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1.
Genet Med ; 26(5): 101075, 2024 05.
Article in English | MEDLINE | ID: mdl-38251460

ABSTRACT

PURPOSE: This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS: The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS: Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION: Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.


Subject(s)
DNA Methylation , Genetic Testing , Rare Diseases , Humans , DNA Methylation/genetics , Rare Diseases/genetics , Rare Diseases/diagnosis , Genetic Testing/standards , Genetic Testing/methods , Female , Promoter Regions, Genetic/genetics , Male , DNA Copy Number Variations/genetics , Child , Adult , Child, Preschool , Genomic Imprinting/genetics
2.
J Pediatr Gastroenterol Nutr ; 77(4): 519-526, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37501225

ABSTRACT

OBJECTIVES: Outpatient inflammatory bowel disease (IBD) care shifted from office visits (OVs) to a model with integrated telemedicine during the 2020 COVID-19 pandemic. We describe the impact of this shift on delivery of pediatric IBD care. METHODS: We collected electronic medical record data from office and telemedicine visits for pediatric patients with IBD at a single center from April 2019 to December 2020. We compared visit volume, duration, and test ordering between 2019 and 2020, and between OV and telemedicine, and assessed for differences in telemedicine adoption by sociodemographic factors. RESULTS: Visit volume was maintained between 2019 and 2020. Median overall appointment time was shorter for telemedicine versus OV [46 (interquartile range, IQR 35-72) vs 62 (IQR 51-80) minutes; P < 0.001] with no significant difference in time spent with provider [28 (IQR 21-41) vs OV 30 (IQR 24-39) minutes; P = 0.08]. Accounting for drive time, telemedicine visits were 2.6 times shorter than office visits in 2020 ( P < 0.001). In univariate analyses, there was no difference in telemedicine utilization by race or gender. Variables significantly associated with telemedicine were older age, English as primary language, being non-Hispanic, commercial insurance, living in an area of very high opportunity, and having a longer drive time to the office ( P < 0.05 for all comparisons). In multivariate analyses, visits among patients with commercial insurance were significantly more likely to be conducted via telemedicine ( P = 0.02). Among those with a telemedicine visit, multivariate analyses demonstrated multiracial patients were significantly more likely to have video visits (vs audio-only; P = 0.02), while patients with public insurance, no or missing insurance, and whose primary language was Arabic were significantly less likely to have video visits ( P < 0.05 for all comparisons). CONCLUSIONS: Integrated telemedicine allowed for continued delivery of pediatric IBD care and significantly decreased appointment time. While telemedicine may improve access for those who live further from the office, concerns remain about the introduction of disparities.


Subject(s)
COVID-19 , Inflammatory Bowel Diseases , Telemedicine , Humans , Child , COVID-19/epidemiology , Pandemics , Ambulatory Care , Inflammatory Bowel Diseases/therapy
3.
J Pediatr Gastroenterol Nutr ; 76(5): 684-694, 2023 05 01.
Article in English | MEDLINE | ID: mdl-36976575

ABSTRACT

Telehealth (TH) broadly encompasses remote activities of clinical care (telemedicine), provider and patient education, and general health services. The use of synchronous video for TH first occurred in 1964 and then catapulted to the forefront in 2020 during the coronavirus disease 2019 public health emergency. Due to the sudden need for increased TH utilization by nearly all health care providers at that time, TH became essential to clinical practice. However, its sustainable future is unclear in part given that best practices for TH in pediatric gastroenterology (GI), hepatology, and nutrition remain undefined and non-standardized. Key areas for review include historical perspective, general and subspeciality usage, health care disparities, quality of care and the provider-patient interaction, logistics and operations, licensure and liability, reimbursement and insurance coverage, research and quality improvement (QI) priorities, and future use of TH in pediatric GI with a call for advocacy. This position paper from the Telehealth Special Interest Group of North American Society of Gastroenterology, Hepatology and Nutrition provides recommendations for pediatric GI-focused TH best practices, reviews areas for research and QI growth, and presents advocacy opportunities.


