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Smith ED, Blanco K, Sajan SA, Hunter JM, Shinde DN, Wayburn B, Rossi M, Huang J, Stevens CA, Muss C, Alcaraz W, Hagman KDF, Tang S, Radtke K. A retrospective review of multiple findings in diagnostic exome sequencing: half are distinct and half are overlapping diagnoses. Genet Med 2019; 21:2199-2207. [PMID: 30894705 PMCID: PMC6774997 DOI: 10.1038/s41436-019-0477-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE We evaluated clinical and genetic features enriched in patients with multiple Mendelian conditions to determine which patients are more likely to have multiple potentially relevant genetic findings (MPRF). METHODS Results of the first 7698 patients who underwent exome sequencing at Ambry Genetics were reviewed. Clinical and genetic features were examined and degree of phenotypic overlap between the genetic diagnoses was evaluated. RESULTS Among patients referred for exome sequencing, 2% had MPRF. MPRF were more common in patients from consanguineous families and patients with greater clinical complexity. The difference in average number of organ systems affected is small: 4.3 (multiple findings) vs. 3.9 (single finding) and may not be distinguished in clinic. CONCLUSION Patients with multiple genetic diagnoses had a slightly higher number of organ systems affected than patients with single genetic diagnoses, largely because the comorbid conditions affected overlapping organ systems. Exome testing may be beneficial for all cases with multiple organ systems affected. The identification of multiple relevant genetic findings in 2% of exome patients highlights the utility of a comprehensive molecular workup and updated interpretation of existing genomic data; a single definitive molecular diagnosis from analysis of a limited number of genes may not be the end of a diagnostic odyssey.
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Affiliation(s)
- Erica D Smith
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Samin A Sajan
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Bess Wayburn
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Mari Rossi
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Candace Muss
- Children's Hospital at Erlanger, Chattanooga, TN, USA
| | - Wendy Alcaraz
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA.
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202
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The Korean undiagnosed diseases program: lessons from a one-year pilot project. Orphanet J Rare Dis 2019; 14:68. [PMID: 30894207 PMCID: PMC6427886 DOI: 10.1186/s13023-019-1041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/28/2019] [Indexed: 11/12/2022] Open
Abstract
Background The Korean Undiagnosed Diseases Program (KUDP) was launched in January 2017 as a one-year pilot project to address the increasing global interest in patients with undiagnosed rare diseases. The purpose of this paper is to summarize the project results and emphasize the unmet research needs among patients with undiagnosed rare diseases in Korea. Results Patient enrollment, assessment, and diagnostic processes were determined by the KUDP clinical expert consortium. Patients followed a diagnostic workflow after being categorized into one of four groups: I) insufficient clinical information or lack of standard diagnostic processes; II) undiagnosed due to low disease awareness; III) clinically diagnosed but unconfirmed genetically due to genetic heterogeneities; or IV) unknown disease due to complex, atypical clinical presentations. After excluding two patients from group I, 97 patients were enrolled, including 10 in group II, 67 in group III, and 20 in group IV. Most of them (92 of 97, 94.8%) were pediatric patients (< 18 years old) and 59 (60.8%) were male. The primary symptoms for 80 patients (82.5%) were neurologic. During the one-year pilot study, 72 patients completed a diagnostic assessment including clinical and molecular genetic analyses; some patients also underwent pathological or biochemical analysis. Twenty-eight of these patients (28/72, 38.9%) achieved molecular genetic diagnosis. Thirteen patients were diagnosed based on traditional tests, including biochemical assay, single or targeted genetic analysis, and chromosomal microarray. We performed whole exome sequencing on 52 patients, among whom 15 (28.8%, 15/52) reached a final diagnosis. One new disorder was identified via international collaboration. Conclusions Using an efficient clinical diagnostic workflow, this KUDP pilot study resulted in a fair diagnostic success rate, improving the potential for additional diagnoses and new scientific discovery of complex and rare diseases. KUDP also satisfied unmet needs for rare diseases with multisystem involvement, highlighting the value of emerging genomic technologies for further research into rare and still-undiagnosed conditions. Electronic supplementary material The online version of this article (10.1186/s13023-019-1041-5) contains supplementary material, which is available to authorized users.
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203
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Bryant D, Liu Y, Datta S, Hariri H, Seda M, Anderson G, Peskett E, Demetriou C, Sousa S, Jenkins D, Clayton P, Bitner-Glindzicz M, Moore GE, Henne WM, Stanier P. SNX14 mutations affect endoplasmic reticulum-associated neutral lipid metabolism in autosomal recessive spinocerebellar ataxia 20. Hum Mol Genet 2019; 27:1927-1940. [PMID: 29635513 DOI: 10.1093/hmg/ddy101] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/15/2018] [Indexed: 12/12/2022] Open
Abstract
Mutations in SNX14 cause the autosomal recessive cerebellar ataxia 20 (SCAR20). Mutations generally result in loss of protein although several coding region deletions have also been reported. Patient-derived fibroblasts show disrupted autophagy, but the precise function of SNX14 is unknown. The yeast homolog, Mdm1, functions in endoplasmic reticulum (ER)-lysosome/vacuole inter-organelle tethering, but functional conservation in mammals is still required. Here, we show that loss of SNX14 alters but does not block autophagic flux. In addition, we find that SNX14 is an ER-associated protein that functions in neutral lipid homeostasis and inter-organelle crosstalk. SNX14 requires its N-terminal transmembrane helices for ER localization, while the Phox homology (PX) domain is dispensable for subcellular localization. Both SNX14-mutant fibroblasts and SNX14KO HEK293 cells accumulate aberrant cytoplasmic vacuoles, suggesting defects in endolysosomal homeostasis. However, ER-late endosome/lysosome contact sites are maintained in SNX14KO cells, indicating that it is not a prerequisite for ER-endolysosomal tethering. Further investigation of SNX14- deficiency indicates general defects in neutral lipid metabolism. SNX14KO cells display distinct perinuclear accumulation of filipin in LAMP1-positive lysosomal structures indicating cholesterol accumulation. Consistent with this, SNX14KO cells display a slight but detectable decrease in cholesterol ester levels, which is exacerbated with U18666A. Finally, SNX14 associates with ER-derived lipid droplets (LD) following oleate treatment, indicating a role in ER-LD crosstalk. We therefore identify an important role for SNX14 in neutral lipid homeostasis between the ER, lysosomes and LDs that may provide an early intervention target to alleviate the clinical symptoms of SCAR20.
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Affiliation(s)
- Dale Bryant
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Yang Liu
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sanchari Datta
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hanaa Hariri
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marian Seda
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Emma Peskett
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Charalambos Demetriou
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Sergio Sousa
- Serviço de Genética Medica, Hospital Pediatrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Dagan Jenkins
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Peter Clayton
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
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204
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Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico. NPJ Genom Med 2019; 4:5. [PMID: 30792901 PMCID: PMC6375919 DOI: 10.1038/s41525-018-0076-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/19/2018] [Indexed: 11/14/2022] Open
Abstract
Patients with rare, undiagnosed, or genetic disease (RUGD) often undergo years of serial testing, commonly referred to as the “diagnostic odyssey”. Patients in resource-limited areas face even greater challenges—a definitive diagnosis may never be reached due to difficulties in gaining access to clinicians, appropriate specialists, and diagnostic testing. Here, we report on a collaboration of the Illumina iHope Program with the Foundation for the Children of the Californias and Hospital Infantil de Las Californias, to enable deployment of clinical whole genome sequencing (cWGS) as first-tier test in a resource-limited dysmorphology clinic in northern Mexico. A total of 60 probands who were followed for a suspected genetic diagnosis and clinically unresolved after expert examination were tested with cWGS, and the ordering clinicians completed a semi-structured survey to investigate change in clinical management resulting from cWGS findings. Clinically significant genomic findings were identified in 68.3% (n = 41) of probands. No recurrent molecular diagnoses were observed. Copy number variants or gross chromosomal abnormalities accounted for 48.8% (n = 20) of the diagnosed cases, including a mosaic trisomy and suspected derivative chromosomes. A qualitative assessment of clinical management revealed 48.8% (n = 20) of those diagnosed had a change in clinical course based on their cWGS results, despite resource limitations. These data suggest that a cWGS first-tier testing approach can benefit patients with suspected genetic disorders. Whole-genome sequencing (WGS) provides a valuable first-tier diagnostic test at pediatric clinics in resource-limited
parts of the world, according to a study of children with suspected genetic disease treated in northern Mexico. A team led by Marilyn Jones from the Rady Children’s Hospital and Ryan Taft from Illumina Inc., both in San Diego, California, USA, describe a collaboration with a volunteer-led clinic in Tijuana, Mexico, where they offered genome sequencing for children with suspected genetic conditions—philanthropically through the iHope Program. Among the 60 families that participated, the clinical laboratory team identified genomic variants with diagnostic relevance in 41 (68%) cases. The genomic information contributed to changes in clinical management for 20 of these children, demonstrating the impact of WGS in places where patients generally don’t have access to medical specialists or other sophisticated molecular tests.
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205
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BoAli A, Tlili-Graiess K, AlHashem A, AlShahwan S, Zuccoli G, Tabarki B. Novel Homozygous Mutation of the AIMP1 Gene: A Milder Neuroimaging Phenotype With Preservation of the Deep White Matter. Pediatr Neurol 2019; 91:57-61. [PMID: 30477741 DOI: 10.1016/j.pediatrneurol.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/05/2018] [Accepted: 09/22/2018] [Indexed: 01/18/2023]
Abstract
BACKGROUND Mutations in AIMP1, which plays an important role in the development and maintenance of axon-cytoskeleton integrity and regulating neurofilaments, cause neurodegeneration of variable severity and white matter abnormalities. METHODS From the patient records we analyzed the clinical evaluation, molecular genetics, neurodiagnostic, and neuroradiological investigations. RESULTS We describe six members of a large consanguineous family with a phenotype of severe neurodegeneration in the form of developmental delays, progressive microcephaly, epilepsy, and failure to thrive. MRI showed callosal atrophy and T2 hyperintensity in the superficial white matter. The periventricular and deep white matter structures were, however, preserved. MR spectroscopy demonstrated N-acetylaspartate preservation without evidence of neuroinflammation. Exome sequencing showed a novel homozygous mutation of the AIMP1 gene in all individuals: c.917A>G (p.(Asp306Gly)). CONCLUSIONS This novel homozygous mutation of the AIMP1 gene is characterized by preserved development of the periventricular and deep white matter structures as demonstrated by MRI and MR spectroscopy correlation.
