29 results on '"Jenny Thies"'
Search Results
2. The low excretor phenotype of glutaric acidemia type I is a source of false negative newborn screening results and challenging diagnoses
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Adam J. Guenzel, Patricia L. Hall, Anna I. Scott, Christina Lam, Irene J. Chang, Jenny Thies, Carlos R. Ferreira, Pavel Pichurin, William Laxen, Kimiyo Raymond, Dimitar K. Gavrilov, Devin Oglesbee, Piero Rinaldo, Dietrich Matern, and Silvia Tortorelli
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glutaric acidemia ,glutarylcarnitine ,glutaryl‐CoA dehydrogenase ,low excretor ,newborn screening ,Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 ,Genetics ,QH426-470 - Abstract
Abstract Background Glutaric acidemia type I (GA1) is an organic acidemia that is often unrecognized in the newborn period until patients suffer an acute encephalopathic crisis, which can be mistaken for nonaccidental trauma. Presymptomatic identification of GA1 patients is possible by newborn screening (NBS). However, the biochemical “low‐excretor” (LE) phenotype with nearly normal levels of disease metabolites can be overlooked, which may result in untreated disease and irreversible neurological sequelae. The LE phenotype is also a potential source of false negative (FN) NBS results that merits further investigation. Methods Samples from six LE GA1 patients were analyzed by biochemical and molecular methods and newborn screen outcomes were retrospectively investigated. Results Five LE GA1 patients were identified that had normal NBS results and three of these presented clinically with GA1 symptoms. One additional symptomatic patient was identified who did not undergo screening. Semiquantitative urine organic acid analysis was consistent with a GA1 diagnosis in two (33%) of the six patients, while plasma glutarylcarnitine was elevated in four (67%) of the six and urine glutarylcarnitine was elevated in four (80%) of five patients. Five GCDH variants were identified in these patients; three of which have not been previously linked to the biochemical LE phenotype. Conclusions The data presented here raise awareness of potential FN NBS results for LE GA1 patients. The LE phenotype is not protective against adverse clinical outcomes, and the possibility of FN NBS results calls for high vigilance amongst clinicians, even in the setting of a normal NBS result.
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- 2021
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3. p.P1379S, a benign variant with reduced ATP7B protein level in Wilson Disease
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Fan Yi, Sheri A. Poskanzer, Candace T. Myers, Jenny Thies, Christopher J. Collins, Remwilyn Dayuha, Phi Duong, Roderick Houwen, and Si Houn Hahn
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ATP7B quantification ,Benign variant ,immuno‐SRM ,newborn screening ,p.P1379S ,Wilson disease ,Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 ,Genetics ,QH426-470 - Abstract
Abstract Background Wilson disease (WD) is an autosomal recessive disorder of copper transport caused by inherited defects in the ATP7B gene and results in toxic accumulation of copper in various organs. We previously reported a family with three consecutive generations affected by WD that carries the variant, p.P1379S, which was classified at the time as likely pathogenic. However, recent investigations of the p.P1379S variant indicate a possible conflict of interpretations regarding its pathogenicity. This led us to explore the quantification of ATP7B in dried blood spots (DBS) using a surrogate peptide to study the effects of the p.P1379S variant on ATP7B concentrations in two unrelated families with the common p.P1379S variant. Methods and results ATP7B was quantified using the peptide immunoaffinity enrichment coupled with selected reaction monitoring mass spectrometry (immuno‐SRM) method which utilizes antibody‐mediated peptide capture from DBS. Two patients affected with WD had undetectable ATP7B level while four compound heterozygous children with one known pathogenic variant and the p.P1379S had significantly reduced ATP7B levels. Of note, all four children remain asymptomatic without abnormal laboratory consequences despite being untreated for WD. Conclusion These two families demonstrated that p.P1379S, when compounded with two known pathogenic variants, resulted in significantly reduced protein levels but retained enough function to maintain normal copper homeostasis. This implies that p.P1379S is benign in nature. A better understanding of the nature and consequences of variants in WD will help in informing patient care and avoiding unnecessary treatments.
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- 2020
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4. The co‐occurrence of Wilson disease and X‐linked agammaglobulinemia in one family highlights the promising diagnostic potential of proteolytic analysis
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Sheri A. Poskanzer, Jenny Thies, Christopher J. Collins, Candace T. Myers, Remwilyn Dayuha, Phi Duong, Fan Yi, Irene J. Chang, Hans D. Ochs, Troy R. Torgerson, and Si Houn Hahn
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co‐occurrence ,immuno‐SRM ,newborn screening ,Wilson disease ,X‐linked agammaglobulinemia ,Genetics ,QH426-470 - Abstract
Abstract Background We report the first case of a family with co‐occurrence of Wilson disease (WD), an autosomal recessive disorder of copper metabolism, and X‐linked agammaglobulinemia (XLA), a primary immunodeficiency disorder (PIDD) that features marked reduction in circulating B lymphocytes and serum immunoglobulins. Methods and Results Through utilization of a multiplexed biomarker peptide quantification method known as the immuno‐SRM assay, we were able to simultaneously and independently identify which family members are affected with WD and which are affected with XLA using dried blood spots (DBS). Conclusion Being able to delineate multiple diagnoses using proteolytic analysis from a single DBS provides support for implementation of this methodology for clinical diagnostic use as well as large‐scale population screening, such as newborn screening (NBS). This could allow for early identification and treatment of affected individuals with WD or XLA, which have been shown to reduce morbidity and decrease mortality in these two populations.
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- 2020
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5. Fractionated plasma N-glycan profiling of novel cohort of ATP6AP1-CDG subjects identifies phenotypic association
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Hana Alharbi, Earnest James Paul Daniel, Jenny Thies, Irene Chang, Dana L. Goldner, Bobby G. Ng, Peter Witters, Amal Aqul, Frances Velez‐Bartolomei, Gregory M. Enns, Evelyn Hsu, Elizabeth Kichula, Esther Lee, Charles Lourenco, Sheri A. Poskanzer, Sara Rasmussen, Katelyn Saarela, YunZu M. Wang, Kimiyo M. Raymond, Matthew J. Schultz, Hudson H. Freeze, Christina Lam, Andrew C. Edmondson, and Miao He
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Genetics ,Genetics (clinical) ,Article - Abstract
ATP6AP1-CDG is an X-linked disorder typically characterized by hepatopathy, immunodeficiency and an abnormal type II transferrin glycosylation pattern. Here, we present eleven new patients and clinical updates with biochemical characterization on one previously reported patient. We also document intrafamilial phenotypic variability and atypical presentations, expanding the symptomatology of ATP6AP1-CDG to include dystonia, hepatocellular carcinoma, and lysosomal abnormalities on hepatic histology. Three of our subjects received successful liver transplantation. We performed N-glycan profiling of total and fractionated plasma proteins for six patients and show associations with varying phenotypes, demonstrating potential diagnostic and prognostic value of fractionated N-glycan profiles. The aberrant N-linked glycosylation in purified transferrin and remaining plasma glycoprotein fractions normalized in one patient post hepatic transplant, while the increases of Man4GlcNAc2 and Man5GlcNAc2 in purified immunoglobulins persisted. Interestingly, in the single patient with isolated immune deficiency phenotype, elevated high-mannose glycans were detected on purified immunoglobulins without glycosylation abnormalities on transferrin or the remaining plasma glycoprotein fractions. Given the diverse and often tissue specific clinical presentations and the need of clinical management post hepatic transplant in ATP6AP1-CDG patients, these results demonstrate that fractionated plasma N-glycan profiling could be a valuable tool in diagnosis and disease monitoring.