Subject(s)
COVID-19 , Gastroenterology , Telemedicine , Child , Humans , Gastroenterology/education , Societies , North America , Societies, Medical
4.
J Pediatr Gastroenterol Nutr ; 77(3): 319-326, 2023 09 01.
Article in English | MEDLINE | ID: mdl-37079871

ABSTRACT

OBJECTIVES: The purpose of our study is to compare in-person and telehealth pediatric care ambulatory visits for gastroenterology (GI) at the Nemours Children's Health System in the Delaware Valley (NCH-DV) based on geospatial, demographic, socioeconomic, and digital disparities. METHODS: Characteristics of 26,565 patient encounters from January 2019 to December 2020 were analyzed. U.S. Census Bureau geographic identifiers were assigned to each participant and aligned with the American Community Survey (2015-2019) socioeconomic and digital outcomes. Reported odds ratios (OR) are telehealth encounter/in-person encounter. RESULTS: GI telehealth usage increased 145-fold in 2020 compared to 2019 for NCH-DV. Comparing telehealth to in-person usage in 2020 revealed that GI patients who required a language translator were 2.2-fold less likely to choose telehealth [individual level adjusted OR (I-OR a ) [95% confidence interval, CI], 0.45 [0.30-0.66], P < 0.001]. Individuals of Hispanic ethnicity or non-Hispanic Black or African American race are 1.3-1.4-fold less likely to utilize telehealth than non-Hispanic Whites (I-OR a [95% CI], 0.73 [0.59-0.89], P = 0.002 and 0.76 [0.60-0.95], P = 0.02, respectively). Households in census block groups (BG) that are more likely to utilize telehealth: have broadband access (BG-OR = 2.51 [1.22-5.31], P = 0.014); are above the poverty level (BG-OR = 4.44 [2.00-10.24], P < 0.001); own their own home (BG-OR = 1.79 [1.25-2.60], P = 0.002); and have a bachelor's degree or higher (BG-OR = 6.55 [3.25-13.80], P < 0.001). CONCLUSIONS: Our study is the largest reported pediatric GI telehealth experience in North America that describes racial, ethnic, socioeconomic, and digital inequities. Advocacy and research for pediatric GI focused on telehealth equity and inclusion is urgently needed.


Subject(s)
Gastroenterology , Healthcare Disparities , Telemedicine , Child , Humans , Ethnicity , Hispanic or Latino , Poverty , Black or African American , White
5.
Genet Med ; 24(4): 905-914, 2022 04.
Article in English | MEDLINE | ID: mdl-35027293

ABSTRACT

PURPOSE: Gabriele-de Vries syndrome (GADEVS) is a rare genetic disorder characterized by developmental delay and/or intellectual disability, hypotonia, feeding difficulties, and distinct facial features. To refine the phenotype and to better understand the molecular basis of the syndrome, we analyzed clinical data and performed genome-wide DNA methylation analysis of a series of individuals carrying a YY1 variant. METHODS: Clinical data were collected for 13 individuals not yet reported through an international call for collaboration. DNA was collected for 11 of these individuals and 2 previously reported individuals in an attempt to delineate a specific DNA methylation signature in GADEVS. RESULTS: Phenotype in most individuals overlapped with the previously described features. We described 1 individual with atypical phenotype, heterozygous for a missense variant in a domain usually not involved in individuals with YY1 pathogenic missense variations. We also described a specific peripheral blood DNA methylation profile associated with YY1 variants. CONCLUSION: We reported a distinct DNA methylation episignature in GADEVS. We expanded the clinical profile of GADEVS to include thin/sparse hair and cryptorchidism. We also highlighted the utility of DNA methylation episignature analysis for classification of variants of unknown clinical significance.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , DNA Methylation/genetics , Genome , Humans , Intellectual Disability/genetics , Intellectual Disability/pathology , Male , Neurodevelopmental Disorders/genetics , Phenotype , Syndrome
6.
Am J Med Genet A ; 188(7): 2217-2225, 2022 07.
Article in English | MEDLINE | ID: mdl-35384273

ABSTRACT

Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.