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Affiliation(s)
- Ahmed BoAli
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kalthoum Tlili-Graiess
- Division of Neuroradiology, Department of Radiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal AlHashem
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Saad AlShahwan
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Giulio Zuccoli
- Division of Neuroradiology, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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206
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Lee JJY, van Karnebeek CDM, Wasserman WW. Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J Am Med Inform Assoc 2019; 26:124-133. [PMID: 30535356 PMCID: PMC6339516 DOI: 10.1093/jamia/ocy153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023] Open
Abstract
Objective The clinical diagnosis of genetic disorders is undergoing transformation, driven by whole exome sequencing and whole genome sequencing (WES/WGS). However, such nucleotide-level resolution technologies create an interpretive challenge. Prior literature suggests that clinicians may employ characteristic cognitive processes during WES/WGS investigations to identify disruptions in genes causal for the observed disease. Based on cognitive ergonomics, we designed and evaluated a gene prioritization workflow that supported these cognitive processes. Materials and Methods We designed a novel workflow in which clinicians recalled known genetic diseases with similarity to patient phenotypes to inform WES/WGS data interpretation. This prototype-based workflow was evaluated against the common computational approach based on physician-specified sets of individual patient phenotypes. The evaluation was conducted as a web-based user study, in which 18 clinicians analyzed 2 simulated patient scenarios using a randomly assigned workflow. Data analysis compared the 2 workflows with respect to accuracy and efficiency in diagnostic interpretation, efficacy in collecting detailed phenotypic information, and user satisfaction. Results Participants interpreted genetic diagnoses faster using prototype-based workflows. The 2 workflows did not differ in other evaluated aspects. Discussion The user study findings indicate that prototype-based approaches, which are designed to model experts’ cognitive processes, can expedite gene prioritization and provide utility in synergy with common phenotype-driven variant/gene prioritization approaches. However, further research of the extent of this effect across diverse genetic diseases is required. Conclusion The findings demonstrate potential for prototype-based phenotype description to accelerate computer-assisted variant/gene prioritization through complementation of skills and knowledge of clinical experts via human–computer interaction.
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Affiliation(s)
- Jessica J Y Lee
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara D M van Karnebeek
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics and Clinical Genetics, Emma Children's Hospital, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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207
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Iqbal Z, Tawamie H, Ba W, Reis A, Halak BA, Sticht H, Uebe S, Kasri NN, Riazuddin S, van Bokhoven H, Abou Jamra R. Loss of function of SVBP leads to autosomal recessive intellectual disability, microcephaly, ataxia, and hypotonia. Genet Med 2019; 21:1790-1796. [DOI: 10.1038/s41436-018-0415-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/07/2018] [Indexed: 01/08/2023] Open
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208
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Gergics P. Pituitary Transcription Factor Mutations Leading to Hypopituitarism. EXPERIENTIA SUPPLEMENTUM (2012) 2019; 111:263-298. [PMID: 31588536 DOI: 10.1007/978-3-030-25905-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Congenital pituitary hormone deficiency is a disabling condition. It is part of a spectrum of disorders including craniofacial midline developmental defects ranging from holoprosencephaly through septo-optic dysplasia to combined and isolated pituitary hormone deficiency. The first genes discovered in the human disease were based on mouse models of dwarfism due to mutations in transcription factor genes. High-throughput DNA sequencing technologies enabled clinicians and researchers to find novel genetic causes of hypopituitarism for the more than three quarters of patients without a known genetic diagnosis to date. Transcription factor (TF) genes are at the forefront of the functional analysis of novel variants of unknown significance due to the relative ease in in vitro testing in a research lab. Genetic testing in hypopituitarism is of high importance to the individual and their family to predict phenotype composition, disease progression and to avoid life-threatening complications such as secondary adrenal insufficiency.This chapter aims to highlight our current understanding about (1) the contribution of TF genes to pituitary development (2) the diversity of inheritance and phenotype features in combined and select isolated pituitary hormone deficiency and (3) provide an initial assessment on how to approach variants of unknown significance in human hypopituitarism. Our better understanding on how transcription factor gene variants lead to hypopituitarism is a meaningful step to plan advanced therapies to specific genetic changes in the future.
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Affiliation(s)
- Peter Gergics
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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209
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Rad A, Altunoglu U, Miller R, Maroofian R, James KN, Çağlayan AO, Najafi M, Stanley V, Boustany RM, Yeşil G, Sahebzamani A, Ercan-Sencicek G, Saeidi K, Wu K, Bauer P, Bakey Z, Gleeson JG, Hauser N, Gunel M, Kayserili H, Schmidts M. MAB21L1 loss of function causes a syndromic neurodevelopmental disorder with distinctive cerebellar, ocular, cranio facial and genital features (COFG syndrome). J Med Genet 2018; 56:332-339. [PMID: 30487245 PMCID: PMC6581149 DOI: 10.1136/jmedgenet-2018-105623] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Putative nucleotidyltransferase MAB21L1 is a member of an evolutionarily well-conserved family of the male abnormal 21 (MAB21)-like proteins. Little is known about the biochemical function of the protein; however, prior studies have shown essential roles for several aspects of embryonic development including the eye, midbrain, neural tube and reproductive organs. OBJECTIVE A homozygous truncating variant in MAB21L1 has recently been described in a male affected by intellectual disability, scrotal agenesis, ophthalmological anomalies, cerebellar hypoplasia and facial dysmorphism. We employed a combination of exome sequencing and homozygosity mapping to identify the underlying genetic cause in subjects with similar phenotypic features descending from five unrelated consanguineous families. RESULTS We identified four homozygous MAB21L1 loss of function variants (p.Glu281fs*20, p.Arg287Glufs*14 p.Tyr280* and p.Ser93Serfs*48) and one missense variant (p.Gln233Pro) in 10 affected individuals from 5 consanguineous families with a distinctive autosomal recessive neurodevelopmental syndrome. Cardinal features of this syndrome include a characteristic facial gestalt, corneal dystrophy, hairy nipples, underdeveloped labioscrotal folds and scrotum/scrotal agenesis as well as cerebellar hypoplasia with ataxia and variable microcephaly. CONCLUSION This report defines an ultrarare but clinically recognisable Cerebello-Oculo-Facio-Genital syndrome associated with recessive MAB21L1 variants. Additionally, our findings further support the critical role of MAB21L1 in cerebellum, lens, genitalia and as craniofacial morphogenesis.
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Affiliation(s)
- Abolfazl Rad
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey
| | - Rebecca Miller
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's, University of London, London, UK
| | - Kiely N James
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA.,Medical Genetics Department, Bilim University School of Medicine, İstanbul, Turkey
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Rose-Mary Boustany
- Department of Pediatrics and Adolescent Medicine, Neurogenetics Program and Division of Pediatric Neurology, American University of Beirut Medical Center Special Kids Clinic, Beirut, Lebanon.,Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Gözde Yeşil
- Medical Genetics Department, Bezmi Alem University School of Medicine, Istanbul, Turkey
| | - Afsaneh Sahebzamani
- Paediatric and Genetic Counselling Center, Kerman Welfare Organization, Kerman, Iran
| | - Gülhan Ercan-Sencicek
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kolsoum Saeidi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medical Genetics, Kerman University of Medical Sciences, Kerman, Iran
| | - Kaman Wu
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Zeineb Bakey
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Natalie Hauser
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Murat Gunel
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Hulya Kayserili
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine (KUSoM), İstanbul, Turkey
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
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210
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Wadhwa RR, Park DY, Natowicz MR. The accuracy of computer-based diagnostic tools for the identification of concurrent genetic disorders. Am J Med Genet A 2018; 176:2704-2709. [PMID: 30475443 DOI: 10.1002/ajmg.a.40651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/09/2018] [Accepted: 09/08/2018] [Indexed: 11/11/2022]
Abstract
The increasing use of next-generation sequencing, especially clinical exome sequencing, has revealed that individuals having two coexisting genetic conditions are not uncommon occurrences. This pilot study evaluates the efficacy of two methodologically distinct computational differential diagnosis generating tools-FindZebra and SimulConsult-in identifying multiple genetic conditions in a single patient. Clinical query terms were generated for each of 15 monogenic disorders that were effective in resulting in the top 10 list of differential diagnoses for each of the 15 monogenic conditions when entered into these bioinformatics tools. Then, the terms of over 125 pairings of these conditions were entered using each tool and the resulting list of diagnoses evaluated to determine how often both diagnoses of a pair were represented in that list. Neither tool was successful in identifying both members of a pair of conditions in greater than 40% of test cases. Disorder detection sensitivity was not homogeneous within a tool, with each tool favoring the identification of a subset of genetic conditions. In view of recent exome sequencing data showing an unexpectedly high prevalence of coexistent monogenic conditions, the results from this pilot study highlight a need for the development of computational tools designed to effectively generate differential diagnoses with consideration of the possibility of coexisting conditions.
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Affiliation(s)
- Raoul R Wadhwa
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Deborah Y Park
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Marvin R Natowicz
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio.,Pathology and Laboratory Medicine, Genomic Medicine, Neurological and Pediatrics Institutes, Cleveland Clinic, Cleveland, Ohio
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211
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Hamanaka K, Miyatake S, Koshimizu E, Tsurusaki Y, Mitsuhashi S, Iwama K, Alkanaq AN, Fujita A, Imagawa E, Uchiyama Y, Tawara N, Ando Y, Misumi Y, Okubo M, Nakashima M, Mizuguchi T, Takata A, Miyake N, Saitsu H, Iida A, Nishino I, Matsumoto N. RNA sequencing solved the most common but unrecognized NEB pathogenic variant in Japanese nemaline myopathy. Genet Med 2018; 21:1629-1638. [PMID: 30467404 DOI: 10.1038/s41436-018-0360-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The diagnostic rate for Mendelian diseases by exome sequencing (ES) is typically 20-40%. The low rate is partly because ES misses deep-intronic or synonymous variants leading to aberrant splicing. In this study, we aimed to apply RNA sequencing (RNA-seq) to efficiently detect the aberrant splicings and their related variants. METHODS Aberrant splicing in biopsied muscles from six nemaline myopathy (NM) cases unresolved by ES were analyzed with RNA-seq. Variants related to detected aberrant splicing events were analyzed with Sanger sequencing. Detected variants were screened in NM patients unresolved by ES. RESULTS We identified a novel deep-intronic NEB pathogenic variant, c.1569+339A>G in one case, and another novel synonymous NEB pathogenic variant, c.24684G>C (p.Ser8228Ser) in three cases. The c.24684G>C variant was observed to be the most frequent among all NEB pathogenic variants in normal Japanese populations with a frequency of 1 in 178 (20 alleles in 3552 individuals), but was previously unrecognized. Expanded screening of the variant identified it in a further four previously unsolved nemaline myopathy cases. CONCLUSION These results indicated that RNA-seq may be able to solve a large proportion of previously undiagnosed muscle diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yoshinori Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Ahmed N Alkanaq
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Nozomu Tawara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - Yukio Ando
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - Yohei Misumi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - Mariko Okubo
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Aritoshi Iida
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.
