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Moon D, Park HW, Surl D, Won D, Lee ST, Shin S, Choi JR, Han J. Precision Medicine through Next-Generation Sequencing in Inherited Eye Diseases in a Korean Cohort. Genes (Basel) 2021; 13:genes13010027. [PMID: 35052368 PMCID: PMC8774510 DOI: 10.3390/genes13010027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
In this study, we investigated medically or surgically actionable genes in inherited eye disease, based on clinical phenotype and genomic data. This retrospective consecutive case series included 149 patients with inherited eye diseases, seen by a single pediatric ophthalmologist, who underwent genetic testing between 1 March 2017 and 28 February 2018. Variants were detected using a target enrichment panel of 429 genes and known deep intronic variants associated with inherited eye disease. Among 149 patients, 38 (25.5%) had a family history, and this cohort includes heterogeneous phenotype including anterior segment dysgenesis, congenital cataract, infantile nystagmus syndrome, optic atrophy, and retinal dystrophy. Overall, 90 patients (60.4%) received a definite molecular diagnosis. Overall, NGS-guided precision care was provided to 8 patients (5.4%). The precision care included cryotherapy to prevent retinal detachment in COL2A1 Stickler syndrome, osteoporosis management in patients with LRP5-associated familial exudative vitreoretinopathy, and avoidance of unnecessary phlebotomy in hyperferritinemia-cataract syndrome. A revision of the initial clinical diagnosis was made in 22 patients (14.8%). Unexpected multi-gene deletions and dual diagnosis were noted in 4 patients (2.7%). We found that precision medical or surgical managements were provided for 8 of 149 patients (5.4%), and multiple locus variants were found in 2.7% of cases. These findings are important because individualized management of inherited eye diseases can be achieved through genetic testing.
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Affiliation(s)
- Dabin Moon
- Department of Medicine, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Hye Won Park
- Department of Ophthalmology, Konyang University College of Medicine, Daejeon 35365, Korea;
| | - Dongheon Surl
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Dongju Won
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (D.W.); (S.-T.L.); (S.S.); (J.R.C.)
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (D.W.); (S.-T.L.); (S.S.); (J.R.C.)
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (D.W.); (S.-T.L.); (S.S.); (J.R.C.)
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (D.W.); (S.-T.L.); (S.S.); (J.R.C.)
| | - Jinu Han
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea;
- Department of Ophthalmology, Institute of Vision Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea
- Correspondence: ; Tel.: +82-2-2019-3445; Fax: +82-2-3463-1049
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Nguyen TV, Tran Vu MT, Do TNP, Tran THN, Do TH, Nguyen TMH, Tran Huynh BN, Le LA, Nguyen Pham NT, Nguyen TDA, Nguyen TMN, Le NHP, Pham Nguyen V, Ho Huynh TD. Genetic Determinants and Genotype-Phenotype Correlations in Vietnamese Patients With Dilated Cardiomyopathy. Circ J 2021; 85:1469-1478. [PMID: 34011823 DOI: 10.1253/circj.cj-21-0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is an important cause of heart failure and cardiac transplantation. This study determined the prevalence of DCM-associated genes and evaluated the genotype-phenotype correlation in Vietnamese patients.Methods and Results:This study analyzed 58 genes from 230 patients. The study cohort consisted of 64.3% men; age at diagnosis 47.9±13.7 years; familial (10.9%) and sporadic DCM (82.2%). The diagnostic yield was 23.5%, 44.0% in familial and 19.6% in sporadic DCM.TTNtruncating variants (TTNtv) were predominant (46.4%), followed byTPM1,DSP,LMNA,MYBPC3,MYH6,MYH7,DES,TNNT2,ACTC1,ACTN2,BAG3,DMD,FKTN,PLN,TBX5,RBM20,TCAP(2-6%). Familial DCM, genotype-positive andTTNtv-positive patients were younger than those with genotype-negative and sporadic DCM. Genotype-positive patients displayed a decreased systolic blood pressure and left ventricular wall thickness compared to genotype-negative patients. Genotype-positive patients, particularly those withTTNtv, had a family history of DCM, higher left atrial volume index and body mass index, and lower right ventricle-fractional area change than genotype-negative patients. Genotype-positive patients reached the combined outcomes more frequently and at a younger age than genotype-negative patients. Major cardiac events occurred more frequently in patients positive with genes other thanTTNtv. CONCLUSIONS The study findings provided an overview of Vietnamese DCM patients' genetic profile and suggested that management of environmental factors may be beneficial for DCM patients.