Subject(s)
Abnormalities, Multiple , Heart Defects, Congenital , Hematologic Diseases , Vestibular Diseases , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , DNA Methylation/genetics , Face/abnormalities , Heart Defects, Congenital/diagnosis , Heart Defects, Congenital/genetics , Hematologic Diseases/diagnosis , Hematologic Diseases/genetics , Humans , Mutation , Vestibular Diseases/diagnosis , Vestibular Diseases/genetics
7.
Am J Med Genet A ; 188(5): 1550-1555, 2022 05.
Article in English | MEDLINE | ID: mdl-35040536

ABSTRACT

Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.


Subject(s)
Abnormalities, Multiple , Hematologic Diseases , Vestibular Diseases , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Abnormalities, Multiple/pathology , Face/abnormalities , Hematologic Diseases/genetics , Humans , Mutation , Students , Vestibular Diseases/genetics
8.
Genet Med ; 23(6): 1065-1074, 2021 06.
Article in English | MEDLINE | ID: mdl-33547396

ABSTRACT

PURPOSE: We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. METHODS: We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). RESULTS: Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. CONCLUSION: This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.


Subject(s)
DNA Methylation , Epigenomics , Canada , Europe , Humans , Syndrome
9.
NMR Biomed ; 34(7): e4514, 2021 07.
Article in English | MEDLINE | ID: mdl-33939204

ABSTRACT

Dynamic nuclear polarization (DNP) of 13 C-labeled substrates enables the use of magnetic resonance imaging (MRI) to monitor specific enzymatic reactions in tumors and offers an opportunity to investigate these differences. In this study, DNP-MRI chemical shift imaging with hyperpolarized [1-13 C] pyruvate was conducted to evaluate the metabolic change in glycolytic profiles after radiation of two glioma stem-like cell-derived gliomas (GBMJ1 and NSC11) and an adherent human glioblastoma cell line (U251) in an orthotopic xenograft mouse model. The DNP-MRI showed an increase in Lac/Pyr at 6 and 16 h after irradiation (18% ± 4% and 14% ± 3%, respectively; mean ± SEM) compared with unirradiated controls in GBMJ1 tumors, whereas no significant change was observed in U251 and NSC11 tumors. Metabolomic analysis likewise showed a significant increase in lactate in GBMJ1 tumors at 16 h. An immunoblot assay showed upregulation of lactate dehydrogenase-A expression in GBMJ1 following radiation exposure, consistent with DNP-MRI and metabolomic analysis. In conclusion, our preclinical study demonstrates that the DNP-MRI technique has the potential to be a powerful diagnostic method with which to evaluate GBM tumor metabolism before and after radiation in the clinical setting.


Subject(s)
Carbon-13 Magnetic Resonance Spectroscopy , Glioblastoma/metabolism , Glioblastoma/radiotherapy , Animals , Cell Line, Tumor , Glioblastoma/diagnostic imaging , Humans , Lactate Dehydrogenase 5/metabolism , Lactic Acid/metabolism , Magnetic Resonance Imaging , Metabolomics , Mice, Nude , Pyruvic Acid/metabolism
10.
Med Care ; 59(12): 1067-1074, 2021 12 01.
Article in English | MEDLINE | ID: mdl-34593709