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212
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van der Sluijs PJ, Jansen S, Vergano SA, Adachi-Fukuda M, Alanay Y, AlKindy A, Baban A, Bayat A, Beck-Wödl S, Berry K, Bijlsma EK, Bok LA, Brouwer AFJ, van der Burgt I, Campeau PM, Canham N, Chrzanowska K, Chu YWY, Chung BHY, Dahan K, De Rademaeker M, Destree A, Dudding-Byth T, Earl R, Elcioglu N, Elias ER, Fagerberg C, Gardham A, Gener B, Gerkes EH, Grasshoff U, van Haeringen A, Heitink KR, Herkert JC, den Hollander NS, Horn D, Hunt D, Kant SG, Kato M, Kayserili H, Kersseboom R, Kilic E, Krajewska-Walasek M, Lammers K, Laulund LW, Lederer D, Lees M, López-González V, Maas S, Mancini GMS, Marcelis C, Martinez F, Maystadt I, McGuire M, McKee S, Mehta S, Metcalfe K, Milunsky J, Mizuno S, Moeschler JB, Netzer C, Ockeloen CW, Oehl-Jaschkowitz B, Okamoto N, Olminkhof SNM, Orellana C, Pasquier L, Pottinger C, Riehmer V, Robertson SP, Roifman M, Rooryck C, Ropers FG, Rosello M, Ruivenkamp CAL, Sagiroglu MS, Sallevelt SCEH, Sanchis Calvo A, Simsek-Kiper PO, Soares G, Solaeche L, Sonmez FM, Splitt M, Steenbeek D, Stegmann APA, Stumpel CTRM, Tanabe S, Uctepe E, Utine GE, Veenstra-Knol HE, Venkateswaran S, Vilain C, Vincent-Delorme C, Vulto-van Silfhout AT, Wheeler P, Wilson GN, Wilson LC, Wollnik B, Kosho T, Wieczorek D, Eichler E, Pfundt R, de Vries BBA, Clayton-Smith J, Santen GWE. The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin-Siris syndrome. Genet Med 2018; 21:1295-1307. [PMID: 30349098 PMCID: PMC6752273 DOI: 10.1038/s41436-018-0330-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/26/2018] [Indexed: 01/09/2023] Open
Abstract
Purpose Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods Clinicians entered clinical data in an extensive web-based survey. Results 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features.
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Affiliation(s)
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of the King's Daughters, Norfolk, VA, USA
| | - Miho Adachi-Fukuda
- Department of Pediatrics, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Yasemin Alanay
- School of Medicine, Department of Pediatrics, Pediatric Genetics Unit, Acibadem University, Istanbul, Turkey
| | - Adila AlKindy
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Anwar Baban
- Pediatric Cardiology and Cardiac Surgery Department, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Allan Bayat
- Copenhagen University Hospital Hvidovre, Copenhagen, Denmark
| | - Stefanie Beck-Wödl
- Department of Molecular Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Katherine Berry
- Department of Medical Genetics, Shodair Hospital, Helena, MT, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Màxima Medical Centre, Veldhoven, The Netherlands
| | - Alwin F J Brouwer
- Department of Paediatrics, Nij Smellinghe Hospital, Drachten, The Netherlands
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Natalie Canham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom.,Cheshire and Merseyside Regional Genetics Service, Liverpool Women's Hospital, Crown Street, Liverpool, United Kingdom
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Yoyo W Y Chu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Brain H Y Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Karin Dahan
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | | | - Anne Destree
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Tracy Dudding-Byth
- Hunter Genetics and University of Newcastle, GrowUpWell Priority Research Centre, Newcastle, Australia
| | - Rachel Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Ellen R Elias
- Department of Pediatrics and Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom
| | - Blanca Gener
- Department of Genetics, Cruces University Hospital, Biocruces Health Research Institute, Vizcayam, Spain
| | - Erica H Gerkes
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ute Grasshoff
- Department of Molecular Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin R Heitink
- Department of Rehabilitation Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Johanna C Herkert
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | | | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin, Berlin, Germany
| | - David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSoM), İstanbul, Turkey
| | - Rogier Kersseboom
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Esra Kilic
- Department of Pediatric Genetics, Hematology Oncology Research & Training Children's Hospital, Ankara, Turkey
| | | | - Kylin Lammers
- Department of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Lone W Laulund
- Department of Paediatrics, Odense University Hospital, Odense, Denmark
| | - Damien Lederer
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatria, Hospital Clinico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER-ISCIII, Murcia, Spain
| | - Saskia Maas
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Francisco Martinez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, Ireland
| | - Sarju Mehta
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | | | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - John B Moeschler
- Department of Pediatrics, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Christian Netzer
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Sharon N M Olminkhof
- Willem Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Carmen Orellana
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Laurent Pasquier
- CRMR Déficiences intellectuelles, Service de Génétique Médicale, CLAD Ouest CHU Hôpital Sud, Rennes, France
| | - Caroline Pottinger
- All Wales Medical Genetics Service, Glan Clwyd Hospital, Rhyl, United Kingdom
| | - Vera Riehmer
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | | | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Fabienne G Ropers
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Monica Rosello
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Suzanne C E H Sallevelt
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Pelin O Simsek-Kiper
- Department of Pediatric Genetics, Ihsan Dogramaci Children's Hospital, Hacettepe University School of Medicine, Ankara, Turkey
| | - Gabriela Soares
- Jacinto de Magalhães Medical Genetics Center, Centro Hospitalar do Porto, Porto, Portugal
| | - Lucia Solaeche
- Departamento de neurometabólicas, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Fatma Mujgan Sonmez
- Karadeniz Technical University, Faculty of Medicine, Dept of Child Neurology, Retired Professor, Trabzon, Turkey
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetics Medicine, Newcastle upon Tyne, United Kingdom
| | - Duco Steenbeek
- Department of Rehabilitation Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Constance T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Saori Tanabe
- Division of Pediatrics, Yamagata Prefectural and Sakata Munici pal Hospital Organization Nihon-Kai General Hospital, Sakata, Japan
| | | | - G Eda Utine
- Department of Pediatric Genetics, Ihsan Dogramaci Children's Hospital, Hacettepe University School of Medicine, Ankara, Turkey
| | - Hermine E Veenstra-Knol
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme. ULB Center of Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Golder N Wilson
- KinderGenome Genetics, Medical City Hospital Dallas, Dallas, TX, USA
| | - Louise C Wilson
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Tomoki Kosho
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Evan Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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213
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Balobaid A, Ben-Omran T, Ramzan K, Altassan R, Almureikhi M, Musa S, Al-Hashmi N, Al-Owain M, Al-Zaidan H, Al-Hassnan Z, Imtiaz F, Al-Sayed M. Delineating the phenotypic spectrum of hyperphosphatasia with mental retardation syndrome 4 in 14 patients of Middle-Eastern origin. Am J Med Genet A 2018; 176:2850-2857. [PMID: 30345601 DOI: 10.1002/ajmg.a.40627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) is a rare autosomal recessive condition caused by an impairment of glycosylphophatidylinositol biosynthesis. The cardinal features of HPMRS4 include; characteristic facial features, severe intellectual disability and various neurologic abnormalities. We report here detailed clinical, biochemical, and molecular findings of 14 patients clinically suspected to have HPMRS4, from three Middle-Eastern Countries; Saudi Arabia, Qatar, and Oman. All patients in our series presented with the cardinal features pointing to HPMRS4 and with an elevated alkaline phosphatase level. Five patients had megalocornea, which have been reported recently in an Arab patient. Additionally, fracture, bilateral coxa valga, camptodactyly, truncal obesity, and hyperpigmented macules of the upper thigh, each was seen once and was not described before with HPMRS4. Additional clinical and radiological findings are described, supporting the novel clinical and radiological findings recently described in Egyptian patients. The utilization of homozygosity mapping coupled with PGAP3 sequencing and whole exome sequencing facilitated the mutation detection in these patients. These missense mutations include c.320C > T (p.S107 L), c.850C > T (p.H284Y), and c.851A > G (p.H284R) in the PGAP3 gene. We believe that the recurrent mutations identified in our cohort may represent founder mutations in big tribes from a certain geographical region of Saudi Arabia, Qatar, and Oman. Therefore, in case of a clinical suspicion of HPMRS4 in these populations, targeted genetic testing for the identified mutations should be performed first to expedite the genetic diagnosis.
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Affiliation(s)
- Ameera Balobaid
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Ruqaiah Altassan
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Mariam Almureikhi
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | - Sara Musa
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | | | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hamad Al-Zaidan
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zuhair Al-Hassnan
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Moeenaldeen Al-Sayed
- Department of Medical Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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214
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Putting genome-wide sequencing in neonates into perspective. Genet Med 2018; 21:1074-1082. [PMID: 30287924 DOI: 10.1038/s41436-018-0293-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/23/2018] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Several studies have reported diagnostic yields up to 57% for rapid exome or genome sequencing (rES/GS) as a single test in neonatal intensive care unit (NICU) patients, but the additional yield of rES/GS compared with other available diagnostic options still remains unquantified in this population. METHODS We retrospectively evaluated all genetic NICU consultations in a 2-year period. RESULTS In 132 retrospectively evaluated NICU consultations 27 of 32 diagnoses (84.4%) were made using standard genetic workup. Most diagnoses (65.6%) were made within 16 days. Diagnostic ES yield was 5/29 (17.2%). Genetic diagnoses had a direct effect on clinical management in 90.6% (29/32) of patients. CONCLUSIONS Our study shows that exome sequencing has a place in NICU diagnostics, but given the associated costs and the high yield of alternative diagnostic strategies, we recommend to first perform clinical genetic consultation.
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215
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Vahidnezhad H, Youssefian L, Saeidian AH, Touati A, Sotoudeh S, Jazayeri A, Guy A, Lovell PA, Liu L, Kariminejad A, McGrath JA, Zeinali S, Uitto J. Next generation sequencing identifies double homozygous mutations in two distinct genes (EXPH5 and COL17A1) in a patient with concomitant simplex and junctional epidermolysis bullosa. Hum Mutat 2018; 39:1349-1354. [PMID: 30016581 DOI: 10.1002/humu.23592] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/23/2018] [Accepted: 07/10/2018] [Indexed: 11/06/2022]
Abstract
Epidermolysis bullosa (EB) is a heterogeneous group of heritable blistering diseases. We developed a next generation sequencing (NGS) panel covering 21 genes associated with skin fragility disorders, and it was applied to DNA from 91 probands with the diagnosis of EB. In one patient, novel homozygous mutations were disclosed in two different, unlinked EB-associated genes: EXPH5, chr11 g.108510085G > A; p.Arg1808Ter and COL17A1, chr10 g.104077423delT; p.Thr68LeufsTer106. Consequences of the COL17A1 mutation were examined by RNAseq which revealed a complex splicing pattern predicting synthesis of a truncated polypeptide (85%) or in-frame deletion of exon 4 (15% of transcripts). Transmission electron microscopy (TEM) and immunostaining revealed findings consistent with EB simplex (EBS) and junctional EB (JEB), and clinical examination revealed a complex phenotype with features of both subtypes. This case illustrates the power of next generation sequencing in identifying mutations in patients with complex EB phenotype, with implications for genotype-phenotype correlations, prenatal testing, and genetic counseling of families at risk for recurrence.
