1
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Liu Y, Zheng Z, Zhu Q. Case Report: Identification of Polygenic Mutations by Exome Sequencing. Front Pediatr 2021; 9:689901. [PMID: 34746046 PMCID: PMC8567987 DOI: 10.3389/fped.2021.689901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/09/2021] [Indexed: 11/18/2022] Open
Abstract
The discovery of rare genetic variation through different gene sequencing methods is a very challenging subject in the field of human genetics. A case of a 1-year-old boy with metabolic acidosis and hypokalemia, a small penis, growth retardation, and G-6PD deficiency was reported. Since the clinical symptoms are complex and seem uncorrelated, the authors hypothesized that the child had chromosome or gene problems, and exome sequencing (ES) was applied to samples from him and his parents. Three main locus mutations in three genes were found in the proband, including SLC4A1, FGFR1, and G6PD genes. A missense mutation (c.1766G>T, p.R589 L) was found in exon 14 of SLC4A1 gene, which was a de novo mutation. Another missense mutation (c.1028 A>G, p.H343R) was found in exon 9 of FGFR1 gene, which was also a de novo mutation. These findings further demonstrate the utility of ES in the diagnosis of rare diseases.
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Affiliation(s)
- Yanfeng Liu
- Department of Endocrinology, Quanzhou Women and Children's Hospital, Quanzhou, China
| | - Zhongshi Zheng
- Department of Endocrinology, Quanzhou Women and Children's Hospital, Quanzhou, China
| | - Qingling Zhu
- Department of Children Health Care, Quanzhou Women and Children's Hospital, Quanzhou, China
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2
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Koboldt DC, Waldrop MA, Wilson RK, Flanigan KM. The Genotypic and Phenotypic Spectrum of
BICD2
Variants in Spinal Muscular Atrophy. Ann Neurol 2020; 87:487-496. [DOI: 10.1002/ana.25704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel C. Koboldt
- Institute for Genomic Medicine Nationwide Children's Hospital Columbus OH
- Department of Pediatrics Ohio State University Columbus OH
| | - Megan A. Waldrop
- Department of Pediatrics Ohio State University Columbus OH
- Center for Gene Therapy Nationwide Children's Hospital Columbus OH
- Department of Neurology Ohio State University Columbus OH
| | - Richard K. Wilson
- Institute for Genomic Medicine Nationwide Children's Hospital Columbus OH
- Department of Pediatrics Ohio State University Columbus OH
| | - Kevin M. Flanigan
- Department of Pediatrics Ohio State University Columbus OH
- Center for Gene Therapy Nationwide Children's Hospital Columbus OH
- Department of Neurology Ohio State University Columbus OH
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3
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Doubková M, Trizuljak J, Vrzalová Z, Hrazdirová A, Blaháková I, Radová L, Pospíšilová Š, Doubek M. Novel genetic variant of HPS1 gene in Hermansky-Pudlak syndrome with fulminant progression of pulmonary fibrosis: a case report. BMC Pulm Med 2019; 19:178. [PMID: 31619213 PMCID: PMC6794755 DOI: 10.1186/s12890-019-0941-4] [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: 05/22/2019] [Accepted: 09/16/2019] [Indexed: 01/22/2023] Open
Abstract
Background Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder that is associated with oculocutaneous albinism, bleeding diathesis, granulomatous colitis, and highly penetrant pulmonary fibrosis in some subtypes. Homozygous or compound heterozygous pathological variants in HPS1, HPS3, HPS4, and several other genes lead to clinical manifestation of the disease. Case presentation A 57-year-old female was admitted with congenital oculocutaneous albinism, thrombocytopathy and late-onset accelerated pulmonary fibrosis (first symptoms from age 50 onwards). Chest high-resolution computed tomography identified thickening of peribronchovascular interstitium, bronchiectasis, reticulations, honeycombing, ground glass opacities and lung parenchyma consolidations. HPS was clinically suspected. We performed whole exome sequencing (WES), a form of massive parallel sequencing, of proband-parents trio. Whole exome libraries were processed using KAPA Hyper Prep Kit, SeqCap EZ MedExome Enrichment Kit and HyperCap Bead Kit according to the SeqCap EZ HyperCap Workflow. The paired-end 2 × 75 bp sequencing was performed on the Illumina NextSeq 500 Sequencer (Illumina Inc., USA). Furthermore, obtained variants by WES were evaluated using a virtual panel of genes: HPS1, AP3B1, HPS3, HPS4, HPS5, HPS6, DTNBP1, BLOC1S3, and PLDN. We identified a compound heterozygous genotype in HPS1 gene in the proband. We identified a pathogenic frameshift variant c.1189delC; p.(Gln397Serfs*2), resulting in a premature stop codon. This variant has been previously associated with HPS. Furthermore, we characterized previously undescribed nonsense variant c.1507C > T; p.(Gln503*), resulting in a premature stop codon and mRNA degradation through nonsense-mediated decay. Sanger sequencing validated the presence of both variants and simultaneously confirmed the heterozygous carrier status of parents. Unfortunately, the patient died due to fulminant progression of pulmonary fibrosis 2 months after diagnostics. Conclusions Compound heterozygous mutations in HPS1 in the proband lead to disruption of HPS1 gene and clinical manifestation of HPS with severe pulmonary fibrosis. This case illustrates the need to consider HPS in differential diagnostics of pulmonary fibrosis. Pulmonary fibrosis is a common cause of death in HPS patients. Earlier diagnosis may enable better treatment for these patients.