ABSTRACT

BACKGROUND: The increase in telehealth in response to the coronavirus disease 2019 pandemic highlights the need to understand patients' capacity to utilize this care modality. Patient portals are a tool whose use requires similar resources and skills as those required for telehealth. Patients' capacity to use patient portals may therefore provide insight regarding patients' readiness and capacity to use telehealth. OBJECTIVE: The aim of this study was to examine factors related to patients' capacity to use a patient portal and test the impact of these factors on patients' portal use. RESEARCH DESIGN AND SUBJECTS: Using data from a large-scale pragmatic randomized controlled trial of patient portal use, 1081 hospitalized patients responded to survey items that were then mapped onto the 4 dimensions of the Engagement Capacity Framework: self-efficacy, resources, willingness, and capabilities. MEASURES: The outcome variable was frequency of outpatient portal use. We evaluated associations between Engagement Capacity Framework dimensions and patient portal use, using regression analyses. RESULTS: Patients with fewer resources, fewer capabilities, lower willingness, and lower overall capacity to use patient portals used the portal less; in contrast, those with lower perceived self-efficacy used the portal more. CONCLUSIONS: Our findings highlight differences in patients' capacity to use patient portals, which provide an initial understanding of factors that may influence the use of telehealth and offer important guidance in efforts to support patients' telehealth use. Offering patients training tailored to the use of telehealth tools may be particularly beneficial.


Subject(s)
Patient Participation/psychology , Patient Portals , Telemedicine , Adult , Aged , Female , Humans , Male , Middle Aged , Models, Psychological , Patient Participation/statistics & numerical data , Self Efficacy , Self-Assessment , Surveys and Questionnaires , United States
11.
Epilepsia ; 62(7): e103-e109, 2021 07.
Article in English | MEDLINE | ID: mdl-34041744

ABSTRACT

CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.


Subject(s)
Developmental Disabilities/genetics , Epilepsy, Generalized/genetics , Adolescent , Adult , Age of Onset , Child , Child, Preschool , Developmental Disabilities/physiopathology , Epilepsies, Myoclonic/diagnosis , Epilepsies, Myoclonic/etiology , Epilepsies, Myoclonic/genetics , Epilepsy, Generalized/diagnosis , Epilepsy, Generalized/etiology , Exome/genetics , Female , Genetic Variation , Humans , Infant , Intellectual Disability/etiology , Intellectual Disability/genetics , Male , Mutation/genetics , Phenotype , Status Epilepticus/diagnosis , Status Epilepticus/etiology , Status Epilepticus/genetics , Young Adult
12.
J Pediatr Gastroenterol Nutr ; 72(5): 700-703, 2021 05 01.
Article in English | MEDLINE | ID: mdl-33720090

ABSTRACT

ABSTRACT: The information blocking (IB) prohibition component of the 21st Century CURES Act (21CCA) comes into effect April 5, 2021, which gives patients and their families near-instant access to almost all clinical notes, lab results, and health data. Exceptions to IB prohibition include risk of harm and patient privacy, but violations can be punished by a fine of up to $1,000,000.00. A committee of pediatric gastroenterologists reviewed the 21CCA regulation and compared local practice policies. Pediatric practitioners need to understand how age will affect local information release policies and to know which note types are released, paying special consideration to trainee notes and confidential information. Extraneous detail should be removed from notes, emotional labeling be avoided, and objective statements be made when referring to the care of other providers. Awareness of the 21CCA provides pediatric gastroenterologists with the opportunity to adapt their medical documentation practices to accommodate the new law.


Subject(s)
Gastroenterology , Child , Humans
13.
J Pediatr Gastroenterol Nutr ; 73(1): 42-47, 2021 07 01.
Article in English | MEDLINE | ID: mdl-33872292