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Affiliation(s)
- Thuy Vy Nguyen
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM [Vietnam National University, Ho Chi Minh City]
| | | | | | | | | | | | | | | | | | | | - Thi My Nuong Nguyen
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM [Vietnam National University, Ho Chi Minh City]
| | - Ngoc Hong Phuong Le
- Research Center for Genetics and Reproductive Health, School of Medicine, VNUHCM [Vietnam National University, Ho Chi Minh City]
| | | | - Thuy Duong Ho Huynh
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM [Vietnam National University, Ho Chi Minh City].,Research Center for Genetics and Reproductive Health, School of Medicine, VNUHCM [Vietnam National University, Ho Chi Minh City].,KTEST Science Company
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3
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Roos D, de Boer M. Mutations in cis that affect mRNA synthesis, processing and translation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166166. [PMID: 33971252 DOI: 10.1016/j.bbadis.2021.166166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
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Affiliation(s)
- Dirk Roos
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Martin de Boer
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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4
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Truty R, Ouyang K, Rojahn S, Garcia S, Colavin A, Hamlington B, Freivogel M, Nussbaum RL, Nykamp K, Aradhya S. Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. Am J Hum Genet 2021; 108:696-708. [PMID: 33743207 PMCID: PMC8059334 DOI: 10.1016/j.ajhg.2021.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.
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Affiliation(s)
| | - Karen Ouyang
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Sarah Garcia
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | | | | | | | | | - Keith Nykamp
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
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Pace NP, Pace Bardon M, Borg I. A respiratory/Hirschsprung phenotype in a three-generation family associated with a novel pathogenic PHOX2B splice donor mutation. Mol Genet Genomic Med 2020; 8:e1528. [PMID: 33047879 PMCID: PMC7767558 DOI: 10.1002/mgg3.1528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/22/2020] [Accepted: 09/25/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Mutations in the PHOX2B gene cause congenital central hypoventilation syndrome (CCHS), a rare autonomic nervous system dysfunction disorder characterized by a decreased ventilatory response to hypercapnia. Affected subjects develop alveolar hypoventilation requiring ventilatory support particularly during the non-REM phase of sleep. In more severe cases, hypoventilation may extend into wakefulness. CCHS is associated with disorders characterized by the defective migration/differentiation of neural crest derivatives, including aganglionic megacolon or milder gastrointestinal phenotypes, such as constipation. Most cases of CCHS are de novo, caused by heterozygosity for polyalanine repeat expansion mutations (PARMs) in exon 3. About 10% of cases are due to heterozygous non-PARM missense, nonsense or frameshift mutations. METHODS We describe a three-generation Maltese-Caucasian family with a variable respiratory/Hirschsprung phenotype, characterized by chronic constipation, three siblings with Hirschsprung disease necessitating surgery, chronic hypoxia, and alveolar hypoventilation requiring non-invasive ventilation. RESULTS The sequencing of PHOX2B revealed a novel heterozygous c.241+2delT splice variant in exon 1 that segregates with the CCHS/Hirschsprung phenotype in the family. The mutation generates a non-functional splice site with a deleterious effect on protein structure and is pathogenic according to ACMG P VS1, PM2, and PP1 criteria. CONCLUSION This report is significant as no PHOX2B splice-site mutations have been reported. Additionally, it highlights the variability in clinical expression and disease severity of non-PARM mutations.
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Affiliation(s)
- Nikolai Paul Pace
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | | | - Isabella Borg
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Medical Genetics Unit, Department of Pathology, Mater Dei Hospital, Msida, Malta.,Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
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6
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Alhenc-Gelas M, Plu-Bureau G, Mauge L, Gandrille S, Présot I. Genotype-Phenotype Relationships in a Large French Cohort of Subjects with Inherited Protein C Deficiency. Thromb Haemost 2020; 120:1270-1281. [PMID: 32717757 DOI: 10.1055/s-0040-1714100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inherited protein C (PC) deficiency caused by mutations in the PROC gene is a well-known risk factor for venous thromboembolism. Few studies have investigated the relationship between PROC genotype and plasma or clinical phenotypes. We addressed this issue in a large retrospective cohort of 1,115 heterozygous carriers of 226 PROC pathogenic or likely pathogenic mutations. Mutations were classified in three categories according to their observed or presumed association with type I, type IIa, or type IIb PC deficiency. The study population comprised 876 carriers of type I category mutations, 55 carriers of type IIa category mutations, and 184 carriers of type IIb category mutations. PC anticoagulant activity significantly influenced risk of first venous thrombosis (p trend < 10-4). No influence of mutation category on risk of whole or unprovoked thrombotic events was observed. Both PC anticoagulant activity and genotype significantly influenced risk of venous thrombosis. Effect of detrimental mutations on plasma phenotype was ambiguous in several carriers, whatever the mutation category. Altogether, our findings confirm that diagnosing PC inherited deficiency based on plasma measurement may be difficult but show that diagnosis can be improved by PROC genotyping.