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Affiliation(s)
- Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Jazayeri
- Department of Information Science, College of Computing and Informatics, Drexel University, Philadelphia, PA, USA
| | - Alyson Guy
- Viapath, St Thomas' Hospital, London, UK
| | | | - Lu Liu
- Viapath, St Thomas' Hospital, London, UK
| | | | - John A McGrath
- Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Kawsar Human Genetics Research Center, Tehran, Iran
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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216
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Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q. Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis. Hereditas 2018; 155:32. [PMID: 30279644 PMCID: PMC6162922 DOI: 10.1186/s41065-018-0069-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000 bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing. RESULTS Here we describe a case study, where WES identified only one heterozygous pathogenic variant for an individual suspected to have glycogen storage disease type Ia (GSD-Ia), which is an autosomal recessive disease caused by bi-allelic mutations in the G6PC gene. Through Nanopore long-read whole-genome sequencing, we identified a 7.1 kb deletion covering two exons on the other allele, suggesting that complex structural variants (SVs) may explain a fraction of cases when the second pathogenic allele is missing from WES on recessive diseases. Both breakpoints of the deletion are within Alu elements, and we designed Sanger sequencing and quantitative PCR assays based on the breakpoints for preimplantation genetic diagnosis (PGD) for the family planning on another child. Four embryos were obtained after in vitro fertilization (IVF), and an embryo without deletion in G6PC was transplanted after PGD and was confirmed by prenatal diagnosis, postnatal diagnosis, and subsequent lack of disease symptoms after birth. CONCLUSIONS In summary, we present one of the first examples of using long-read sequencing to identify causal yet complex SVs in exome-negative patients, which subsequently enabled successful personalized PGD.
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Affiliation(s)
- Hefan Miao
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
| | | | - Qi Yang
- GrandOmics Biosciences, Beijing, 102206 China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, 102206 China
| | - Depeng Wang
- GrandOmics Biosciences, Beijing, 102206 China
| | - Na Ma
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
| | - Bodi Gao
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078 Hunan China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078 Hunan China
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217
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Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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A survey of undetected, clinically relevant chromosome abnormalities when replacing postnatal karyotyping by Whole Genome Sequencing. Eur J Med Genet 2018; 62:103543. [PMID: 30248410 DOI: 10.1016/j.ejmg.2018.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/30/2018] [Accepted: 09/18/2018] [Indexed: 11/21/2022]
Abstract
Whole genome sequencing (WGS) holds the potential to identify pathogenic gene mutations, copy number variation, uniparental disomy and structural rearrangements in a single genetic test. With its high diagnostic yield and decreasing costs, the question arises whether WGS can serve as a single test for all referrals to diagnostic genome laboratories ("one test fits all"). Here, we provide an estimate for the proportion of clinically relevant aberrations identified by light microscopy in postnatal referrals that would go undetected by WGS. To this end, we compiled the clinically relevant abnormal findings for each of the different referral categories in our laboratory during the period 2006-2015. We assumed that WGS would be performed on 300-500 bp DNA fragments with 150-bp paired sequence reads, and that the mean genome coverage is 30x, corresponding to current practice. For the detection of chromosomal mosaicism we set minimum thresholds of 10% for monosomy and 20% for trisomy. Based on the literature we assumed that balanced Robertsonian translocations and ∼9% of other, balanced chromosome rearrangements would not be detectable because of breakpoints in sequences of repetitive DNA. Based on our analysis of all 14,957 referrals, including 1455 abnormal cases, we show that at least 8.1% of these abnormalities would escape detection (corresponding to 0.79% of all referrals). The highest rate occurs in referrals of premature ovarian failure, as 73.3% of abnormalities would not be identified because of the frequent occurrence of low-level sex chromosome mosaicism. Among referrals of recurrent miscarriage, 25.6% of abnormalities would go undetected, mainly because of a high proportion of balanced Robertsonian translocations. In referrals of mental retardation (with or without multiple congenital anomalies) the abnormality would be missed in only 0.35% of referrals. These include cases without imbalances of unique DNA sequences but of clinical relevance, as for example, r(20) epilepsy syndrome. The expected shift to large-scale implementation of WGS ("one test fits most") as initial genetic test will be beneficial to patients and their families, since a cause for the clinical phenotype can be identified in more cases by a single genetic test at an early phase in the diagnostic process. However, a niche for genome analysis by light microscopy will remain. For example, in referrals of newborns with a suspicion of Down syndrome, karyotyping is not only a cost-effective method for providing a quick diagnosis, but also discriminates between trisomy 21 and a Robertsonian translocation involving chromosome 21. Thus, when replacing karyotyping by WGS, one must be aware of the rates and spectra of undetected abnormalities. In addition, it is equally important that requirements for cytogenetic follow-up studies are recognized.
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Fujiwara T, Yamamoto Y, Kim JD, Buske O, Takagi T. PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases. Am J Hum Genet 2018; 103:389-399. [PMID: 30173820 DOI: 10.1016/j.ajhg.2018.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/01/2018] [Indexed: 01/29/2023] Open
Abstract
Recently, to speed up the differential-diagnosis process based on symptoms and signs observed from an affected individual in the diagnosis of rare diseases, researchers have developed and implemented phenotype-driven differential-diagnosis systems. The performance of those systems relies on the quantity and quality of underlying databases of disease-phenotype associations (DPAs). Although such databases are often developed by manual curation, they inherently suffer from limited coverage. To address this problem, we propose a text-mining approach to increase the coverage of DPA databases and consequently improve the performance of differential-diagnosis systems. Our analysis showed that a text-mining approach using one million case reports obtained from PubMed could increase the coverage of manually curated DPAs in Orphanet by 125.6%. We also present PubCaseFinder (see Web Resources), a new phenotype-driven differential-diagnosis system in a freely available web application. By utilizing automatically extracted DPAs from case reports in addition to manually curated DPAs, PubCaseFinder improves the performance of automated differential diagnosis. Moreover, PubCaseFinder helps clinicians search for relevant case reports by using phenotype-based comparisons and confirm the results with detailed contextual information.
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Alsultan A, Al-Suliman AM, Aleem A, AlGahtani FH, Alfadhel M. Utilizing Whole-Exome Sequencing to Characterize the Phenotypic Variability of Sickle Cell Disease. Genet Test Mol Biomarkers 2018; 22:561-567. [PMID: 30183354 DOI: 10.1089/gtmb.2018.0058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Sickle cell disease (SCD) is a monogenic disease that has wide variety of phenotypes with both and environmental factors contributing to its severity. METHODS We performed whole-exome sequencing (WES) in 22 Saudi SCD patients to identify variants that could explain differences in disease phenotypes. All variants, except those that were benign and likely benign, described in the ClinVar database, were considered in our analysis. Gene-based association testing using sequence kernel association optimal unified test (SKAT-O) with small sample adjustment was performed to evaluate the effect of multiple variants in genes on SCD phenotypes. RESULTS The mean age of participants was 28 (range, 10-48 years). All patients were homozygous for the sickle cell mutation. The Benin haplotype was present in 15 patients and the Arab-Indian haplotype in 7 patients. One patient who had both SCD and CHARGE association was heterozygous for pathogenic mutation p.Arg987Ter in the CHD7 gene. One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance. Two patients with steady hemoglobin levels of 7.5 and 7.1 g/dL were carriers of the pathogenic mutation p.Gly140Ser in the RPL5 gene that is associated with Diamond-Blackfan anemia. None of the patients were transfusion dependent. A heterozygous pathogenic mutation in the LDLR gene associated with autosomal dominant familial hypercholesterolemia was present in one patient with deep venous thrombosis, although their cholesterol level was normal. One individual with stroke was a carrier for the p.Arg284Ter variant in the NLRP12 gene, which is associated with familial cold autoinflammatory syndrome 2. Another patient with stroke and a pulmonary embolism was heterozygous for the p.Pro106Leu variant of the MPL gene, which has been associated with thrombocytosis. Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study. SKAT-O analysis did not explain SCD heterogeneity. CONCLUSION WES provided limited information to explain the severity of SCD. Whole genome sequencing, epigenetic studies, and assessment of environmental factors might expand our knowledge of SCD heterogeneity.
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Affiliation(s)
- Abdulrahman Alsultan
- 1 Department of Pediatrics, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | | | - Aamer Aleem
- 3 Department of Internal Medicine, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Farjah H AlGahtani
- 3 Department of Internal Medicine, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Majid Alfadhel
- 4 Department of Pediatrics, King Abdullah Specialist Children's Hospital , King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia .,5 King Saud bin Abdulaziz University for Health Sciences , Riyadh, Saudi Arabia
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221
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Bramswig NC, Bertoli-Avella AM, Albrecht B, Al Aqeel AI, Alhashem A, Al-Sannaa N, Bah M, Bröhl K, Depienne C, Dorison N, Doummar D, Ehmke N, Elbendary HM, Gorokhova S, Héron D, Horn D, James K, Keren B, Kuechler A, Ismail S, Issa MY, Marey I, Mayer M, McEvoy-Venneri J, Megarbane A, Mignot C, Mohamed S, Nava C, Philip N, Ravix C, Rolfs A, Sadek AA, Segebrecht L, Stanley V, Trautman C, Valence S, Villard L, Wieland T, Engels H, Strom TM, Zaki MS, Gleeson JG, Lüdecke HJ, Bauer P, Wieczorek D. Genetic variants in components of the NALCN-UNC80-UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies). Hum Genet 2018; 137:753-768. [PMID: 30167850 PMCID: PMC6671679 DOI: 10.1007/s00439-018-1929-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/30/2022]
Abstract
NALCN is a conserved cation channel, which conducts a permanent sodium leak current and regulates resting membrane potential and neuronal excitability. It is part of a large ion channel complex, the "NALCN channelosome", consisting of multiple proteins including UNC80 and UNC79. The predominant neuronal expression pattern and its function suggest an important role in neuronal function and disease. So far, biallelic NALCN and UNC80 variants have been described in a small number of individuals leading to infantile hypotonia, psychomotor retardation, and characteristic facies 1 (IHPRF1, OMIM 615419) and 2 (IHPRF2, OMIM 616801), respectively. Heterozygous de novo NALCN missense variants in the S5/S6 pore-forming segments lead to congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD, OMIM 616266) with some clinical overlap. In this study, we present detailed clinical information of 16 novel individuals with biallelic NALCN variants, 1 individual with a heterozygous de novo NALCN missense variant and an interesting clinical phenotype without contractures, and 12 individuals with biallelic UNC80 variants. We report for the first time a missense NALCN variant located in the predicted S6 pore-forming unit inherited in an autosomal-recessive manner leading to mild IHPRF1. We show evidence of clinical variability, especially among IHPRF1-affected individuals, and discuss differences between the IHPRF1- and IHPRF2 phenotypes. In summary, we provide a comprehensive overview of IHPRF1 and IHPRF2 phenotypes based on the largest cohort of individuals reported so far and provide additional insights into the clinical phenotypes of these neurodevelopmental diseases to help improve counseling of affected families.