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- 2023
6. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
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Zou Pan, Marielle E. van Gijn, Marjolein H. Willemsen, Mariet W. Elting, Susanne Koning, Daniel C. Koboldt, Rebecca Baud, Renzo Guerrini, Ghayda M. Mirzaa, Laurence E. Walsh, Kim L. McBride, Jenny Thies, Andrew E. Timms, Shaoping Huang, Gretchen E. Rosso, Joshua Scheck, Haley McConkey, Matthew A. Deardorff, Peter D. Turnpenny, Suzanne M. Leal, Sanjay M. Sisodiya, Lin Yang, Melissa Lees, Cacha M.P.C.D. Peeters-Scholte, Henry Houlden, Marielle Alders, J. Austin Hamm, Karla A. Peña-Guerra, Richard E. Person, Leena Lauronen, Hannah K. Robinson, Theresa Mihalic Mosher, Alexandra Garza-Flores, Victoria Harrison, Tuomo Määttä, Daniela Q.C.M. Barge-Schaapveld, James R. Lupski, Houda Zghal Elloumi, Francisco J. Guzmán-Vega, Tamison Jewett, Siddharth Banka, Barbara W. van Paassen, J. Lawrence Merritt, Angela Sun, Yana Lara-Taranchenko, Irma Järvelä, Ivan K. Chinn, Claudia A. L. Ruivenkamp, Nicholas M. Allen, Xiaodong Wang, Amy Crunk, Selina H. Banu, Maura R.Z. Ruzhnikov, Jeffery McGlothlin, Mashaya Zaman, Adam Jackson, Stefan T. Arold, Bert B.A. de Vries, Jing Peng, Lauren Schenck, Isabelle Schrauwen, Marjon van Slegtenhorst, Luis Alberto Pedroza, Bekim Sadikovic, Annalisa Vetro, Reshmi Ramakrishnan, Kristin G. Monaghan, Kelly J. Cardona-Londoño, Catherine Quindipan, Kristina Lanko, Rolph Pfundt, Caroline M. Kehoe, Martino Montomoli, Christian Gilissen, Hamid Galehdari, Yolande van Bever, Jennifer Keller-Ramey, Sadegheh Haghshenas, Neda Mazaheri, Stephanie Efthymiou, Reza Maroofian, Lewis Pang, Fleur Vansenne, Abeltje M. Polstra, Kara C. Klemp, Marjolein J.A. Weerts, Xi Lin, Julia Baptista, Tahsin Stefan Barakat, Anneke Kievit, Adi Reich, Stephen R. Braddock, Shehla Mohammed, Abbey M. Putnam, Jennifer Kerkhof, Matthew Pastore, Sally Ann Lynch, Graduate School, ANS - Neuroinfection & -inflammation, Human Genetics, ACS - Pulmonary hypertension & thrombosis, ARD - Amsterdam Reproduction and Development, MUMC+: DA KG Polikliniek (9), RS: FHML non-thematic output, Human genetics, VU University medical center, Amsterdam Reproduction & Development (AR&D), Clinical Genetics, Irma Järvelä / Principal Investigator, Medicum, Department of Medical and Clinical Genetics, HUS Medical Imaging Center, Clinicum, BioMag Laboratory, HUS Children and Adolescents, and Kliinisen neurofysiologian yksikkö
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Male ,INTELLECTUAL DISABILITY ,GENES ,Language delay ,VARIANTS ,Biology ,Bioinformatics ,3124 Neurology and psychiatry ,Article ,12Q24.31 ,SETD1B ,03 medical and health sciences ,Epilepsy ,0302 clinical medicine ,Neurodevelopmental disorder ,Seizures ,Intellectual disability ,medicine ,Humans ,MICRODELETION ,Global developmental delay ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,3112 Neurosciences ,RECOGNITION ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Histone-Lysine N-Methyltransferase ,medicine.disease ,Penetrance ,Human genetics ,Phenotype ,Neurodevelopmental Disorders ,MOTIF ,Autism ,METHYLTRANSFERASE ,3111 Biomedicine ,030217 neurology & neurosurgery - Abstract
Contains fulltext : 243955.pdf (Publisher’s version ) (Open Access) PURPOSE: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. METHODS: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. RESULTS: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. CONCLUSION: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.
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- 2021
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7. A rapid and non-invasive proteomic analysis using DBS and buccal swab for multiplexed second-tier screening of Pompe disease and Mucopolysaccharidosis type I
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Tong Zhang, Phi Duong, Remwilyn Dayuha, Christopher J. Collins, Erika Beckman, Jenny Thies, Irene Chang, Christina Lam, Angela Sun, Anna I. Scott, John Thompson, Aranjeet Singh, Hamid Khaledi, Michael H. Gelb, and Si Houn Hahn
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Proteomics ,Endocrinology ,Neonatal Screening ,Glycogen Storage Disease Type II ,Endocrinology, Diabetes and Metabolism ,Mucopolysaccharidosis I ,Genetics ,Infant, Newborn ,Humans ,Reproducibility of Results ,Molecular Biology ,Biochemistry - Abstract
Current newborn screening programs for Pompe disease (PD) and mucopolysaccharidosis type I (MPS I) suffer from a high false positive rate and long turnaround time for clinical follow up. This study aimed to develop a novel proteomics-based assay for rapid and accurate second-tier screening of PD and MPS I. A fast turnaround assay would enable the identification of severe cases who need immediate clinical follow up and treatment.We developed an immunocapture coupled with mass spectrometry-based proteomics (Immuno-SRM) assay to quantify GAA and IDUA proteins in dried blood spots (DBS) and buccal swabs. Sensitivity, linearity, reproducibility, and protein concentration range in healthy control samples were determined. Clinical performance was evaluated in known PD and MPS I patients as well as pseudodeficiency and carrier cases.Using three 3.2 mm punches (~13.1 μL of blood) of DBS, the assay showed reproducible and sensitive quantification of GAA and IDUA. Both proteins can also be quantified in buccal swabs with high reproducibility and sensitivity. Infantile onset Pompe disease (IOPD) and severe MPS I cases are readily identifiable due to the absence of GAA and IDUA, respectively. In addition, late onset Pompe disease (LOPD) and attenuated MPS I patients showed much reduced levels of the target protein. By contrast, pseudodeficiency and carrier cases exhibited significant higher target protein levels compared to true patients.Direct quantification of endogenous GAA and IDUA peptides in DBS by Immuno-SRM can be used for second-tier screening to rapidly identify severe PD and MPS I patients with a turnaround time of1 week. Such patients could benefit from immediate clinical follow up and possibly earlier treatment.
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- 2022
8. Immune dysfunction in <scp>MGAT2‐CDG</scp> : A clinical report and review of the literature
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Anita E. Beck, Piero Rinaldo, Sheri A. Poskanzer, Matthew J. Schultz, Christina Lam, Kris Liedtke, Silvia Tortorelli, James T. Bennett, Irene J. Chang, Jenny Thies, Noemi Vidal-Folch, Eric J. Allenspach, Coleman T. Turgeon, Devin Oglesbee, Kimiyo Raymond, Dimitar Gavrilov, and Dietrich Matern
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0301 basic medicine ,congenital, hereditary, and neonatal diseases and abnormalities ,Glycosylation ,business.industry ,Lymphocyte ,030105 genetics & heredity ,medicine.disease ,Article ,Hypotonia ,Hypogammaglobulinemia ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,medicine.anatomical_structure ,Immune system ,chemistry ,Antigen ,Immunology ,Genetics ,medicine ,medicine.symptom ,business ,Congenital disorder of glycosylation ,Genetics (clinical) ,Immunodeficiency - Abstract
Glycosylation is a critical post/peri-translational modification required for the appropriate development and function of the immune system. As an example, abnormalities in glycosylation can cause antibody deficiency and reduced lymphocyte signaling, although the phenotype can be complex given the diverse roles of glycosylation. Human MGAT2 encodes N-acetylglucosaminyltransferase II, which is a critical enzyme in the processing of oligomannose to complex N-glycans. Complex N-glycans are essential for immune system functionality, but only one individual with MGAT2-CDG has been described to have an abnormal immunologic evaluation. MGAT2-CDG (CDG-IIa) is a congenital disorder of glycosylation (CDG) associated with profound global developmental disability, hypotonia, early onset epilepsy, and other multisystem manifestations. Here, we report a 4-year old female with MGAT2-CDG due to a novel homozygous pathogenic variant in MGAT2, a 4-base pair deletion, c.1006_1009delGACA. In addition to clinical features previously described in MGAT2-CDG, she experienced episodic asystole, persistent hypogammaglobulinemia, and defective ex vivo mitogen and antigen proliferative responses, but intact specific vaccine antibody titers. Her infection history has been mild despite the testing abnormalities. We compare this patient to the 15 previously reported patients in the literature, thus expanding both the genotypic and phenotypic spectrum for MGAT2-CDG.