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Affiliation(s)
- Martine Alhenc-Gelas
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
| | - Geneviève Plu-Bureau
- Unité d'hémostase, Unité de Gynécologie Endocrinienne, AP-HP, Hôpital Cochin, QUP Centre Université de Paris, Paris, France
| | - Laetitia Mauge
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
| | - Sophie Gandrille
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France.,Innovative Therapies in Haemostasis, Université de Paris, Paris, France
| | - Isabelle Présot
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
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7
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Pricolo MR, Herrero-Galán E, Mazzaccara C, Losi MA, Alegre-Cebollada J, Frisso G. Protein Thermodynamic Destabilization in the Assessment of Pathogenicity of a Variant of Uncertain Significance in Cardiac Myosin Binding Protein C. J Cardiovasc Transl Res 2020; 13:867-877. [PMID: 32034629 DOI: 10.1007/s12265-020-09959-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/20/2020] [Indexed: 12/29/2022]
Abstract
In the era of next generation sequencing (NGS), genetic testing for inherited disorders identifies an ever-increasing number of variants whose pathogenicity remains unclear. These variants of uncertain significance (VUS) limit the reach of genetic testing in clinical practice. The VUS for hypertrophic cardiomyopathy (HCM), the most common familial heart disease, constitute over 60% of entries for missense variants shown in ClinVar database. We have studied a novel VUS (c.1809T>G-p.I603M) in the most frequently mutated gene in HCM, MYBPC3, which codes for cardiac myosin-binding protein C (cMyBPC). Our determinations of pathogenicity integrate bioinformatics evaluation and functional studies of RNA splicing and protein thermodynamic stability. In silico prediction and mRNA analysis indicated no alteration of RNA splicing induced by the variant. At the protein level, the p.I603M mutation maps to the C4 domain of cMyBPC. Although the mutation does not perturb much the overall structure of the C4 domain, the stability of C4 I603M is severely compromised as detected by circular dichroism and differential scanning calorimetry experiments. Taking into account the highly destabilizing effect of the mutation in the structure of C4, we propose reclassification of variant p.I603M as likely pathogenic. Looking into the future, the workflow described here can be used to refine the assignment of pathogenicity of variants of uncertain significance in MYBPC3.
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Affiliation(s)
- Maria Rosaria Pricolo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain. .,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Naples, Italy.
| | - Elías Herrero-Galán
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Cristina Mazzaccara
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate s.c. a r.l., Naples, Italy
| | - Maria Angela Losi
- Dipartimento di Scienze Biomediche Avanzate, Università Federico II, Naples, Italy
| | | | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate s.c. a r.l., Naples, Italy
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8
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Bryen SJ, Joshi H, Evesson FJ, Girard C, Ghaoui R, Waddell LB, Testa AC, Cummings B, Arbuckle S, Graf N, Webster R, MacArthur DG, Laing NG, Davis MR, Lührmann R, Cooper ST. Pathogenic Abnormal Splicing Due to Intronic Deletions that Induce Biophysical Space Constraint for Spliceosome Assembly. Am J Hum Genet 2019; 105:573-587. [PMID: 31447096 DOI: 10.1016/j.ajhg.2019.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022] Open
Abstract
A precise genetic diagnosis is the single most important step for families with genetic disorders to enable personalized and preventative medicine. In addition to genetic variants in coding regions (exons) that can change a protein sequence, abnormal pre-mRNA splicing can be devastating for the encoded protein, inducing a frameshift or in-frame deletion/insertion of multiple residues. Non-coding variants that disrupt splicing are extremely challenging to identify. Stemming from an initial clinical discovery in two index Australian families, we define 25 families with genetic disorders caused by a class of pathogenic non-coding splice variant due to intronic deletions. These pathogenic intronic deletions spare all consensus splice motifs, though they critically shorten the minimal distance between the 5' splice-site (5'SS) and branchpoint. The mechanistic basis for abnormal splicing is due to biophysical constraint precluding U1/U2 spliceosome assembly, which stalls in A-complexes (that bridge the 5'SS and branchpoint). Substitution of deleted nucleotides with non-specific sequences restores spliceosome assembly and normal splicing, arguing against loss of an intronic element as the primary causal basis. Incremental lengthening of 5'SS-branchpoint length in our index EMD case subject defines 45-47 nt as the critical elongation enabling (inefficient) spliceosome assembly for EMD intron 5. The 5'SS-branchpoint space constraint mechanism, not currently factored by genomic informatics pipelines, is relevant to diagnosis and precision medicine across the breadth of Mendelian disorders and cancer genomics.