ABSTRACT

OBJECTIVE: Use of telemedicine in pediatric gastroenterology has increased dramatically in response to the coronavirus disease 2019 (COVID-19) pandemic. The goal of this study was to systematically assess the usability of telemedicine in the field of pediatric gastroenterology. METHODS: The previously validated Telehealth Usability Questionnaire was distributed to physician pediatric gastroenterologist members of North American Society for Pediatric Gastroenterology Hepatology and Nutrition. Physician demographic and practice characteristics were collected. Data were analyzed using descriptive, linear mixed-effect, and ordinary least squares regression methods. RESULTS: One hundred sixty pediatric gastroenterologists completed the survey. The majority were from academic practice (77%) with experience ranging from trainee (11%) to over 20 years of clinical practice (34%). Most (82%) had no experience with telemedicine before the pandemic. The average usability score (scale 1-5) was 3.87 (σ = 0.67) with the highest domain in the usefulness of telemedicine (µâ€Š= 4.29, σ = 0.69) and physician satisfaction (µâ€Š= 4.13, σ = 0.79) and the lowest domain in reliability (µâ€Š= 3.02, σ = 0.87). When comparing trainees to attending physicians, trainees' responses were almost one point lower on satisfaction with telemedicine (trainee effect = -0.97, Bonferroni adjusted 95% confidence interval = -1.71 to -0.23). CONCLUSION: Pediatric gastroenterologists who responded to the survey reported that the technology for telemedicine was usable, but trainees indicated lower levels of satisfaction when compared to attending physicians. Future study is needed to better understand user needs and the impacts of telemedicine on providers with different levels are experience to inform efforts to promote implementation and use of telemedicine beyond the pandemic.


Subject(s)
COVID-19 , Physicians , Telemedicine , Child , Humans , Reproducibility of Results , SARS-CoV-2
14.
Hum Mutat ; 41(1): 150-168, 2020 01.
Article in English | MEDLINE | ID: mdl-31448840

ABSTRACT

Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.


Subject(s)
Chromosome Deletion , Chromosomes, Human, X , Genetic Association Studies , Genetic Predisposition to Disease , Nervous System Diseases/diagnosis , Nervous System Diseases/genetics , Quantitative Trait, Heritable , Child , Child, Preschool , Chromosome Breakpoints , Chromosome Mapping , Comparative Genomic Hybridization , Female , Genetic Association Studies/methods , Humans , Male , Pedigree , Phenotype , Repetitive Sequences, Nucleic Acid , Sex Factors , Syndrome , X Chromosome Inactivation
15.
J Hum Genet ; 64(6): 561-572, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30858506

ABSTRACT

Variants have been identified in the embryonic ectoderm development (EED) gene in seven patients with syndromic overgrowth similar to that observed in Weaver syndrome. Here, we present three additional patients with missense variants in the EED gene. All the missense variants reported to date (including the three presented here) have localized to one of seven WD40 domains of the EED protein, which are necessary for interaction with enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2). In addition, among the seven patients reported in the literature and the three new patients presented here, all of the reported pathogenic variants except one occurred at one of four amino acid residues in the EED protein. The recurrence of pathogenic variation at these loci suggests that these residues are functionally important (mutation hotspots). In silico modeling and calculations of the free energy changes resulting from these variants suggested that they not only destabilize the EED protein structure but also adversely affect interactions between EED, EZH2, and/or H3K27me3. These cases help demonstrate the mechanism(s) by which apparently deleterious variants in the EED gene might cause overgrowth and lend further support that amino acid residues in the WD40 domain region may be mutation hotspots.


Subject(s)
Abnormalities, Multiple/genetics , Congenital Hypothyroidism/genetics , Craniofacial Abnormalities/genetics , Enhancer of Zeste Homolog 2 Protein/genetics , Hand Deformities, Congenital/genetics , Histone-Lysine N-Methyltransferase/genetics , Polycomb Repressive Complex 2/genetics , Abnormalities, Multiple/etiology , Abnormalities, Multiple/physiopathology , Adolescent , Child , Computer Simulation , Congenital Hypothyroidism/etiology , Congenital Hypothyroidism/physiopathology , Craniofacial Abnormalities/etiology , Craniofacial Abnormalities/physiopathology , Enhancer of Zeste Homolog 2 Protein/chemistry , Female , Hand Deformities, Congenital/etiology , Hand Deformities, Congenital/physiopathology , Histone-Lysine N-Methyltransferase/chemistry , Humans , Male , Molecular Dynamics Simulation , Mutation Rate , Mutation, Missense/genetics , Polycomb Repressive Complex 2/chemistry , Protein Conformation , WD40 Repeats/genetics , Exome Sequencing
17.
Hum Mutat ; 39(11): 1485-1493, 2018 11.
Article in English | MEDLINE | ID: mdl-30311384