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- 2020
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9. p.P1379S, a benign variant with reduced ATP7B protein level in Wilson Disease
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Phi Duong, Remwilyn Dayuha, Roderick H. J. Houwen, Jenny Thies, Christopher J. Collins, Si Houn Hahn, Candace T. Myers, Fan Yi, and Sheri A. Poskanzer
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lcsh:QH426-470 ,Endocrinology, Diabetes and Metabolism ,Case Report ,Disease ,Case Reports ,Biology ,Compound heterozygosity ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Asymptomatic ,lcsh:Diseases of the endocrine glands. Clinical endocrinology ,Internal Medicine ,medicine ,Dried blood ,Likely pathogenic ,Wilson disease ,Genetics ,Newborn screening ,lcsh:RC648-665 ,newborn screening ,p.P1379S ,Protein level ,immuno‐SRM ,Pathogenicity ,ATP7B quantification ,lcsh:Genetics ,Benign variant ,medicine.symptom - Abstract
Background Wilson disease (WD) is an autosomal recessive disorder of copper transport caused by inherited defects in the ATP7B gene and results in toxic accumulation of copper in various organs. We previously reported a family with three consecutive generations affected by WD that carries the variant, p.P1379S, which was classified at the time as likely pathogenic. However, recent investigations of the p.P1379S variant indicate a possible conflict of interpretations regarding its pathogenicity. This led us to explore the quantification of ATP7B in dried blood spots (DBS) using a surrogate peptide to study the effects of the p.P1379S variant on ATP7B concentrations in two unrelated families with the common p.P1379S variant. Methods and results ATP7B was quantified using the peptide immunoaffinity enrichment coupled with selected reaction monitoring mass spectrometry (immuno‐SRM) method which utilizes antibody‐mediated peptide capture from DBS. Two patients affected with WD had undetectable ATP7B level while four compound heterozygous children with one known pathogenic variant and the p.P1379S had significantly reduced ATP7B levels. Of note, all four children remain asymptomatic without abnormal laboratory consequences despite being untreated for WD. Conclusion These two families demonstrated that p.P1379S, when compounded with two known pathogenic variants, resulted in significantly reduced protein levels but retained enough function to maintain normal copper homeostasis. This implies that p.P1379S is benign in nature. A better understanding of the nature and consequences of variants in WD will help in informing patient care and avoiding unnecessary treatments.
- Published
- 2020
10. PRE AND PERINATAL FINDINGS IN A CASE OF -RELATED ENCEPHALOCARDIOMYOPATHY
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Monica Penon Portmann, Anna Scott, Gail Deutsch, Anna Hedstrom, Angela Sun, Jenny Thies, Erika Beckman, and Irene Chang
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Endocrinology ,Endocrinology, Diabetes and Metabolism ,Genetics ,Molecular Biology ,Biochemistry - Published
- 2023
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11. Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder
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Joshua J. Ziarek, Manju A. Kurian, Daniel Scott, Rebekah Barrick, Kate Baker, Jasper J. van der Smagt, Anna Kolesnik-Taylor, Jenny Thies, Holly Melland, Lucy Loong, Shelagh Joss, Marjolein H. Willemsen, Fabian Bumbak, Sarah L. Gordon, Abinayah John, Elise Ng-Cordell, R. Pfundt, Christina Fagerberg, Majid Alfadhel, Frances Emslie, Martin Jakob Larsen, Panayiotis Constantinou, Tjitske Kleefstra, Mathilde Nizon, and Richard Chang
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Sleep disorder ,Movement disorders ,business.industry ,Cognition ,medicine.disease ,Phenotype ,Genotype-phenotype distinction ,Neurodevelopmental disorder ,Intellectual disability ,Medicine ,Missense mutation ,medicine.symptom ,business ,Neuroscience - Abstract
PurposeSynaptotagmin-1 (SYT1) is a critical mediator of neurotransmitter release in the central nervous system. Previously reported missense SYT1 variants in the C2B domain are associated with severe intellectual disability, movement disorders, behavioural disturbance and EEG abnormalities. Here, we expand the genotypes and phenotypes and identify discriminating features of this disorder.MethodsWe describe 22 individuals with 15 de novo missense SYT1 variants. Evidence for pathogenicity is discussed, including ACMG criteria, known structure-function relationships, and molecular dynamics simulations. Quantitative behavioural data for 14 cases are compared to other monogenic neurodevelopmental disorders.ResultsFour variants lie in the C2A domain with the remainder in the C2B. We classify 6 variants as pathogenic, 4 as likely pathogenic, and 5 as variants of uncertain significance. Prevalent clinical phenotypes include delayed developmental milestones, ophthalmic problems, abnormal EEG, movement disorders and sleep disturbance. Discriminating behavioural characteristics were severity of motor and communication impairment, presence of motor stereotypies and mood instability.ConclusionSYT1 variants associated with neurodevelopmental disorder extend beyond previously reported regions, and the phenotypic spectrum encompasses a broader range of severity than initially reported. This work guides diagnosis and molecular understanding of this rare neurodevelopmental disorder, and highlights a key role for SYT1 function in emotional regulation, motor control and emergent cognitive function.
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- 2021
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12. A rapid and non-invasive proteomic analysis using DBS and buccal swab for multiplexed second-tier screening of Pompe disease and Hurler syndrome
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Angela Sun, Tong Zhang, Phi Duong, Remwilyn Dayuha, Andy Dang, Christopher Collins, Anna Scott, Erika Beckman, Jenny Thies, Irene Chang, Christina Lam, Hamid Kahledi, Michael Gelb, and Sihoun Hahn
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Endocrinology ,Endocrinology, Diabetes and Metabolism ,Genetics ,Molecular Biology ,Biochemistry - Published
- 2022
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13. Clinical Exome Studies Have Inconsistent Coverage
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Chao Xing, Luis A. Umaña, Donnice Michel, Crescenda L. Uhles, Jason Y. Park, Julia Kozlitina, Judy Fan, Angela E. Scheuerle, Jenny Thies, Christine Quinn, Callie Hornbuckle, Garrett Gotway, and Eric Crossley
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0301 basic medicine ,Oncology ,medicine.medical_specialty ,Epilepsy ,BRCA1 Protein ,Biochemistry (medical) ,Clinical Biochemistry ,Sequencing data ,Diagnostic test ,Guidelines as Topic ,Exons ,030204 cardiovascular system & hematology ,Biology ,Laboratories, Hospital ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Internal medicine ,Exome Sequencing ,medicine ,Humans ,Exome ,MutL Protein Homolog 1 ,Exome sequencing - Abstract
BACKGROUND Exome sequencing has become a commonly used clinical diagnostic test. Multiple studies have examined the diagnostic utility and individual laboratory performance of exome testing; however, no previous study has surveyed and compared the data quality from multiple clinical laboratories. METHODS We examined sequencing data from 36 clinical exome tests from 3 clinical laboratories. Exome data were compared in terms of overall characteristics and coverage of specific genes and nucleotide positions. The sets of genes examined included genes in Consensus Coding Sequence (CCDS) (n = 17723), a subset of genes clinically relevant to epilepsy (n = 108), and genes that are recommended for reporting of secondary findings (n = 57; excludes X-linked genes). RESULTS The average exome nucleotide coverage (≥20×) of each laboratory varied at 96.49% (CV = 3%), 96.54% (CV = 1%), and 91.68% (CV = 4%), for laboratories A, B, and C, respectively. For CCDS genes, the average number of completely covered genes varied at 12184 (CV = 29%), 11687 (CV = 13%), and 5989 (CV = 37%), for laboratories A, B, and C, respectively. With smaller subsets of genes related to epilepsy and secondary findings, the CV revealed low consistency, with a maximum CV seen in laboratory C for both epilepsy genes (CV = 60%) and secondary findings genes (CV = 71%). CONCLUSIONS Poor consistency in complete gene coverage was seen in the clinical exome laboratories surveyed. The degree of consistency varied widely between the laboratories.