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Affiliation(s)
- Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | | | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Aida I Al Aqeel
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- American University of Beirut, Beirut, Lebanon
- Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Nouriya Al-Sannaa
- John Hopkins Aramco Health Care, Pediatric Services, Dhahran, Saudi Arabia
| | - Maissa Bah
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Katharina Bröhl
- Internal Medicine Department, Waldkrankenhaus Evangelical Hospital, Berlin, Germany
| | - Christel Depienne
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, 75013, Paris, France
| | - Nathalie Dorison
- Service de Neurochirurgie Pédiatrique, Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Diane Doummar
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Nadja Ehmke
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Hasnaa M Elbendary
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Svetlana Gorokhova
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Delphine Héron
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Denise Horn
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kiely James
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Boris Keren
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Samira Ismail
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Isabelle Marey
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Michèle Mayer
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Jennifer McEvoy-Venneri
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Andre Megarbane
- CEMEDIPP-Centre Medico Psychopedagogique, Beirut, Lebanon
- Institut Jerome Lejeune, Paris, France
| | - Cyril Mignot
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
| | - Sarar Mohamed
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Prince Abdullah bin Khaled Coeliac Disease Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Caroline Nava
- Groupe de Recherche Clinique sorbonne Université "Déficiences Intellectuelles et Autisme", Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, 75013, Paris, France
| | - Nicole Philip
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Cecile Ravix
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Arndt Rolfs
- CENTOGENE AG, The Rare Disease Company, Rostock, Germany
- Albrecht Kossel Institute, University of Rostock, Rostock, Germany
| | - Abdelrahim Abdrabou Sadek
- Pediatric Neurology Unit, Department of Pediatrics, Faculty of Medicine, Sohag University, Sohâg, Egypt
| | - Lara Segebrecht
- Institute of Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Camille Trautman
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Stephanie Valence
- AP-HP, Département de neuropédiatrie, GHUEP, Hôpital Armand Trousseau, Paris, France
| | - Laurent Villard
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Univ, MMG, INSERM, Marseille, France
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Howard Hughes Medical Institute, University of California San Diego, Rady Children's Institute for Genomic Medicine, La Jolla, CA, 92093, USA
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Peter Bauer
- CENTOGENE AG, The Rare Disease Company, Rostock, Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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Bellai‐Dussault K, Nguyen TTM, Baratang NV, Jimenez‐Cruz DA, Campeau PM. Clinical variability in inherited glycosylphosphatidylinositol deficiency disorders. Clin Genet 2018; 95:112-121. [DOI: 10.1111/cge.13425] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Kara Bellai‐Dussault
- Medical Genetics DivisionChildren's Hospital of Eastern Ontario Ottawa ON Canada
| | | | - Nissan V. Baratang
- CHU Sainte‐Justine Research CenterUniversity of Montreal Montreal QC Canada
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Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population. Genet Med 2018; 21:53-61. [PMID: 30100613 PMCID: PMC6752300 DOI: 10.1038/s41436-018-0016-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 11/29/2022] Open
Abstract
Purpose Next-generation sequencing (NGS) is rapidly replacing Sanger sequencing in genetic diagnostics. Sensitivity and specificity of NGS approaches are not well-defined, but can be estimated from applying NGS and Sanger sequencing in parallel. Utilizing this strategy, we aimed at optimizing exome sequencing (ES)–based diagnostics of a clinically diverse patient population. Methods Consecutive DNA samples from unrelated patients with suspected genetic disease were exome-sequenced; comparatively nonstringent criteria were applied in variant calling. One thousand forty-eight variants in genes compatible with the clinical diagnosis were followed up by Sanger sequencing. Based on a set of variant-specific features, predictors for true positives and true negatives were developed. Results Sanger sequencing confirmed 81.9% of ES-derived variants. Calls from the lower end of stringency accounted for the majority of the false positives, but also contained ~5% of the true positives. A predictor incorporating three variant-specific features classified 91.7% of variants with 100% specificity and 99.75% sensitivity. Confirmation status of the remaining variants (8.3%) was not predictable. Conclusions Criteria for variant calling in ES-based diagnostics impact on specificity and sensitivity. Confirmatory sequencing for a proportion of variants, therefore, remains a necessity. Our study exemplifies how these variants can be defined on an empirical basis.
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Wattacheril J, Shea PR, Mohammad S, Behling C, Aggarwal V, Wilson LA, Yates KP, Ito J, Fishbein M, Stong N, Lavine JE, Goldstein DB. Exome sequencing of an adolescent with nonalcoholic fatty liver disease identifies a clinically actionable case of Wilson disease. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003087. [PMID: 30026388 PMCID: PMC6169823 DOI: 10.1101/mcs.a003087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022] Open
Abstract
Diagnostic whole-exome sequencing has proven highly successful in a range of rare diseases, particularly early-onset genetic conditions. In more common conditions, however, exome sequencing for diagnostic purposes remains the exception. Here we describe a patient initially diagnosed with a common, complex liver disease, nonalcoholic fatty liver disease (NAFLD), who was determined to have Wilson disease (WD) upon research-related exome sequencing. The patient presented as a 14.5-yr-old adolescent with chronically elevated aminotransferases, normal ceruloplasmin, and histologic examination consistent with NAFLD with advanced fibrosis. He was enrolled in a large longitudinal study of patients with NAFLD and was found to have WD by exome sequencing performed 4 yr later. This new diagnosis, confirmed clinically by 24 h urine copper quantification, led to a change in the therapy from lifestyle counseling to directed treatment with d-penicillamine, a copper chelating agent. In this case, the likelihood of making the correct diagnosis and thereby choosing the appropriate treatment was increased by exome sequencing and careful interpretation. This example illustrates the utility of exome sequencing diagnostically in more common conditions not currently considered as targets for genome-wide evaluation and adds to a growing body of evidence that patients diagnosed with more common conditions often in fact have rarer genetically determined syndromes that have escaped clinical detection.
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Affiliation(s)
- Julia Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, New York 10032, USA
| | - Patrick R Shea
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Saeed Mohammad
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Cynthia Behling
- Department of Pathology, University of California, San Diego, La Jolla, California 90293, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Laura A Wilson
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Katherine P Yates
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joy Ito
- Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Mark Fishbein
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Joel E Lavine
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, Children's Hospital of New York, New York, New York 10032, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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225
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 PMCID: PMC6037748 DOI: 10.1038/s41525-018-0053-8] [Citation(s) in RCA: 359] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 12/14/2022] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011–August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34–0.48, I2 = 44%) and WES (0.36, 95% CI 0.33–0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08–0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62–2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38–0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27–0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17–0.40, I2 = 54%) and WES (0.17, 95% CI 0.12–0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05–0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases. Children with suspected genetic disease are more likely to receive a diagnosis when gene sequencing technologies are employed. At present, a microarray test for short pieces of missing or extra chromosomes (chromosomal microarray, CMA) is the recommended test for diagnosing genetic disease in children. The recent use of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for diagnosing genetic disease prompted Stephen Kingsmore at Rady Children’s Institute for Genomic Medicine in San Diego, California, USA, and colleagues to examine the effectiveness of these methods compared with CMA. Analyses of studies comprising over 20,000 children showed that using WGS and WES increased the likelihood of diagnosis and led to a change in inpatient management to prevent or ameliorate adverse health outcomes. The authors advocate the use of WGS or WES as a first-line genomic test for genetic disease in children.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA.,3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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226
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Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. Am J Hum Genet 2018; 103:58-73. [PMID: 29961570 DOI: 10.1016/j.ajhg.2018.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.
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227
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Suleiman J, Al Hashem AM, Tabarki B, Al-Thihli K, Bi W, El-Hattab AW. PPP1R21 homozygous null variants associated with developmental delay, muscle weakness, distinctive facial features, and brain abnormalities. Clin Genet 2018; 94:351-355. [PMID: 29808498 DOI: 10.1111/cge.13387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/19/2023]
Abstract
We present 3 children with homozygous null variants in the PPP1R21 gene. A 3-year-old girl had profound developmental delay, hypotonia and weakness, poor feeding, recurrent chest infections and respiratory failure, rotatory nystagmus, absent reflexes, and a homozygous nonsense variant c.2089C>T (p.Arg697*). A 2-year-old boy had profound developmental delay, weakness and hypotonia, recurrent chest infections and respiratory distress, undescended testes, rotatory nystagmus, hyporeflexia, and a homozygous nonsense variant c.427C>T (p.Arg143*). An 11-year-old girl with profound developmental delay, weakness and hypotonia, stereotypic movements, growth failure, hyporeflexia, and a homozygous frameshift variant c.87_88delAG (p.Gly30Cysfs*4). In addition, these children shared common facial features (thick eyebrows, hypertelorism, broad nasal bridge, short nose with upturned nasal tip and broad low-hanging columella, thick lips, low-set ears, and coarse facies with excessive facial hair), and brain abnormalities (cerebellar vermis hypoplasia, ventricular dilatation, and reduced white matter volume). Although PPP1R21 has not yet been linked to human disease, the consistency in the phenotype of individuals from unrelated families, the nature of the variants which result in truncated proteins, and the expected vital role for PPP1R21 in cellular function, all support that PPP1R21 is a novel disease-associated gene responsible for the phenotype observed in these individuals.
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Affiliation(s)
- J Suleiman
- Division of Neurology, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates.,Department of Pediatrics, College of Medicine and Health sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - A M Al Hashem
- Division of Genetics, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - B Tabarki
- Division of Neurology, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - K Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - W Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - A W El-Hattab
- Division of Genetic and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates
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228
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Heyne HO, Singh T, Stamberger H, Abou Jamra R, Caglayan H, Craiu D, De Jonghe P, Guerrini R, Helbig KL, Koeleman BPC, Kosmicki JA, Linnankivi T, May P, Muhle H, Møller RS, Neubauer BA, Palotie A, Pendziwiat M, Striano P, Tang S, Wu S, Poduri A, Weber YG, Weckhuysen S, Sisodiya SM, Daly MJ, Helbig I, Lal D, Lemke JR. De novo variants in neurodevelopmental disorders with epilepsy. Nat Genet 2018; 50:1048-1053. [DOI: 10.1038/s41588-018-0143-7] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/09/2018] [Indexed: 12/31/2022]
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229
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Smigiel R, Landsberg G, Schilling M, Rydzanicz M, Pollak A, Walczak A, Stodolak A, Stawinski P, Mierzewska H, Sasiadek MM, Gruss OJ, Ploski R. Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs. Eur J Hum Genet 2018; 26:1502-1511. [PMID: 29899372 DOI: 10.1038/s41431-018-0179-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/20/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023] Open
Abstract
PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies. Here, we describe a pediatric proband with severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI. Whole exome sequencing and family study showed two novel PTPN23 variants, c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)), in compound heterozygous state, which are predicted in silico to be damaging. When studying patient's fibroblasts we found similar expression of SMN but a dramatic reduction of cells displaying SMN accumulation in Cajal bodies (CB). SMN strongly accumulated in CB in more than 50% of unrelated control cell fibroblasts as well as in fibroblasts from the parent carrying only the c.2974delC (p.(Leu992Tyrfs*168)) variant (predicted to cause loss-of-function). In contrast, only 22% of cells showed respective SMN accumulations in patient fibroblasts (p = 1.9-2.5 × 10-7) while showing a higher level of nucleoplasmic SMN. Furthermore, the remaining accumulations in patient cells displayed weaker SMN signals than control or heterozygous wt/c.2974delC (p.(Leu992Tyrfs*168)) fibroblasts. Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study.
