerous previous studies (27)(28)(29)(30). ...
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... Our aim was to leverage a publicly available dataset of single-cell RNA seq (scRNAseq) of EoE patients [18] to identify fibroblast sub-populations, and related transcriptomes, disease status-specific pathways and cell-cell interactions in active and remission states. Active EoE was defined by histologic findings of ≥15 eosinophils per high-power field in esophageal biopsies and clinical symptoms. ...
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... Finally, it is important to remark that most of deleterious or potentially deleterious variants were identified in the TTN gene, the main gene associated with G-DCM in adult and pediatric population. Re-evaluation was also higher in TNNT2, RBM20, MYH7, and LMNA, in concordance with reports related to aggressive phenotypes, especially in the pediatric population [22,23]. Therefore, if a variant is re-analyzed in a pediatric patient, it should be also taken into account. ...
... The incidence is estimated at 0.54 cases per 1 million person-years overall and 2.32 cases per 1 million person-years in individuals aged ≤ 20 years, without predilection for gender. They represent 10-15% of all pediatric brain tumors and 75% of all pediatric tumors of the brainstem [5]. ...
... This finding corroborates reports from previous registry and consortium studies. 20,21 Furthermore, the overall yield of genetic testing was also high, exceeding 60% in HCM, ARVC, and RCM. Dilated cardiomyopathy had the lowest overall yield of genetic testing (41%), but this was higher for those aged 10-18 years (59.1%). ...
... Nonetheless, correlations between the absolute abundances of members of the core taxa and gut inflammation were observed when we considered levels of expression of 13 genes in an adjacent duodenal biopsy. These genes were previously identified as being expressed at significantly higher levels in biopsies adjacent to the one selected here for histopatho logic analysis compared to their expression in duodenal biopsies obtained from 2-yearold USA children who had undergone EGD for Celiac disease and had no histopathologic evidence of EED (15). The absolute abundance of Granulicatella adiacens was significantly positively correlated with levels of expression of (i) dual oxidase type 2 (DUOX2; Pearson r = 0.32; P = 0.05), an enzyme whose increased expression is associated with epithelial barrier dysfunction and production of cytokines/chemokines, and (ii) serum amyloid A2 (SAA2; r = 0.32; P = 0.05), an acute phase protein. ...
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... 8 MRI features have been used to predict H3K27M mutation status 9 and correlate with patient prognosis . [10][11][12][13][14][15] However, the features utilized in these studies were either simple without high-dimensional image features 10,11,[13][14][15] or only based on texture analysis. 12 The statistical analysis that most of these studies relied on tend to identify inconsistent and inconclusive biomarkers among different studies and datasets. ...