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Affiliation(s)
- Martina Doubková
- Department of Pulmonary Diseases and Tuberculosis, Masaryk University, Faculty of Medicine and University Hospital, Brno, Czech Republic
| | - Jakub Trizuljak
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Vrzalová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Hrazdirová
- Department of Pulmonary Diseases and Tuberculosis, Masaryk University, Faculty of Medicine and University Hospital, Brno, Czech Republic
| | - Ivona Blaháková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Šárka Pospíšilová
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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4
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Wright CF, West B, Tuke M, Jones SE, Patel K, Laver TW, Beaumont RN, Tyrrell J, Wood AR, Frayling TM, Hattersley AT, Weedon MN. Assessing the Pathogenicity, Penetrance, and Expressivity of Putative Disease-Causing Variants in a Population Setting. Am J Hum Genet 2019; 104:275-286. [PMID: 30665703 PMCID: PMC6369448 DOI: 10.1016/j.ajhg.2018.12.015] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
More than 100,000 genetic variants are classified as disease causing in public databases. However, the true penetrance of many of these rare alleles is uncertain and might be over-estimated by clinical ascertainment. Here, we use data from 379,768 UK Biobank (UKB) participants of European ancestry to assess the pathogenicity and penetrance of putatively clinically important rare variants. Although rare variants are harder to genotype accurately than common variants, we were able to classify as high quality 1,244 of 4,585 (27%) putatively clinically relevant rare (MAF < 1%) variants genotyped on the UKB microarray. We defined as "clinically relevant" variants that were classified as either pathogenic or likely pathogenic in ClinVar or are in genes known to cause two specific monogenic diseases: maturity-onset diabetes of the young (MODY) and severe developmental disorders (DDs). We assessed the penetrance and pathogenicity of these high-quality variants by testing their association with 401 clinically relevant traits. 27 of the variants were associated with a UKB trait, and we were able to refine the penetrance estimate for some of the variants. For example, the HNF4A c.340C>T (p.Arg114Trp) (GenBank: NM_175914.4) variant associated with diabetes is <10% penetrant by the time an individual is 40 years old. We also observed associations with relevant traits for heterozygous carriers of some rare recessive conditions, e.g., heterozygous carriers of the ERCC4 c.2395C>T (p.Arg799Trp) variant that causes Xeroderma pigmentosum were more susceptible to sunburn. Finally, we refute the previous disease association of RNF135 in developmental disorders. In conclusion, this study shows that very large population-based studies will help refine our understanding of the pathogenicity of rare genetic variants.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
| | - Ben West
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Kashyap Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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5
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Naugler C, Church DL. Clinical laboratory utilization management and improved healthcare performance. Crit Rev Clin Lab Sci 2019. [DOI: 10.1080/10408363.2018.1526164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christopher Naugler
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Family Medicine, University of Calgary, Calgary, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, Canada
| | - Deirdre L. Church
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Medicine, University of Calgary, Calgary, Canada
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6
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Matthews AM, Blydt-Hansen I, Al-Jabri B, Andersen J, Tarailo-Graovac M, Price M, Selby K, Demos M, Connolly M, Drögemoller B, Shyr C, Mwenifumbo J, Elliott AM, Lee J, Ghani A, Stöckler S, Salvarinova R, Vallance H, Sinclair G, Ross CJ, Wasserman WW, McKinnon ML, Horvath GA, Goez H, van Karnebeek CD. Atypical cerebral palsy: genomics analysis enables precision medicine. Genet Med 2018; 21:1621-1628. [DOI: 10.1038/s41436-018-0376-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022] Open
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7
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Theunissen TEJ, Nguyen M, Kamps R, Hendrickx AT, Sallevelt SCEH, Gottschalk RWH, Calis CM, Stassen APM, de Koning B, Mulder-Den Hartog ENM, Schoonderwoerd K, Fuchs SA, Hilhorst-Hofstee Y, de Visser M, Vanoevelen J, Szklarczyk R, Gerards M, de Coo IFM, Hellebrekers DMEI, Smeets HJM. Whole Exome Sequencing Is the Preferred Strategy to Identify the Genetic Defect in Patients With a Probable or Possible Mitochondrial Cause. Front Genet 2018; 9:400. [PMID: 30369941 PMCID: PMC6194163 DOI: 10.3389/fgene.2018.00400] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/03/2018] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial disorders, characterized by clinical symptoms and/or OXPHOS deficiencies, are caused by pathogenic variants in mitochondrial genes. However, pathogenic variants in some of these genes