ABSTRACT

The RASopathies are a complex group of conditions regarding phenotype and genetic etiology. The ClinGen RASopathy Expert Panel (RAS EP) assessed published and other publicly available evidence supporting the association of 19 genes with RASopathy conditions. Using the semiquantitative literature curation method developed by the ClinGen Gene Curation Working Group, evidence for each gene was curated and scored for Noonan syndrome (NS), Costello syndrome, cardiofaciocutaneous syndrome, NS with multiple lentigines, and Noonan-like syndrome with loose anagen hair. The curated evidence supporting each gene-disease relationship was then discussed and approved by the ClinGen RASopathy Expert Panel. Each association's strength was classified as definitive, strong, moderate, limited, disputed, or no evidence. Eleven genes were classified as definitively associated with at least one RASopathy condition. Two genes classified as strong for association with at least one RASopathy condition while one gene was moderate and three were limited. The RAS EP also disputed the association of two genes for all RASopathy conditions. Overall, our results provide a greater understanding of the different gene-disease relationships within the RASopathies and can help in guiding and directing clinicians, patients, and researchers who are identifying variants in individuals with a suspected RASopathy.


Subject(s)
ras Proteins/metabolism , Costello Syndrome/genetics , Ectodermal Dysplasia/genetics , Facies , Failure to Thrive/genetics , Heart Defects, Congenital/genetics , Humans , MAP Kinase Signaling System/genetics , MAP Kinase Signaling System/physiology , Mutation/genetics , Noonan Syndrome/genetics , ras Proteins/genetics
18.
Genet Med ; 20(11): 1334-1345, 2018 11.
Article in English | MEDLINE | ID: mdl-29493581

ABSTRACT

PURPOSE: Standardized and accurate variant assessment is essential for effective medical care. To that end, Clinical Genome (ClinGen) Resource clinical domain working groups (CDWGs) are systematically reviewing disease-associated genes for sufficient evidence to support disease causality and creating disease-specific specifications of American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines for consistent and accurate variant classification. METHODS: The ClinGen RASopathy CDWG established an expert panel to curate gene information and generate gene- and disease-specific specifications to ACMG-AMP variant classification framework. These specifications were tested by classifying 37 exemplar pathogenic variants plus an additional 66 variants in ClinVar distributed across nine RASopathy genes. RESULTS: RASopathy-related specifications were applied to 16 ACMG-AMP criteria, with 5 also having adjustable strength with availability of additional evidence. Another 5 criteria were deemed not applicable. Key adjustments to minor allele frequency thresholds, multiple de novo occurrence events and/or segregation, and strength adjustments impacted 60% of variant classifications. Unpublished case-level data from participating laboratories impacted 45% of classifications supporting the need for data sharing. CONCLUSION: RAS-specific ACMG-AMP specifications optimized the utility of available clinical evidence and Ras/MAPK pathway-specific characteristics to consistently classify RASopathy-associated variants. These specifications highlight how grouping genes by shared features promotes rapid multigenic variant assessment without sacrificing specificity and accuracy.