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- 2019
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14. Expansion of the Primrose syndrome phenotype through the comparative analysis of two new case reports with ZBTB20 variants
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Rhonda E. Schnur, Rayssa L. Borges-Medeiros, Jenny Thies, João Ricardo Mendes de Oliveira, Laura Durão Ferreira, and Christina Lam
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Male ,Pediatrics ,medicine.medical_specialty ,Nerve Tissue Proteins ,Intellectual Disability ,Intellectual disability ,Genetics ,medicine ,Humans ,Missense mutation ,Abnormalities, Multiple ,Genetic Predisposition to Disease ,Medical history ,Ear Diseases ,Wasting ,Genetic Association Studies ,Genetics (clinical) ,business.industry ,Genetic disorder ,Macrocephaly ,Calcinosis ,Infant ,medicine.disease ,Primrose syndrome ,Natural history ,Muscular Atrophy ,Phenotype ,Mutation ,medicine.symptom ,business ,Transcription Factors - Abstract
Primrose syndrome (PRIMS), a rare genetic disorder with several clinical findings including intellectual disability, macrocephaly, typical facial features, and muscle wasting, is caused by heterozygous variants in the ZBTB20 gene. We report the cases of two males diagnosed with PRIMS at different ages, emphasizing the likely progressive nature of the disorder, as well as the differences and similarities of presentation during infancy and adulthood. Patient 1 is a 2-year-old American male with a medical history marked by impaired hearing, developmental delays, and fainting spells. Patient 2 is a 28-year-old Brazilian male, who presents with a phenotype similar to that seen in Patient 1 with additional features of ectopic calcifications and prominent muscular and skeletal abnormalities. Additionally, Patient 2 has a history of fainting spells and diminished body height and weight, with the latter features having only been reported in one PRIMS patient so far. Both Patients 1 and 2 were found to carry heterozygous likely pathogenic missense variants, detected in the last coding exon of ZBTB20 (c.1822T>C, p.Cys608Arg, de novo, and c.1873A>G, p.Met625Val, respectively), consistent with PRIMS. Overall, these case reports highlight PRIMS's likely progressive nature and contribute to the understanding of the natural history of this condition.
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- 2019
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15. Targeted long-read sequencing identifies missing disease-causing variation
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Tim Cherry, Seth J. Perlman, Rando Allikmets, Christina Lam, Katrina M Dipple, Alexias Safi, Hailey Loucks, Penny M Chow, Ian A. Glass, Xue Zou, Heather C Mefford, Angela Sun, Deborah A. Nickerson, Danny E. Miller, Dawn L. Earl, James T. Bennett, Alexandra P. Lewis, Stephanie Austin, Margaret P Adam, Apoorva K Iyengar, Arvis Sulovari, Edith P Almanza Fuerte, Andrew S. Allen, Audrey Squire, Karynne E. Patterson, Erin Huggins, Winston Lee, William H. Majoros, Emily S Bonkowski, Tianyun Wang, Priya S. Kishnani, Robin L. Bennett, Mary Claire King, Tara L. Wenger, Erika Beckman, Kendra Hoekzema, Gregory E. Crawford, Timothy E. Reddy, Evan E. Eichler, Irene Chang, Anne V. Hing, Zoe Nelson, Thomas J. Walsh, Dan Doherty, Megan C. Sikes, Michael J. Bamshad, Catherine R Paschal, Jessica X. Chong, Jenny Thies, and Katherine M. Munson
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Male ,DNA Copy Number Variations ,Computational biology ,Disease ,Biology ,Article ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Genetics ,Humans ,Genetic Predisposition to Disease ,Genetic Testing ,Gene ,Genetics (clinical) ,030304 developmental biology ,Sequence (medicine) ,Data source ,Chromosome Aberrations ,0303 health sciences ,Genome, Human ,Genetic Diseases, Inborn ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Phenotype ,Karyotyping ,Mutation (genetic algorithm) ,Cytogenetic Analysis ,Mutation ,Mendelian inheritance ,symbols ,Female ,Nanopore sequencing ,030217 neurology & neurosurgery - Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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- 2021
16. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
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Reshmi Ramakrishnan, Catherine Quindipan, Claudia A. L. Ruivenkamp, Nicholas M. Allen, Mashaya Zaman, Daniela Q.C.M. Barge-Schaapveld, Annalisa Vetro, Stephanie Efthymiou, James R. Lupski, Kara C. Klemp, Zou Pan, Adam Jackson, Marielle E. van Gijn, Joshua Scheck, Marielle Alders, Mariet W. Elting, Karla A. Peña-Guerra, Stephen R. Braddock, Rolph Pfundt, Ivan K. Chinn, Lin Yang, Lauren Schenck, Xiaodong Wang, Melissa Lees, Houda Zghal Elloumi, Shehla Mohammed, Sally Ann Lynch, Henry Houlden, Jennifer Keller-Ramey, Stefan T. Arold, Anneke Kievit, Jefferey McGlothlin, Marjon van Slegtenhorst, Marjolein H. Willemsen, Hannah K. Robinson, Bert B.A. de Vries, Irma Järvelä, Kelly J. Cardona-Londoño, Yolande van Bever, Abeltje M. Polstra, Neda Mazaheri, Barbara W. van Paassen, Maura R.Z. Ruzhnikov, Lewis Pang, Theresa Mihalic Mosher, J. Lawrence Merritt, Jing Peng, Sadegheh Haghshenas, Amy Crunk, Christian Gilissen, Fleur Vansenne, Cacha M.P.C.D. Peeters-Scholte, Richard E. Person, Hamid Galehdari, Leena Lauronen, Abbey M. Putnam, Jennifer Kerkhof, Matthew Pastore, Angela Sun, Caroline M. Kehoe, Alexandra Garza-Flores, Julia Baptista, Martino Montomoli, Selina H. Banu, Tahsin Stefan Barakat, Adi Reich, Luis Alberto Pedroza, Laurence E. Walsh, Renzo Guerrini, Ghayda M. Mirzaa, Peter D. Turnpenny, J. Austin Hamm, Xi Lin, Kristina Lanko, Reza Maroofian, Tuomo Määttä, Yana Lara-Taranchenko, Kim L. McBride, Jenny Thies, Andrew E. Timms, Shaoping Huang, Suzanne M. Leal, Daniel C. Koboldt, Rebecca Baud, Gretchen E. Rosso, Haley McConkey, Matthew A. Deardorff, Marjolein J.A. Weerts, Francisco J. Guzmán-Vega, Tamison Jewett, Siddharth Banka, Kristin G. Monaghan, Isabelle Schrauwen, Bekim Sadikovic, Sanjay M. Sisodiya, Victoria Harrison, and Susanne Koning
- Subjects
Genetics ,0303 health sciences ,Language delay ,Mechanism (biology) ,Biology ,medicine.disease ,Penetrance ,03 medical and health sciences ,0302 clinical medicine ,Neurodevelopmental disorder ,Intellectual disability ,medicine ,Autism ,Global developmental delay ,Epigenetics ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay and seizures. To date, clinical features have been described for eleven patients with (likely) pathogenic SETD1B sequence variants. We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Interestingly, males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. Finally, despite the possibility of non-redundant contributions of SETD1B and its paralogue SETD1A to epigenetic control, the clinical phenotypes of the related disorders share many similarities, indicating that elucidating shared and divergent downstream targets of both genes will help to understand the mechanism leading to the neurobehavioral phenotypes. Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.