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Affiliation(s)
- Robert Smigiel
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Gerd Landsberg
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Maximilian Schilling
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Anna Stodolak
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.,Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Hanna Mierzewska
- Department of Child and Adolescent Neurology, Institute of Mother and Child, Warsaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Oliver J Gruss
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.
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230
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Trinh J, Hüning I, Yüksel Z, Baalmann N, Imhoff S, Klein C, Rolfs A, Gillessen-Kaesbach G, Lohmann K. A KAT6A variant in a family with autosomal dominantly inherited microcephaly and developmental delay. J Hum Genet 2018; 63:997-1001. [DOI: 10.1038/s10038-018-0469-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/12/2018] [Accepted: 04/30/2018] [Indexed: 11/09/2022]
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231
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Seong E, Insolera R, Dulovic M, Kamsteeg EJ, Trinh J, Brüggemann N, Sandford E, Li S, Ozel AB, Li JZ, Jewett T, Kievit AJ, Münchau A, Shakkottai V, Klein C, Collins C, Lohmann K, van de Warrenburg BP, Burmeister M. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. Ann Neurol 2018; 83:1075-1088. [PMID: 29604224 PMCID: PMC6105379 DOI: 10.1002/ana.25220] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/11/2018] [Accepted: 03/19/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To identify novel causes of recessive ataxias, including spinocerebellar ataxia with saccadic intrusions, spastic ataxias, and spastic paraplegia. METHODS In an international collaboration, we independently performed exome sequencing in 7 families with recessive ataxia and/or spastic paraplegia. To evaluate the role of VPS13D mutations, we evaluated a Drosophila knockout model and investigated mitochondrial function in patient-derived fibroblast cultures. RESULTS Exome sequencing identified compound heterozygous mutations in VPS13D on chromosome 1p36 in all 7 families. This included a large family with 5 affected siblings with spinocerebellar ataxia with saccadic intrusions (SCASI), or spinocerebellar ataxia, recessive, type 4 (SCAR4). Linkage to chromosome 1p36 was found in this family with a logarithm of odds score of 3.1. The phenotypic spectrum in our 12 patients was broad. Although most presented with ataxia, additional or predominant spasticity was present in 5 patients. Disease onset ranged from infancy to 39 years, and symptoms were slowly progressive and included loss of independent ambulation in 5. All but 2 patients carried a loss-of-function (nonsense or splice site) mutation on one and a missense mutation on the other allele. Knockdown or removal of Vps13D in Drosophila neurons led to changes in mitochondrial morphology and impairment in mitochondrial distribution along axons. Patient fibroblasts showed altered morphology and functionality including reduced energy production. INTERPRETATION Our study demonstrates that compound heterozygous mutations in VPS13D cause movement disorders along the ataxia-spasticity spectrum, making VPS13D the fourth VPS13 paralog involved in neurological disorders. Ann Neurol 2018.
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Affiliation(s)
- Eunju Seong
- Molecular & Behavioral Neuroscience Institute, University of
Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Insolera
- Department of Molecular, Cellular, and Developmental Biology,
University of Michigan, Ann Arbor, MI 48109, USA
| | - Marija Dulovic
- Institute of Neurogenetics, University of Lübeck,
Germany
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Centre,
Nijmegen, The Netherlands
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck,
Germany
| | | | - Erin Sandford
- Molecular & Behavioral Neuroscience Institute, University of
Michigan, Ann Arbor, MI 48109, USA
| | | | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
48109, USA
| | - Jun Z. Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
48109, USA
- Department of Computational Medicine & Bioinformatics,
University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamison Jewett
- Department of Pediatrics, Section on Medical Genetics, Wake Forest
School of Medicine, Winston-Salem, North Carolina, USA
| | | | | | - Vikram Shakkottai
- Departments of Neurology and of Molecular and Integrative
Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Catherine Collins
- Department of Molecular, Cellular, and Developmental Biology,
University of Michigan, Ann Arbor, MI 48109, USA
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck,
Germany
| | - Bart P. van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and
Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of
Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
48109, USA
- Department of Computational Medicine & Bioinformatics,
University of Michigan, Ann Arbor, MI 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI
48109, USA
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232
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Smith HS, Swint JM, Lalani SR, Yamal JM, de Oliveira Otto MC, Castellanos S, Taylor A, Lee BH, Russell HV. Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature. Genet Med 2018; 21:3-16. [PMID: 29760485 DOI: 10.1038/s41436-018-0024-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS. METHODS PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized. RESULTS Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type. CONCLUSION Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.
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Affiliation(s)
- Hadley Stevens Smith
- Baylor College of Medicine, The University of Texas School of Public Health, Houston, Texas, USA
| | - J Michael Swint
- The University of Texas School of Public Health, The Center for Clinical Research and Evidence-Based Medicine, The University of Texas McGovern Medical School, Houston, Texas, USA
| | - Seema R Lalani
- Baylor College of Medicine, Baylor Genetics Laboratory, Houston, Texas, USA
| | - Jose-Miguel Yamal
- The University of Texas School of Public Health, Houston, Texas, USA
| | | | | | - Amy Taylor
- Texas Medical Center Library, Houston, Texas, USA
| | | | - Heidi V Russell
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
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233
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Torrezan GT, de Almeida FGDSR, Figueiredo MCP, Barros BDDF, de Paula CAA, Valieris R, de Souza JES, Ramalho RF, da Silva FCC, Ferreira EN, de Nóbrega AF, Felicio PS, Achatz MI, de Souza SJ, Palmero EI, Carraro DM. Complex Landscape of Germline Variants in Brazilian Patients With Hereditary and Early Onset Breast Cancer. Front Genet 2018; 9:161. [PMID: 29868112 PMCID: PMC5949367 DOI: 10.3389/fgene.2018.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Pathogenic variants in known breast cancer (BC) predisposing genes explain only about 30% of Hereditary Breast Cancer (HBC) cases, whereas the underlying genetic factors for most families remain unknown. Here, we used whole-exome sequencing (WES) to identify genetic variants associated to HBC in 17 patients of Brazil with familial BC and negative for causal variants in major BC risk genes (BRCA1/2, TP53, and CHEK2 c.1100delC). First, we searched for rare variants in 27 known HBC genes and identified two patients harboring truncating pathogenic variants in ATM and BARD1. For the remaining 15 negative patients, we found a substantial vast number of rare genetic variants. Thus, for selecting the most promising variants we used functional-based variant prioritization, followed by NGS validation, analysis in a control group, cosegregation analysis in one family and comparison with previous WES studies, shrinking our list to 23 novel BC candidate genes, which were evaluated in an independent cohort of 42 high-risk BC patients. Rare and possibly damaging variants were identified in 12 candidate genes in this cohort, including variants in DNA repair genes (ERCC1 and SXL4) and other cancer-related genes (NOTCH2, ERBB2, MST1R, and RAF1). Overall, this is the first WES study applied for identifying novel genes associated to HBC in Brazilian patients, in which we provide a set of putative BC predisposing genes. We also underpin the value of using WES for assessing the complex landscape of HBC susceptibility, especially in less characterized populations.
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Affiliation(s)
- Giovana T Torrezan
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | | | - Márcia C P Figueiredo
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Bruna D de Figueiredo Barros
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Cláudia A A de Paula
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Renan Valieris
- Laboratory of Bioinformatics and Computational Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Jorge E S de Souza
- Instituto de Bioinformática e Biotecnologia-2bio, Natal, Brazil.,Instituto Metrópole Digital, Federal University of Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rodrigo F Ramalho
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Felipe C C da Silva
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Elisa N Ferreira
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,Research and Development, Fleury Group, São Paulo, Brazil
| | | | - Paula S Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | - Maria I Achatz
- Oncogenetics Department, A.C. Camargo Cancer Center, São Paulo, Brazil.,Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, United States
| | - Sandro J de Souza
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil.,Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil.,Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Dirce M Carraro
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
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234
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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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235
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Mattick JS, Dinger M, Schonrock N, Cowley M. Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing. Med J Aust 2018; 209:197-199. [DOI: 10.5694/mja17.01176] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- John S Mattick
- Garvan Institute of Medical Research, Sydney, NSW
- St Vincentˈs Clinical School, UNSW Sydney, Sydney, NSW
| | - Marcel Dinger
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Nicole Schonrock
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Mark Cowley
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
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236
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Zaman T, Helbig I, Božović IB, DeBrosse SD, Bergqvist AC, Wallis K, Medne L, Maver A, Peterlin B, Helbig KL, Zhang X, Goldberg EM. Mutations in SCN3A cause early infantile epileptic encephalopathy. Ann Neurol 2018; 83:703-717. [PMID: 29466837 DOI: 10.1002/ana.25188] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/01/2018] [Accepted: 02/18/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Voltage-gated sodium (Na+ ) channels underlie action potential generation and propagation and hence are central to the regulation of excitability in the nervous system. Mutations in the genes SCN1A, SCN2A, and SCN8A, encoding the Na+ channel pore-forming (α) subunits Nav1.1, 1.2, and 1.6, respectively, and SCN1B, encoding the accessory subunit β1 , are established causes of genetic epilepsies. SCN3A, encoding Nav1.3, is known to be highly expressed in brain, but has not previously been linked to early infantile epileptic encephalopathy. Here, we describe a cohort of 4 patients with epileptic encephalopathy and heterozygous de novo missense variants in SCN3A (p.Ile875Thr in 2 cases, p.Pro1333Leu, and p.Val1769Ala). METHODS All patients presented with treatment-resistant epilepsy in the first year of life, severe to profound intellectual disability, and in 2 cases (both with the variant p.Ile875Thr), diffuse polymicrogyria. RESULTS Electrophysiological recordings of mutant channels revealed prominent gain of channel function, with a markedly increased amplitude of the slowly inactivating current component, and for 2 of 3 mutants (p.Ile875Thr and p.Pro1333Leu), a leftward shift in the voltage dependence of activation to more hyperpolarized potentials. Gain of function was not observed for Nav1.3 variants known or presumed to be inherited (p.Arg1642Cys and p.Lys1799Gln). The antiseizure medications phenytoin and lacosamide selectively blocked slowly inactivating over transient current in wild-type and mutant Nav1.3 channels. INTERPRETATION These findings establish SCN3A as a new gene for infantile epileptic encephalopathy and suggest a potential pharmacologic intervention. These findings also reinforce the role of Nav1.3 as an important regulator of neuronal excitability in the developing brain, while providing additional insight into mechanisms of slow inactivation of Nav1.3. Ann Neurol 2018;83:703-717.