Subject(s)
Genetic Testing/methods , Genome, Human/genetics , Genomics/methods , High-Throughput Nucleotide Sequencing , Gene Frequency , Genetic Variation , Humans , Information Dissemination , Mutation , Software , United States
19.
J Hum Genet ; 63(3): 349-356, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29279609

ABSTRACT

Cornelia de Lange syndrome (CdLS) is a rare neurodevelopmental syndrome for which mutations in five causative genes that encode (SMC1A, SMC3, RAD21) or regulate (NIPBL, HDAC8) the cohesin complex, account for ~70% of cases. Herein we report on four female Subjects who were found to carry novel intragenic deletions in HDAC8. In one case, the deletion was found in mosaic state and it was determined to be present in ~38% of blood lymphocytes and in nearly all cells of a buccal sample. All deletions, for which parental blood samples were available, were shown to have arisen de novo. X-chromosome inactivation studies demonstrated marked skewing, suggesting strong selection against the mutated HDAC8 allele. Based on an investigation of the deletion breakpoints, we hypothesize that microhomology-mediated replicative mechanisms may be implicated in the formation of some of these rearrangements. This study broadens the mutational spectrum of HDAC8, provides the first description of a causative HDAC8 somatic mutation and increases the knowledge on possible mutational mechanisms underlying copy number variations in HDAC8. Moreover our findings highlight the clinical utility of considering copy number analysis in HDAC8 as well as the analysis on DNA from more than one tissue as an indispensable part of the routine molecular diagnosis of individuals with CdLS or CdLS-overlapping features.


Subject(s)
De Lange Syndrome/diagnosis , De Lange Syndrome/genetics , Genetic Association Studies , Histone Deacetylases/genetics , Phenotype , Repressor Proteins/genetics , Sequence Deletion , Base Sequence , Child , Child, Preschool , Chromosome Breakpoints , Comparative Genomic Hybridization , DNA Copy Number Variations , Exons , Facies , Female , Gene Duplication , Humans , Sequence Analysis, DNA , X Chromosome Inactivation
20.
HPB (Oxford) ; 20(9): 834-840, 2018 09.
Article in English | MEDLINE | ID: mdl-30060910

ABSTRACT

BACKGROUND: In a single trial, perioperative pasireotide demonstrated reduction in postoperative pancreatic fistula (POPF) following pancreatectomy, yet recent studies question the efficacy of this drug. METHODS: All patients who underwent pancreatic resection between January 2014 and August 2017 at a single institution were prospectively followed. Starting in February 2016, pasireotide was administered to all pancreatectomies. Pancreaticoduodenectomy (PD) patients were additionally risk-stratified using a validated clinical risk score. The primary endpoint was the development of clinically relevant POPF (CR-POPF), and was compared between patients who received pasireotide and controls. RESULTS: Of 116 patients, 87 patients (75%) underwent PD, and 43 patients (37.1%) received pasireotide. CR-POPF occurred in 28.4% patients. The use of pasireotide was not associated with reduced CR-POPF among the total cohort (25.6% vs. 30.1%, P = 0.599), distal pancreatectomy patients (P = 0.339), PD (P = 0.274), or PD patients with elevated risk scores (P = 0.073). Pasireotide did not decrease hospital length of stay, use of parenteral nutrition, delayed gastric emptying, surgical site wound infection, or readmission rate. CONCLUSION: Use of pasireotide after pancreatic resection does not decrease CR-POPF, nor is it associated with reduced length of stay or postoperative complications. A multi-center randomized trial is warranted to study its true effect on outcomes after pancreatectomy.


Subject(s)
Gastrointestinal Agents/therapeutic use , Pancreatectomy/adverse effects , Pancreatic Fistula/prevention & control , Pancreaticoduodenectomy/adverse effects , Somatostatin/analogs & derivatives , Adolescent , Adult , Aged , Aged, 80 and over , Databases, Factual , Female , Humans , Length of Stay , Los Angeles , Male , Middle Aged , Pancreatic Fistula/diagnosis , Pancreatic Fistula/etiology , Patient Readmission , Prospective Studies , Risk Factors , Somatostatin/therapeutic use , Time Factors , Treatment Outcome , Young Adult
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