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- 2021
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17. Biallelic variants in KARS1 are associated with neurodevelopmental disorders and hearing loss recapitulated by the knockout zebrafish
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Sheng-Jia Lin, Barbara Vona, Patricia G. Barbalho, Rauan Kaiyrzhanov, Reza Maroofian, Cassidy Petree, Mariasavina Severino, Valentina Stanley, Pratishtha Varshney, Paulina Bahena, Fatema Alzahrani, Amal Alhashem, Alistair T. Pagnamenta, Gudrun Aubertin, Juvianee I. Estrada-Veras, Héctor Adrián Díaz Hernández, Neda Mazaheri, Andrea Oza, Jenny Thies, Deborah L. Renaud, Sanmati Dugad, Jennifer McEvoy, Tipu Sultan, Lynn S. Pais, Brahim Tabarki, Daniel Villalobos-Ramirez, Aboulfazl Rad, J.C. Ambrose, P. Arumugam, M. Bleda, F. Boardman-Pretty, C.R. Boustred, H. Brittain, M.J. Caulfield, G.C. Chan, T. Fowler, A. Giess, A. Hamblin, S. Henderson, T.J.P. Hubbard, R. Jackson, L.J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, S.E.A. Leigh, I.U.S. Leong, F.J. Lopez, F. Maleady-Crowe, L. Moutsianas, M. Mueller, N. Murugaesu, A.C. Need, P. O‘Donovan, C.A. Odhams, C. Patch, D. Perez-Gil, M.B. Pereira, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R.H. Scott, A. Siddiq, A. Sieghart, S.C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, E.R.A. Thomas, S.R. Thompson, A. Tucci, E. Walsh, M.J. Welland, E. Williams, K. Witkowska, S.M. Wood, Hamid Galehdari, Farah Ashrafzadeh, Afsaneh Sahebzamani, Kolsoum Saeidi, Erin Torti, Houda Z. Elloumi, Sara Mora, Timothy B. Palculict, Hui Yang, Jonathan D. Wren, null Ben Fowler, Manali Joshi, Martine Behra, Shawn M. Burgess, Swapan K. Nath, Michael G. Hanna, Margaret Kenna, J. Lawrence Merritt, Henry Houlden, Ehsan Ghayoor Karimiani, Maha S. Zaki, Thomas Haaf, Fowzan S. Alkuraya, Joseph G. Gleeson, and Gaurav K. Varshney
- Subjects
Genetics ,Lysine-tRNA Ligase ,biology ,Disease ,biology.organism_classification ,medicine.disease ,Phenotype ,Human genetics ,Disease Models, Animal ,Neurodevelopmental Disorders ,medicine ,Missense mutation ,Autism ,Animals ,Humans ,Allele ,Hearing Loss ,Zebrafish ,Genetics (clinical) ,Gene knockout ,Alleles - Abstract
Pathogenic variants in Lysyl-tRNA synthetase 1 (KARS1) have increasingly been recognized as a cause of early-onset complex neurological phenotypes. To advance the timely diagnosis of KARS1-related disorders, we sought to delineate its phenotype and generate a disease model to understand its function in vivo. Through international collaboration, we identified 22 affected individuals from 16 unrelated families harboring biallelic likely pathogenic or pathogenic in KARS1 variants. Sequencing approaches ranged from disease-specific panels to genome sequencing. We generated loss-of-function alleles in zebrafish. We identify ten new and four known biallelic missense variants in KARS1 presenting with a moderate-to-severe developmental delay, progressive neurological and neurosensory abnormalities, and variable white matter involvement. We describe novel KARS1-associated signs such as autism, hyperactive behavior, pontine hypoplasia, and cerebellar atrophy with prevalent vermian involvement. Loss of kars1 leads to upregulation of p53, tissue-specific apoptosis, and downregulation of neurodevelopmental related genes, recapitulating key tissue-specific disease phenotypes of patients. Inhibition of p53 rescued several defects of kars1−/− knockouts. Our work delineates the clinical spectrum associated with KARS1 defects and provides a novel animal model for KARS1-related human diseases revealing p53 signaling components as potential therapeutic targets.
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- 2021
18. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
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Genomics England Research Consortium, M.J.A. (Marjolein) Weerts, K. (Kristina) Lanko, Francisco J. Guzmán-Vega, Adam Jackson, Reshmi Ramakrishnan, Kelly J. Cardona-Londoño, Karla A. Peña-Guerra, Yolande van Bever, B.W. (Barbara) van Paassen, J.A. (Anneke) Kievit, Marjon van Slegtenhorst, Nicholas M. Allen, Caroline M. Kehoe, Hannah K. Robinson, Lewis Pang, Selina H. Banu, Mashaya Zaman, Stephanie Efthymiou, Henry Houlden, Irma Järvelä, Leena Lauronen, Tuomo Määttä, Isabelle Schrauwen, Suzanne M. Leal, Claudia Ruivenkamp, Daniela Q.C.M. Barge-Schaapveld, Cacha Peeters-Scholte, Hamid Galehdari, Neda Mazaheri, Sanjay M. Sisodiya, Victoria Harrison, Angela Sun, Jenny Thies, Luis Alberto Pedroza, Yana Lara-Taranchenko, Ivan K. Chinn, James R. Lupski, Alexandra Garza-Flores, Jeffery McGlothlin, L Yang, Shaoping Huang, Xiaodong Wang, Tamison Jewett, Gretchen Rosso, Xi Lin, Shehla Mohammed, J. Lawrence Merritt, M Willemsen, C Gilissen, T.S. (Stefan) Barakat, Genomics England Research Consortium, M.J.A. (Marjolein) Weerts, K. (Kristina) Lanko, Francisco J. Guzmán-Vega, Adam Jackson, Reshmi Ramakrishnan, Kelly J. Cardona-Londoño, Karla A. Peña-Guerra, Yolande van Bever, B.W. (Barbara) van Paassen, J.A. (Anneke) Kievit, Marjon van Slegtenhorst, Nicholas M. Allen, Caroline M. Kehoe, Hannah K. Robinson, Lewis Pang, Selina H. Banu, Mashaya Zaman, Stephanie Efthymiou, Henry Houlden, Irma Järvelä, Leena Lauronen, Tuomo Määttä, Isabelle Schrauwen, Suzanne M. Leal, Claudia Ruivenkamp, Daniela Q.C.M. Barge-Schaapveld, Cacha Peeters-Scholte, Hamid Galehdari, Neda Mazaheri, Sanjay M. Sisodiya, Victoria Harrison, Angela Sun, Jenny Thies, Luis Alberto Pedroza, Yana Lara-Taranchenko, Ivan K. Chinn, James R. Lupski, Alexandra Garza-Flores, Jeffery McGlothlin, L Yang, Shaoping Huang, Xiaodong Wang, Tamison Jewett, Gretchen Rosso, Xi Lin, Shehla Mohammed, J. Lawrence Merritt, M Willemsen, C Gilissen, and T.S. (Stefan) Barakat
- Abstract
Purpose: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. Methods: We p
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- 2021
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19. Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants
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Ting Wang, Karynne E. Patterson, Penny M Chow, Alexandra P. Lewis, Bonkowski Es, Adam Mp, Katherine M. Munson, Catherine R Paschal, Deborah A. Nickerson, Won Hee Lee, Audrey Squire, Dipple Km, Fuerte Epa, Angela Sun, Dan Doherty, Loucks H, Christina Lam, Ian A. Glass, Danny E. Miller, Dawn L. Earl, Rando Allikmets, Jenny Thies, Chang I, Beckman E, Arvis Sulovari, Evan E. Eichler, Jessica X. Chong, Perlman Sj, Nelson Z, Kendra Hoekzema, Robin L. Bennett, Anne V. Hing, Timothy J. Cherry, Megan C. Sikes, Michael J. Bamshad, Heather C Mefford, and James T. Bennett
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Candidate gene ,symbols.namesake ,Mutation (genetic algorithm) ,Mendelian inheritance ,symbols ,Computational biology ,Nanopore sequencing ,Copy-number variation ,Biology ,Gene ,Phenotype ,Sequence (medicine) - Abstract