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Affiliation(s)
- Tariq Zaman
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ingo Helbig
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrecht University, Kiel, Germany.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ivana Babić Božović
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Suzanne D DeBrosse
- Departments of Genetics and Genome Sciences, Pediatrics, and Neurology, and Center for Human Genetics, Case Western Reserve University School of Medicine, Cleveland, OH
| | - A Christina Bergqvist
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kimberly Wallis
- Departments of Genetics and Genome Sciences, Pediatrics, and Neurology, and Center for Human Genetics, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katherine L Helbig
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA.,Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Xiaohong Zhang
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ethan M Goldberg
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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237
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Faqeih EA, Almannai M, Saleh MM, AlWadei AH, Samman MM, Alkuraya FS. Phenotypic characterization of KCTD3-related developmental epileptic encephalopathy. Clin Genet 2018; 93:1081-1086. [PMID: 29406573 DOI: 10.1111/cge.13227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/03/2018] [Accepted: 01/31/2018] [Indexed: 12/01/2022]
Abstract
The association between KCTD3 gene and neurogenetic disorders has only been published recently. In this report, we describe the clinical phenotype associated with 2 pathogenic variants in KCTD3 gene. Seven individuals (including one set of monozygotic twin) from 4 consanguineous families presented with developmental epileptic encephalopathy, global developmental delay, central hypotonia, progressive peripheral hypertonia, and variable dysmorphic facial features. Posterior fossa abnormalities (ranging from Dandy-Walker malformation to isolated hypoplasia of the cerebellar vermis) were consistently observed in addition to other variable neuroradiological abnormalities such as hydrocephalus and abnormal brain myelination. One patient also had a multicystic kidney. Whole exome sequencing revealed 2 probably pathogenic homozygous variants in KCTD3 gene that fully segregated with the disease. KCTD3 gene belongs to a family of accessory subunits that regulate the biophysical properties of ion channels, and is highly expressed in the kidney and brain. In this largest series to date on KCTD3-mutated patients, we show that biallelic loss of function mutations in KCTD3 lead to a consistent phenotype of developmental epileptic encephalopathy and abnormal cerebellum on brain imaging.
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Affiliation(s)
- E A Faqeih
- Section of Medial Genetics, Department of Pediatrics Subspecialties, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - M Almannai
- Section of Medial Genetics, Department of Pediatrics Subspecialties, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - M M Saleh
- Section of Medial Genetics, Department of Pediatrics Subspecialties, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - A H AlWadei
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - M M Samman
- Pathology and Clinical Laboratory Administration, Section of Molecular Pathology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - F S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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238
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Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL. A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001978. [PMID: 29555671 DOI: 10.1161/circgen.117.001978] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/18/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS Whole-exome sequencing was performed with the DNA of multiple family members. We utilized a 2-tiered whole-exome variant screening and interpretation procedure. First, we manually curated a high-confidence list of 90 genes known to cause CHD in humans, identified predicted damaging variants in genes on this list, and rated their pathogenicity using American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS In 3 families (10%), we found pathogenic variants in known CHD genes TBX5, TFAP2B, and PTPN11, explaining the cardiac lesions. Second, exomes were comprehensively analyzed to identify additional predicted damaging variants that segregate with disease in CHD candidate genes. In 10 additional families (33%), likely disease-causal variants were uncovered in PBX1, CNOT1, ZFP36L2, TEK, USP34, UPF2, KDM5A, KMT2C, TIE1, TEAD2, and FLT4. CONCLUSIONS The pathogenesis of CHD could be explained using our high-confidence CHD gene list for variant filtering in a subset of cases. Furthermore, our unbiased screening procedure of family exomes implicates additional genes and variants in the pathogenesis of CHD, which suggest themselves for functional validation. This 2-tiered approach provides a means of (1) identifying clinically actionable variants and (2) identifying additional disease-causal genes, both of which are essential for improving the molecular diagnosis of CHD.
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Affiliation(s)
- Justin O Szot
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Hartmut Cuny
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gillian M Blue
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David T Humphreys
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eddie Ip
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Katrina Harrison
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gary F Sholler
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eleni Giannoulatou
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Paul Leo
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Emma L Duncan
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Duncan B Sparrow
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Joshua W K Ho
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Robert M Graham
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Nicholas Pachter
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gavin Chapman
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David S Winlaw
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Sally L Dunwoodie
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.).
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239
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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240
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Clinical and genetic spectrum of AMPD2-related pontocerebellar hypoplasia type 9. Eur J Hum Genet 2018; 26:695-708. [PMID: 29463858 DOI: 10.1038/s41431-018-0098-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/28/2017] [Accepted: 01/09/2018] [Indexed: 11/08/2022] Open
Abstract
Pontocerebellar hypoplasia (PCH) represents a group of autosomal-recessive progressive neurodegenerative disorders of prenatal onset. Eleven PCH subtypes are classified according to clinical, neuroimaging and genetic findings. Individuals with PCH type 9 (PCH9) have a unique combination of postnatal microcephaly, hypoplastic cerebellum and pons, and hypoplastic or absent corpus callosum. PCH9 is caused by biallelic variants in AMPD2 encoding adenosine monophosphate deaminase 2; however, a homozygous AMPD2 frameshift variant has recently been reported in two family members with spastic paraplegia type 63 (SPG63). We identified homozygous or compound heterozygous AMPD2 variants in eight PCH-affected individuals from six families. The eight variants likely affect function and comprise one frameshift, one nonsense and six missense variants; seven of which were novel. The main clinical manifestations in the eight new patients and 17 previously reported individuals with biallelic AMPD2 variants were postnatal microcephaly, severe global developmental delay, spasticity, and central visual impairment. Brain imaging data identified hypomyelination, hypoplasia of the cerebellum and pons, atrophy of the cerebral cortex, complete or partial agenesis of the corpus callosum and the "figure 8" shape of the hypoplastic midbrain as consistent features. We broaden the AMPD2-related clinical spectrum by describing one individual without microcephaly and absence of the characteristic "figure 8" shape of the midbrain. The existence of various AMPD2 isoforms with different functions possibly explains the variability in phenotypes associated with AMPD2 variants: variants leaving some of the isoforms intact may cause SPG63, while those affecting all isoforms may result in the severe and early-onset PCH9.
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241
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Bertoli-Avella AM, Garcia-Aznar JM, Brandau O, Al-Hakami F, Yüksel Z, Marais A, Grüning NM, Abbasi Moheb L, Paknia O, Alshaikh N, Alameer S, Marafi MJ, Al-Mulla F, Al-Sannaa N, Rolfs A, Bauer P. Biallelic inactivating variants in the GTPBP2 gene cause a neurodevelopmental disorder with severe intellectual disability. Eur J Hum Genet 2018; 26:592-598. [PMID: 29449720 DOI: 10.1038/s41431-018-0097-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/06/2017] [Accepted: 01/05/2018] [Indexed: 11/09/2022] Open
Abstract
Congenital neurological disorders are genetically highly heterogeneous. Rare forms of hereditary neurological disorders are still difficult to be adequately diagnosed. Pertinent studies, especially when reporting only single families, need independent confirmation. We present three unrelated families in which whole-exome sequencing identified the homozygous non-sense variants c.430[C>T];[C>T] p.(Arg144*), c.1219[C>T];[C>T] p.(Gln407*) and c.1408[C>T];[C>T] p.(Arg470*) in GTPBP2. Their clinical presentations include early onset and apparently non-progressive motor and cognitive impairment, and thereby overlap with findings in a recently described family harbouring a homozygous GTPBP2 splice site variant. Notable differences include structural brain abnormalities (e.g., agenesis of the corpus callosum, exclusive to our patients), and evidence for brain iron accumulation (exclusive to the previously described family). This report confirms pathogenicity of biallelic GTPBP2 inactivation and broadens the phenotypic spectrum. It also underlines that a potential involvement of brain iron accumulation needs clarification. Further patients will have to be identified and characterised in order to fully define the core features of GTPBP2-associated neurological disorder, but future approaches to molecular diagnosis of neurodevelopmental disorders should implement GTPBP2.
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Affiliation(s)
| | | | | | - Fahad Al-Hakami
- Molecular Medicine Section, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,King Saud Bin Abdulaziz University For Health Sciences, Ministry of National Guard Health Affairs,, Jeddah, Saudi Arabia
| | | | | | | | | | | | - Nahla Alshaikh
- King Saud Bin Abdulaziz University For Health Sciences, Ministry of National Guard Health Affairs,, Jeddah, Saudi Arabia.,Pediatric Neurology Section, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Seham Alameer
- King Saud Bin Abdulaziz University For Health Sciences, Ministry of National Guard Health Affairs,, Jeddah, Saudi Arabia.,Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | | | - Fahd Al-Mulla
- Genatak Center for Genomic Medicine, Kuwait City, Kuwait
| | - Nouriya Al-Sannaa
- John Hopkins Aramco Health Care, Pediatric Services, Dhahran, Saudi Arabia
| | - Arndt Rolfs
- Centogene AG, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
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242
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Werner-Lin A, Zaspel L, Carlson M, Mueller R, Walser SA, Desai R, Bernhardt BA. Gratitude, protective buffering, and cognitive dissonance: How families respond to pediatric whole exome sequencing in the absence of actionable results. Am J Med Genet A 2018; 176:578-588. [DOI: 10.1002/ajmg.a.38613] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/26/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Allison Werner-Lin
- School of Social Policy and Practice; University of Pennsylvania; Philadelphia Pennsylvania
| | - Lori Zaspel
- School of Social Policy and Practice; University of Pennsylvania; Philadelphia Pennsylvania
| | - Mae Carlson
- School of Social Policy and Practice; University of Pennsylvania; Philadelphia Pennsylvania
| | - Rebecca Mueller
- Department of History and Sociology of Science; University of Pennsylvania; Philadelphia Pennsylvania
| | - Sarah A. Walser
- Department of Medicine; Perelman School of Medicine; University of Pennsylvania; Philadelphia Pennsylvania
| | - Ria Desai
- College of Arts and Science; University of Pennsylvania; Philadelphia Pennsylvania
| | - Barbara A. Bernhardt
- Department of Medicine; Perelman School of Medicine; University of Pennsylvania; Philadelphia Pennsylvania
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243
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Normand EA, Alaimo JT, Van den Veyver IB. Exome and genome sequencing in reproductive medicine. Fertil Steril 2018; 109:213-220. [PMID: 29395096 DOI: 10.1016/j.fertnstert.2017.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/07/2017] [Indexed: 12/15/2022]
Abstract
The advent of next-generation sequencing has enabled clinicians to assess many genes simultaneously and at high resolution. This is advantageous for diagnosing patients in whom a genetic disorder is suspected but who have a nonspecific or atypical phenotype or when the disorder has significant genetic heterogeneity. Herein, we describe common clinical applications of next-generation sequencing technology, as well as their respective benefits and limitations. We then discuss key considerations of variant interpretation and reporting, clinical utility, pre- and posttest genetic counseling, and ethical challenges. We will present these topics with an emphasis on their applicability to the reproductive medicine setting.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.