can lead to clinical manifestations which overlap with other neuromuscular diseases, which can be caused by pathogenic variants in non-mitochondrial genes as well. Mitochondrial pathogenic variants can be found in the mitochondrial DNA (mtDNA) or in any of the 1,500 nuclear genes with a mitochondrial function. We have performed a two-step next-generation sequencing approach in a cohort of 117 patients, mostly children, in whom a mitochondrial disease-cause could likely or possibly explain the phenotype. A total of 86 patients had a mitochondrial disorder, according to established clinical and biochemical criteria. The other 31 patients had neuromuscular symptoms, where in a minority a mitochondrial genetic cause is present, but a non-mitochondrial genetic cause is more likely. All patients were screened for pathogenic variants in the mtDNA and, if excluded, analyzed by whole exome sequencing (WES). Variants were filtered for being pathogenic and compatible with an autosomal or X-linked recessive mode of inheritance in families with multiple affected siblings and/or consanguineous parents. Non-consanguineous families with a single patient were additionally screened for autosomal and X-linked dominant mutations in a predefined gene-set. We identified causative pathogenic variants in the mtDNA in 20% of the patient-cohort, and in nuclear genes in 49%, implying an overall yield of 68%. We identified pathogenic variants in mitochondrial and non-mitochondrial genes in both groups with, obviously, a higher number of mitochondrial genes affected in mitochondrial disease patients. Furthermore, we show that 31% of the disease-causing genes in the mitochondrial patient group were not included in the MitoCarta database, and therefore would have been missed with MitoCarta based gene-panels. We conclude that WES is preferable to panel-based approaches for both groups of patients, as the mitochondrial gene-list is not complete and mitochondrial symptoms can be secondary. Also, clinically and genetically heterogeneous disorders would require sequential use of multiple different gene panels. We conclude that WES is a comprehensive and unbiased approach to establish a genetic diagnosis in these patients, able to resolve multi-genic disease-causes.
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Affiliation(s)
- Tom E J Theunissen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Minh Nguyen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Rick Kamps
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Alexandra T Hendrickx
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Suzanne C E H Sallevelt
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Ralph W H Gottschalk
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Chantal M Calis
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Alphons P M Stassen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Bart de Koning
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | | | | | - Sabine A Fuchs
- Department of Metabolic Disorders, University Medical Centre Utrecht, Utrecht, Netherlands
| | | | - Marianne de Visser
- Department of Neurology, Academic Medical Centre Amsterdam, Amsterdam, Netherlands
| | - Jo Vanoevelen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Radek Szklarczyk
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Mike Gerards
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Maastricht Center for Systems Biology (MaCSBio), Maastricht University Medical Centre, Maastricht, Netherlands
| | - Irenaeus F M de Coo
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Department of Pediatric Neurology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Debby M E I Hellebrekers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Hubert J M Smeets
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
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Strande NT, Brnich SE, Roman TS, Berg JS. Navigating the nuances of clinical sequence variant interpretation in Mendelian disease. Genet Med 2018; 20:918-926. [PMID: 29988079 PMCID: PMC6679919 DOI: 10.1038/s41436-018-0100-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding clinical genetic test results in the era of next-generation sequencing has become increasingly complex, necessitating clear and thorough guidelines for sequence variant interpretation. To meet this need the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for a systematic approach for sequence variant interpretation in 2015. This framework is intended to be adaptable to any Mendelian condition, promoting transparency and consistency in variant interpretation, yet its comprehensive nature yields important challenges and caveats that end users must understand. In this review, we address some of these nuances and discuss the evolving efforts to refine and adapt this framework. We also consider the added complexity of distinguishing between variant-level interpretations and case-level conclusions, particularly in the context of the large gene panel approach to clinical diagnostics.
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Affiliation(s)
- Natasha T Strande
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tamara S Roman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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