BACKGROUNDDespite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take advantage of state-of-the-art treatments. In such instances, testing sometimes reveals difficult-to-evaluate complex structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in specific genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted.METHODSTargeted long-read sequencing (T-LRS) was performed on 33 individuals using Read Until on the Oxford Nanopore platform. This method allowed us to computationally target up to 100 Mbp of sequence per experiment, resulting in an average of 20x coverage of target regions, a 500% increase over background. We analyzed patient DNA for pathogenic substitutions, structural variants, and methylation differences using a single data source.RESULTSThe effectiveness of T-LRS was validated by detecting all genomic aberrations, including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences, previously identified by prior clinical testing. In 6/7 individuals who had complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, which led, in one case, to a change in clinical management. In nine individuals with suspected Mendelian conditions who lacked a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in five and variants of uncertain significance in two others.CONCLUSIONST-LRS can accurately predict pathogenic copy number variants and triplet repeat expansions, resolve complex rearrangements, and identify single-nucleotide variants not detected by other technologies, including short-read sequencing. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority candidate genes and regions or to further evaluate complex clinical testing results. The application of T-LRS will likely increase the diagnostic rate of rare disorders.
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- 2020
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20. Tutorial: Triheptanoin and Nutrition Management for Treatment of Long-Chain Fatty Acid Oxidation Disorders
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Kelly N. McKean, Anna I. Scott, Sihoun Hahn, Melissa Gunnarson, Angela Sun, Irene J. Chang, Christina Lam, Marie K. Norris, Sarah Sullivan, J. Lawrence Merritt, and Jenny Thies
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medicine.medical_specialty ,030309 nutrition & dietetics ,Cardiomyopathy ,Medicine (miscellaneous) ,Gastroenterology ,Lipid Metabolism, Inborn Errors ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Internal medicine ,Carnitine ,Medicine ,Humans ,Carnitine-acylcarnitine translocase deficiency ,Medical nutrition therapy ,Beta oxidation ,Triglycerides ,0303 health sciences ,Nutrition and Dietetics ,Triglyceride ,business.industry ,Fatty Acids ,Dietary management ,medicine.disease ,Triheptanoin ,Discontinuation ,chemistry ,030211 gastroenterology & hepatology ,business ,Oxidation-Reduction - Abstract
Background Patients with severe long-chain fatty acid oxidation disorders (LC-FAODs) experience serious morbidity and mortality despite traditional dietary management including medium-chain triglyceride (MCT)-supplemented, low-fat diets. Triheptanoin is a triglyceride oil that is broken down to acetyl-coenzyme A (CoA) and propionyl-CoA, which replenishes deficient tricarboxylic acid cycle intermediates. We report the complex medical and nutrition management of triheptanoin therapy initiated emergently for 3 patients with LC-FAOD. Methods Triheptanoin (Ultragenyx Pharmaceutical, Inc, Novato, CA, USA) was administered to 3 patients with LC-FAOD on a compassionate-use basis. Triheptanoin was mixed with non-MCT-containing low-fat formula. Patients were closely followed with regular cardiac and laboratory monitoring. Results Cardiac ejection fraction normalized after triheptanoin initiation. Patients experienced fewer hospitalizations related to metabolic crises while on triheptanoin. Patient 1 has tolerated oral administration without difficulty since birth. Patients 2 and 3 experienced increased diarrhea. Recurrent breakdown of the silicone gastrostomy tube occurred in patient 3, whereas the polyurethane nasogastric tube for patient 2 remained intact. Patient 3 experiences recurrent episodes of elevated creatine kinase levels and muscle weakness associated with illness. Patient 3 had chronically elevated C10-acylcarnitines while on MCT supplementation, which normalized after initiation of triheptanoin and discontinuation of MCT oil. Conclusions Triheptanoin can ameliorate acute cardiomyopathy and increase survival in patients with severe LC-FAOD. Substituting triheptanoin for traditional MCT-based treatment improves clinical outcomes. MCT oil might be less effective in carnitine-acylcarnitine translocase deficiency patients compared with other FAODs and needs further investigation.
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- 2020
21. CHRNB1-associated congenital myasthenia syndrome: Expanding the clinical spectrum
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Shilpi Chabra, Amanda S. Freed, Sarah V. Clowes Candadai, Jenny Thies, Anisha Chandra Schwarz, Leo H. Wang, Brianna K Brei, A. Micheil Innes, James T. Bennett, and Jean K. Mah
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0301 basic medicine ,Adult ,Male ,030105 genetics & heredity ,Congenital myasthenia ,Receptors, Nicotinic ,Bioinformatics ,Neuromuscular junction ,03 medical and health sciences ,Exon ,Genetics ,Medicine ,Humans ,Abnormalities, Multiple ,Genetics (clinical) ,Exome sequencing ,Genetic testing ,Acetylcholine receptor ,Retrospective Studies ,Myasthenic Syndromes, Congenital ,medicine.diagnostic_test ,business.industry ,Genetic heterogeneity ,Infant, Newborn ,Prognosis ,Pedigree ,030104 developmental biology ,medicine.anatomical_structure ,Fetal akinesia deformation sequence ,Mutation ,Female ,business - Abstract
CHRNB1 encodes the β subunit of the acetylcholine receptor (AChR) at the neuromuscular junction. Inherited defects in the neuromuscular junction can lead to congenital myasthenia syndrome (CMS), a clinically and genetically heterogeneous group of disorders which includes fetal akinesia deformation sequence (FADS) on the severe end of the spectrum. Here, we report two unrelated families with biallelic CHRNB1 variants, and in each family, one child presented with lethal FADS. We contrast the diagnostic odysseys in the two families, one of which lasted 16 years while the other, utilizing rapid exome sequencing, led to specific treatment in the first 2 weeks of life. Furthermore, we note that CHRNB1 variants may be under-recognized because in both families, one of the variants is a single exon deletion that has been previously described but may not easily be detected in clinically available genetic testing.