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244
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Dragojlovic N, Elliott AM, Adam S, van Karnebeek C, Lehman A, Mwenifumbo JC, Nelson TN, du Souich C, Friedman JM, Lynd LD. The cost and diagnostic yield of exome sequencing for children with suspected genetic disorders: a benchmarking study. Genet Med 2018; 20:1013-1021. [PMID: 29300375 DOI: 10.1038/gim.2017.226] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE This study aimed to generate benchmark estimates for the cost, diagnostic yield, and cost per positive diagnosis of diagnostic exome sequencing (ES) in heterogeneous pediatric patient populations and to illustrate how the design of an ES service can influence its cost and yield. METHODS A literature review and Monte Carlo simulations were used to generate benchmark estimates for singleton and trio ES. A cost model for the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, which is testing a proposed delivery model for diagnostic ES in British Columbia, is used to illustrate the potential effects of changing the service design. RESULTS The benchmark diagnostic yield was 34.3% (95% confidence interval (CI): 23.2-46.5) for trio ES and 26.5% (95% CI: 12.9-42.9) for singleton ES. The benchmark cost of delivery was C$6,437 (95% CI: $5,305-$7,704) in 2016 Canadian dollars (US$4,859; 4,391€) for trio ES and C$2,576 (95% CI: $1,993-$3,270) (US$1,944; 1,757€) for singleton ES. Scenario models for CAUSES suggest that alternative service designs could reduce costs but might lead to a higher cost per diagnosis due to lower yields. CONCLUSION Broad conclusions about the cost-effectiveness of ES should be drawn with caution when relying on studies that use cost or yield assumptions that lie at the extremes of the benchmark ranges.
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Affiliation(s)
- Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Shelin Adam
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.,Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Anna Lehman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jill C Mwenifumbo
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tanya N Nelson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, British Columbia, Canada.
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245
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 DOI: 10.1101/255299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 05/22/2023] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011-August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34-0.48, I2 = 44%) and WES (0.36, 95% CI 0.33-0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08-0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62-2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38-0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27-0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17-0.40, I2 = 54%) and WES (0.17, 95% CI 0.12-0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05-0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
- 3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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Kong L, Wang D, Li S, Zhang C, Jiang X, Guan Q, Zhang Z, Jing F, Xu J. Clinical Diagnosis of X-Linked Spondyloepiphyseal Dysplasia Tarda and a Novel Missense Mutation in the Sedlin Gene (SEDL). Int J Endocrinol 2018; 2018:8263136. [PMID: 30647738 PMCID: PMC6311833 DOI: 10.1155/2018/8263136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/04/2018] [Accepted: 10/25/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Spondyloepiphyseal dysplasia tarda (SEDT) is a rare hereditary bone disease characterized by spinal and epiphyseal anomalies. We identified the disease by gene sequencing in a Chinese pedigree with SEDT. METHODS We extracted genomic DNA from five members of a four-generation Chinese SEDT kindred with three affected males and then analyzed the genetic mutation by PCR and DNA sequencing. RESULTS DNA sequencing showed that the genetic missense mutation occurred one bp upstream of exon 6 in the SEDL gene in two families, and a heterozygous mutation was found in a female carrier. In addition, no mutation was found in the other members of the family. CONCLUSION SEDT in this family was caused by a G/C missense mutation in exon 6 of the SEDL gene, previously not shown to be associated with X-linked SEDT.
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Affiliation(s)
- Lei Kong
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, China
- Shandong Clinical Medical Centre of Endocrinology and Metabolism, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, China
| | | | - Shanshan Li
- Metabolic Bone Disease and Genetics Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
- Shanghai Key Clinical Centre for Metabolic Disease, China
| | | | - Xiuyun Jiang
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, China
- Shandong Clinical Medical Centre of Endocrinology and Metabolism, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, China
| | - Qingbo Guan
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, China
- Shandong Clinical Medical Centre of Endocrinology and Metabolism, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, China
| | - Zhenlin Zhang
- Metabolic Bone Disease and Genetics Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
- Shanghai Key Clinical Centre for Metabolic Disease, China
| | - Fei Jing
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, China
- Shandong Clinical Medical Centre of Endocrinology and Metabolism, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, China
| | - Jin Xu
- Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, China
- Shandong Clinical Medical Centre of Endocrinology and Metabolism, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, China
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Martin S, Chamberlin A, Shinde DN, Hempel M, Strom TM, Schreiber A, Johannsen J, Ousager LB, Larsen MJ, Hansen LK, Fatemi A, Cohen JS, Lemke J, Sørensen KP, Helbig KL, Lessel D, Abou Jamra R. De Novo Variants in GRIA4 Lead to Intellectual Disability with or without Seizures and Gait Abnormalities. Am J Hum Genet 2017; 101:1013-1020. [PMID: 29220673 DOI: 10.1016/j.ajhg.2017.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 01/21/2023] Open
Abstract
Using trio whole-exome sequencing, we have identified de novo heterozygous pathogenic variants in GRIA4 in five unrelated individuals with intellectual disability and other symptoms. GRIA4 encodes an AMPA receptor subunit known as GluR4, which is found on excitatory glutamatergic synapses and is important for learning and memory. Four of the variants are located in the highly conserved SYTANLAAF motif in the transmembrane protein M3, and the fifth is in an extra-cellular domain. Molecular modeling of the altered protein showed that three of the variants in the SYTANLAAF motif orient toward the center of the pore region and most likely lead to disturbance of the gating mechanism. The fourth variant in the SYTANLAAF motif most likely results in reduced permeability. The variant in the extracellular domain potentially interferes with the binding between the monomers. On the basis of clinical information and genetic results, and the fact that other subunits of the AMPA receptor have already been associated with neurodevelopmental disorders, we suggest that pathogenic de novo variants in GRIA4 lead to intellectual disability with or without seizures, gait abnormalities, problems of social behavior, and other variable features.
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248
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Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, Zhang J, He W, Dharmadhikari AV, Qu C, Ward P, Braxton A, Narayanan S, Ge X, Tokita MJ, Santiago-Sim T, Dai H, Chiang T, Smith H, Azamian MS, Robak L, Bostwick BL, Schaaf CP, Potocki L, Scaglia F, Bacino CA, Hanchard NA, Wangler MF, Scott D, Brown C, Hu J, Belmont JW, Burrage LC, Graham BH, Sutton VR, Craigen WJ, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Muzny DM, Miller MJ, Wang X, Leduc MS, Xiao R, Liu P, Shaw C, Walkiewicz M, Bi W, Xia F, Lee B, Eng C, Yang Y, Lalani SR. Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. JAMA Pediatr 2017; 171:e173438. [PMID: 28973083 PMCID: PMC6359927 DOI: 10.1001/jamapediatrics.2017.3438] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined. Objective To determine the diagnostic yield and use of clinical exome sequencing in critically ill infants. Design, Setting, and Participants Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants. Main Outcomes and Measures Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders. Results The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling. Conclusions and Relevance Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.
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Affiliation(s)
- Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine, Houston, Texas
| | - Anirudh Saronwala
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrew Ray Ghazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Jing Zhang
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin He
- Baylor Genetics Laboratory, Houston, Texas
| | | | | | - Patricia Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Swetha Narayanan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mari J. Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Theodore Chiang
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Hadley Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret L. Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas
| | - Daryl Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston Texas
| | - Chester Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Jianhong Hu
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Vernon Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - William J. Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Donna M. Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Marcus J. Miller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Magalie S. Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
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249
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Sowada N, Hashem MO, Yilmaz R, Hamad M, Kakar N, Thiele H, Arold ST, Bode H, Alkuraya FS, Borck G. Mutations of PTPN23 in developmental and epileptic encephalopathy. Hum Genet 2017; 136:1455-1461. [PMID: 29090338 DOI: 10.1007/s00439-017-1850-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/22/2017] [Indexed: 11/26/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) are a heterogeneous group of neurodevelopmental disorders with poor prognosis. Recent discoveries have greatly expanded the repertoire of genes that are mutated in epileptic encephalopathies and DEE, often in a de novo fashion, but in many patients, the disease remains molecularly uncharacterized. Here, we describe a new form of DEE in patients with likely deleterious biallelic variants in PTPN23. The phenotype is characterized by early onset drug-resistant epilepsy, severe and global developmental delay, microcephaly, and sometimes premature death. PTPN23 encodes a tyrosine phosphatase with strong brain expression, and its knockout in mouse is embryonically lethal. Structural modeling supports a deleterious effect of the identified alleles. Our data suggest that PTPN23 mutations cause a rare severe form of autosomal-recessive DEE in humans, a finding that requires confirmation.
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Affiliation(s)
- Nadine Sowada
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mais Omar Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rüstem Yilmaz
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Muddathir Hamad
- Department of Pediatrics, King Khalid University Hospital, Riyadh, Saudi Arabia
| | - Naseebullah Kakar
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Harald Bode
- Division of Pediatric Neurology, Children's Hospital, University of Ulm, Ulm, Germany
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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250
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Molecular diversity of combined and complex dystonia: insights from diagnostic exome sequencing. Neurogenetics 2017; 18:195-205. [PMID: 28849312 DOI: 10.1007/s10048-017-0521-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/10/2017] [Indexed: 12/22/2022]
Abstract
Combined and complex dystonias are heterogeneous movement disorders combining dystonia with other motor and/or systemic signs. Although we are beginning to understand the diverse molecular causes of these disease entities, clinical pattern recognition and conventional genetic workup achieve an etiological diagnosis only in a minority of cases. Our goal was to provide a window into the variable genetic origins and distinct clinical patterns of combined/complex dystonia more broadly. Between August 2016 and January 2017, we applied whole-exome sequencing to a cohort of nine patients with varied combined and/or complex dystonic presentations, being on a diagnostic odyssey. Bioinformatics analyses, co-segregation studies, and sequence-interpretation algorithms were employed to detect causative mutations. Comprehensive clinical review was undertaken to define the phenotypic spectra and optimal management strategies. On average, we observed a delay in diagnosis of 23 years before whole-exome analysis enabled determination of each patient's genetic defect. Whereas mutations in ACTB, ATP1A3, ADCY5, and SGCE were associated with particular phenotypic clues, trait manifestations arising from mutations in PINK1, MRE11A, KMT2B, ATM, and SLC6A1 were different from those previously reported in association with these genes. Apart from improving counseling for our entire cohort, genetic findings had actionable consequences on preventative measures and therapeutic interventions for five patients. Our investigation confirms unique genetic diagnoses, highlights key clinical features and phenotypic expansions, and suggests whole-exome sequencing as a first-tier diagnostic for combined/complex dystonia. These results might stimulate independent teams to extend the scope of agnostic genetic screening to this particular phenotypic group that remains poorly characterized through existing studies.
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