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- 2020
22. eP036: Not your typical newborn screen for X-ALD: Outcomes from Washington State
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Jenny Thies, Erika Beckman, Anna Scott, Irene Chang, Angela Sun, and Christina Lam
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Genetics (clinical) - Published
- 2022
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23. Expanding clinical phenotype in CACNA1C related disorders: From neonatal onset severe epileptic encephalopathy to late-onset epilepsy
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Jenny Thies, Jennifer N. Dines, Heather C Mefford, Edward J. Novotny, J. Lawrence Merritt, Ghayda M. Mirzaa, Xiuhua Bozarth, Qian Cong, and Kimberly Foss
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Heart Defects, Congenital ,Models, Molecular ,0301 basic medicine ,Pediatrics ,medicine.medical_specialty ,Calcium Channels, L-Type ,Genotype ,Protein Conformation ,Cardiomyopathy ,Timothy syndrome ,Neonatal onset ,Article ,Structure-Activity Relationship ,03 medical and health sciences ,Epilepsy ,Genetics ,medicine ,Humans ,Missense mutation ,Alleles ,Genetic Association Studies ,Genetics (clinical) ,Exome sequencing ,Brugada syndrome ,Comparative Genomic Hybridization ,Learning Disabilities ,business.industry ,Epileptic encephalopathy ,Infant, Newborn ,Facies ,medicine.disease ,Phenotype ,030104 developmental biology ,Cytogenetic Analysis ,Mutation ,business - Abstract
CACNA1C (NM_000719.6) encodes an L-type calcium voltage-gated calcium channel (Ca(v)1.2), and pathogenic variants have been associated with two distinct clinical entities: Timothy syndrome and Brugada syndrome. Thus far, CACNA1C has not been reported as a gene associated with epileptic encephalopathy (EE) and is less commonly associated with epilepsy. We report three individuals from two families with variants in CACNA1C. Patient 1 presented with neonatal onset severe epileptic encephalopathy (NOEE) and was found to have a de novo missense variant in CACNA1C (c.4087G>A (p.V1363M)) on exome sequencing. In family 2, Patient 2 presented with congenital cardiac anomalies and cardiomyopathy and was found to have a paternally inherited splice site variant, c.3717+1_3717+2insA, on a cardiomyopathy panel. Her father, Patient 3, presented with learning difficulties, late-onset epilepsy, and congenital cardiac anomalies. Family 2 highlights variable expressivity seen within a family. This case series expands the clinical and molecular phenotype of CACNA1C-related disorders and highlights the need to include CACNA1C on epilepsy gene panels.
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- 2018
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24. TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants
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Alison M. Muir, Dianne Laboy Cintrón, Katherine H. Kim, Amber Begtrup, Peter I. Karachunski, Almuth Caliebe, Heather C Mefford, Amy Lacroix, J. Lawrence Merritt, Kirsty McWalter, Angela Sun, Sharon F. Suchy, Barbara K. Burton, Ingo Helbig, René Santer, Joline C. Dalton, Dmitriy Niyazov, Rachel Westman, Ganka Douglas, Leah Fleming, Hiltrud Muhle, Kristin G. Monaghan, Alice Basinger, Katherine L. Helbig, Jenny Thies, Kolja Becker, Manuela Pendziwiat, Can Ficicioglu, Megan T. Cho, Jennifer N. Dines, Francisca Millan, and Katie Golden-Grant
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Male ,0301 basic medicine ,Adolescent ,DNA Copy Number Variations ,Genotype ,Developmental Disabilities ,Encephalopathy ,developmental delay DNA copy-number variation ,030105 genetics & heredity ,Compound heterozygosity ,Bioinformatics ,Article ,03 medical and health sciences ,Epilepsy ,Genotype-phenotype distinction ,Seizures ,Intellectual Disability ,Intellectual disability ,medicine ,Humans ,Exome ,Family ,intragenic deletion ,Child ,Genetics (clinical) ,Exome sequencing ,Brain Diseases ,business.industry ,Aryl Hydrocarbon Receptor Nuclear Translocator ,Correction ,medicine.disease ,Phenotype ,Pedigree ,3. Good health ,030104 developmental biology ,Child, Preschool ,epilepsy ,Female ,business ,exome sequencing - Abstract
Purpose TANGO2-related disorders were first described in 2016 and prior to this publication, only 15 individuals with TANGO2-related disorder were described in the literature. Primary features include metabolic crisis with rhabdomyolysis, encephalopathy, intellectual disability, seizures, and cardiac arrhythmias. We assess whether genotype and phenotype of TANGO2-related disorder has expanded since the initial discovery and determine the efficacy of exome sequencing (ES) as a diagnostic tool for detecting variants. Methods We present a series of 14 individuals from 11 unrelated families with complex medical and developmental histories, in whom ES or microarray identified compound heterozygous or homozygous variants in TANGO2. Results The initial presentation of patients with TANGO2-related disorders can be variable, including primarily neurological presentations. We expand the phenotype and genotype for TANGO2, highlighting the variability of the disorder. Conclusion TANGO2-related disorders can have a more diverse clinical presentation than previously anticipated. We illustrate the utility of routine ES data reanalysis whereby discovery of novel disease genes can lead to a diagnosis in previously unsolved cases and the need for additional copy-number variation analysis when ES is performed.
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- 2018
25. COQ2 nephropathy: a treatable cause of nephrotic syndrome in children
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Austin Larson, Irene J. Chang, Johan L.K. Van Hove, Sangeeta Hingorani, Angela Sun, Laura S. Finn, Michelle C. Starr, Jenny Thies, Jens Goebel, Christina Lam, and Coral Hanevold
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Male ,0301 basic medicine ,Nephrology ,medicine.medical_specialty ,Mitochondrial Diseases ,Nephrotic Syndrome ,Ubiquinone ,Biopsy ,030232 urology & nephrology ,Disease ,030105 genetics & heredity ,Kidney ,Gastroenterology ,Article ,Nephropathy ,03 medical and health sciences ,0302 clinical medicine ,Focal segmental glomerulosclerosis ,Internal medicine ,medicine ,Humans ,Genetic Testing ,Child ,Alkyl and Aryl Transferases ,Muscle Weakness ,Proteinuria ,medicine.diagnostic_test ,business.industry ,food and beverages ,medicine.disease ,Kidney Transplantation ,Treatment Outcome ,Child, Preschool ,Pediatrics, Perinatology and Child Health ,Ataxia ,Coenzyme Q10 deficiency ,medicine.symptom ,business ,Nephrotic syndrome - Abstract
BACKGROUND: Nephrotic syndrome can be caused by a subgroup of mitochondrial diseases classified as primary coenzyme Q(10) (CoQ(10)) deficiency. Pathogenic COQ2 variants are a cause of primary CoQ(10) deficiency and present with phenotypes ranging from isolated nephrotic syndrome to fatal multisystem disease. CASE REPORT: We report three pediatric patients with COQ2 variants presenting with nephrotic syndrome. Two of these patients had normal leukocyte CoQ(10) levels prior to treatment. Pathologic findings varied from mesangial sclerosis to focal segmental glomerulosclerosis, with all patients having abnormal appearing mitochondria on kidney biopsy. In two of three patients treated with CoQ(10) supplementation, the nephrotic syndrome resolved and at follow-up both have normal renal function and stable proteinuria. CONCLUSIONS: COQ2 nephropathy should be suspected in patients presenting with nephrotic syndrome, although less common than disease due to mutations in NPHS1, NPHS2, and WT1. The index of suspicion should remain high and we suggest that providers consider genetic evaluation even in patients with normal leukocyte CoQ(10) levels, as levels may be within normal range even with significant clinical disease. Early molecular diagnosis and specific treatment are essential in the management of this severe yet treatable condition.
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- 2018
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26. The co-occurrence of Wilson disease and X-linked agammaglobulinemia in one family highlights the promising diagnostic potential of proteolytic analysis
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Phi Duong, Fan Yi, Jenny Thies, Sheri A. Poskanzer, Christopher J. Collins, Remwilyn Dayuha, Candace T. Myers, Troy R. Torgerson, Si Houn Hahn, Irene J. Chang, and Hans D. Ochs
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0301 basic medicine ,Adult ,Male ,lcsh:QH426-470 ,Adolescent ,Copper metabolism ,X‐linked agammaglobulinemia ,X-linked agammaglobulinemia ,Disease ,030105 genetics & heredity ,Immunologic Tests ,Mass Spectrometry ,03 medical and health sciences ,Hepatolenticular Degeneration ,Agammaglobulinemia ,hemic and lymphatic diseases ,Genetics ,medicine ,Humans ,Dried blood ,Child ,Molecular Biology ,Genetics (clinical) ,Wilson disease ,Newborn screening ,Clinical Report ,co‐occurrence ,biology ,business.industry ,newborn screening ,Genetic Diseases, X-Linked ,immuno‐SRM ,medicine.disease ,Pedigree ,lcsh:Genetics ,030104 developmental biology ,Immunology ,Proteolysis ,biology.protein ,Primary immunodeficiency ,Biomarker (medicine) ,Female ,Dried Blood Spot Testing ,Antibody ,business ,Peptides ,Biomarkers - Abstract
Background We report the first case of a family with co‐occurrence of Wilson disease (WD), an autosomal recessive disorder of copper metabolism, and X‐linked agammaglobulinemia (XLA), a primary immunodeficiency disorder (PIDD) that features marked reduction in circulating B lymphocytes and serum immunoglobulins. Methods and Results Through utilization of a multiplexed biomarker peptide quantification method known as the immuno‐SRM assay, we were able to simultaneously and independently identify which family members are affected with WD and which are affected with XLA using dried blood spots (DBS). Conclusion Being able to delineate multiple diagnoses using proteolytic analysis from a single DBS provides support for implementation of this methodology for clinical diagnostic use as well as large‐scale population screening, such as newborn screening (NBS). This could allow for early identification and treatment of affected individuals with WD or XLA, which have been shown to reduce morbidity and decrease mortality in these two populations., This is the first family case with co‐occurrence of Wilson disease and X‐linked Agammaglobulinemia detected through our novel multiplex Immuno‐SRM‐MS analysis.
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- 2019
27. Rapid clinical exome sequencing in a pediatric ICU: genetic counselor impacts and challenges
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Jenny Thies, Amanda S. Freed, Sarah V. Clowes Candadai, Megan C. Sikes, and James T. Bennett
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Male ,medicine.medical_specialty ,Genetic counseling ,Genetic Counseling ,Disease ,Intensive Care Units, Pediatric ,Article ,Informed consent ,Exome Sequencing ,Medicine ,Humans ,Genetic Testing ,Intensive care medicine ,Child ,Genetics (clinical) ,Utilization management ,Exome sequencing ,Retrospective Studies ,business.industry ,Infant, Newborn ,Infant ,Inpatient setting ,Increased risk ,Counselors ,Child, Preschool ,Female ,Personalized medicine ,business - Abstract
Exome sequencing (ES) has revolutionized molecular diagnosis in children with genetic disease over the past decade. However, exome sequencing in the inpatient setting has traditionally been discouraged, in part due to an increased risk of providers failing to retrieve and act upon results, as many patients are discharged before results return. The development of rapid turn-around-times (TATs) for genomic testing has begun to shift this paradigm. Rapid exome sequencing (rES) is increasingly being used as a diagnostic tool for critically ill infants with likely genetic disease and presents significant challenges to execute. We implemented a program, entitled the Rapid Inpatient Genomic Testing (RIGhT) project, to identify critically ill children for whom a molecular diagnosis is likely to change inpatient management. Two important goals of the RIGhT project were to provide appropriate genetic counseling, and to develop protocols to ensure efficient test coordination- both of which relied heavily on laboratory and clinic-based genetic counselors (GCs). Here, rES was performed on 27 inpatient trios from October 2016 to August 2018; laboratory and clinical GCs encountered significant challenges in the coordination of this testing. The GCs involved retrospectively reviewed these cases and identified three common challenges encountered during pretest counseling and coordination. The aim of this paper is to define these challenges using illustrative case examples that highlight the importance of including GCs to support rES programs.
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- 2019
28. The Impact of Rapid Exome Sequencing on Medical Management of Critically Ill Children
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Margaret P. Adam, Mallory B Smith, Heather M. Byers, Jennifer N. Dines, Mesaki Kenneth Ndugga-Kabuye, Amanda S. Freed, Katrina M. Dipple, Robert DiGeronimo, Heather C Mefford, James T. Bennett, Gail H. Deutsch, Katie Fogus, Jenny Thies, Zeenia Billimoria, Sarah V. Clowes Candadai, John K. McGuire, Angela Sun, Christina Lam, and Megan C. Sikes
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medicine.medical_specialty ,Critically ill ,business.industry ,Genetic counseling ,Disease ,Geneticist ,Reference laboratory ,03 medical and health sciences ,0302 clinical medicine ,030225 pediatrics ,Family medicine ,Pediatrics, Perinatology and Child Health ,medicine ,030212 general & internal medicine ,Personalized medicine ,business ,Exome sequencing ,Utilization management - Abstract
Objectives To evaluate the clinical usefulness of rapid exome sequencing (rES) in critically ill children with likely genetic disease using a standardized process at a single institution. To provide evidence that rES with should become standard of care for this patient population. Study design We implemented a process to provide clinical-grade rES to eligible children at a single institution. Eligibility included (a) recommendation of rES by a consulting geneticist, (b) monogenic disorder suspected, (c) rapid diagnosis predicted to affect inpatient management, (d) pretest counseling provided by an appropriate provider, and (e) unanimous approval by a committee of 4 geneticists. Trio exome sequencing was sent to a reference laboratory that provided verbal report within 7-10 days. Clinical outcomes related to rES were prospectively collected. Input from geneticists, genetic counselors, pathologists, neonatologists, and critical care pediatricians was collected to identify changes in management related to rES. Results There were 54 patients who were eligible for rES over a 34-month study period. Of these patients, 46 underwent rES, 24 of whom (52%) had at least 1 change in management related to rES. In 20 patients (43%), a molecular diagnosis was achieved, demonstrating that nondiagnostic exomes could change medical management in some cases. Overall, 84% of patients were under 1 month old at rES request and the mean turnaround time was 9 days. Conclusions rES testing has a significant impact on the management of critically ill children with suspected monogenic disease and should be considered standard of care for tertiary institutions who can provide coordinated genetics expertise.
- Published
- 2020
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29. Correction: TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants
- Author
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Amber Begtrup, Heather C Mefford, Hiltrud Muhle, Sharon F. Suchy, Barbara K. Burton, Angela Sun, Ingo Helbig, René Santer, J. Lawrence Merritt, Kolja Becker, Megan T. Cho, Katherine L. Helbig, Katie Golden-Grant, Amy Lacroix, Rachel Westman, Alison M. Muir, Ganka Douglas, Dmitriy Niyazov, Kristin G. Monaghan, Jennifer N. Dines, Almuth Caliebe, Jenny Thies, Leah Fleming, Manuela Pendziwiat, Can Ficicioglu, Alice Basinger, Dianne Laboy Cintrón, Katherine H. Kim, Kirsty McWalter, Francisca Millan, Joline C. Dalton, and Peter I. Karachunski
- Subjects
Computer science ,business.industry ,Artificial intelligence ,Clinical phenotype ,business ,computer.software_genre ,Spectrum (topology) ,computer ,Genetics (clinical) ,Natural language processing ,Spelling - Abstract
The original version of this Article contained an error in the spelling of the author J. Lawrence Merritt, which was incorrectly given as Lawrence Merritt. This has now been corrected in both the PDF and HTML versions of the Article.
- Published
- 2019
- Full Text
- View/download PDF
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