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9
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A novel CUL4B splice site variant in a young male exhibiting less pronounced features. Hum Genome Var 2019; 6:43. [PMID: 31645981 PMCID: PMC6804535 DOI: 10.1038/s41439-019-0074-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 11/20/2022] Open
Abstract
Patients with variants in CUL4B exhibit syndromic intellectual disability (MIM #300354). A seven-year-old boy presented with intellectual disability, a history of seizure, characteristic facial features, and short stature. Whole-exome sequencing detected a c.974+3A>G variant in CUL4B, which was subsequently confirmed to disrupt mRNA splicing. The current patient showed less pronounced phenotypic features compared with the previously reported cases. This report, therefore, provides evidence of genotype–phenotype correlations in CUL4B-related disorders.
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10
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Tran Vu MT, Nguyen TV, Huynh NV, Nguyen Thai HT, Pham Nguyen V, Ho Huynh TD. Presence of Hypertrophic Cardiomyopathy Related Gene Mutations and Clinical Manifestations in Vietnamese Patients With Hypertrophic Cardiomyopathy. Circ J 2019; 83:1908-1916. [PMID: 31308319 DOI: 10.1253/circj.cj-19-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is associated primarily with pathogenic mutations in sarcomeric genes. The aim of this study was to identify the prevalence and distribution of disease-causing mutations in HCM-associated genes and the genotype-phenotype relationship in Vietnamese patients with HCM.Methods and Results:Genetic testing was performed by next-generation sequencing in 104 unrelated probands for 23 HCM-related genes and in 57 family members for the mutation(s) detected. Clinical manifestations were recorded for genotype-phenotype correlation analysis. Mutation detection rate was 43.4%. Mutations inMYBPC3accounted for 38.6%, followed byTPM1(20.5%),MYH7(18.2%),TNNT2(9.1%),TNNI3(4.5%) andMYL2(2.3%). A mutation inGLAassociated with Fabry disease was found in 1 patient. A mutation inTPM1(c.842T>C, p.Met281Thr) was identified in 8 unrelated probands (18.2%) and 8 family members from 5 probands. Genotype-positive status related toMYH7,TPM1, andTNNT2mutations was associated with severe clinical manifestations.MYH7-positive patients displayed worse prognosis compared withMYBPC3-positive patients. Interestingly,TPM1c.842T>C mutation was associated with high penetrance and severe HCM phenotype. CONCLUSIONS We report for the first time the prevalence of HCM-related gene variants in Vietnamese patients with HCM.MYH7,TPM1, andTNNT2mutations were associated with unfavorable prognosis.
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Affiliation(s)
| | - Thuy Vy Nguyen
- Research Center for Genetics and Reproductive Health, School of Medicine, Viet Nam National University.,Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM
| | | | - Hoang Tam Nguyen Thai
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM
| | | | - Thuy Duong Ho Huynh
- Research Center for Genetics and Reproductive Health, School of Medicine, Viet Nam National University.,Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNUHCM.,KTEST Science Company
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11
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Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel) 2019; 11:cancers11030295. [PMID: 30832263 PMCID: PMC6468917 DOI: 10.3390/cancers11030295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Highly penetrant variants of BRCA1/2 genes are involved in hereditary predisposition to breast and ovarian cancer. The detection of pathogenic BRCA variants has a considerable clinical impact, allowing appropriate cancer-risk management. However, a major drawback is represented by the identification of variants of uncertain significance (VUS). Many VUS potentially affect mRNA splicing, making transcript analysis an essential step for the definition of their pathogenicity. Here, we characterize the impact on splicing of ten BRCA1/2 variants. Aberrant splicing patterns were demonstrated for eight variants whose alternative transcripts were fully characterized. Different events were observed, including exon skipping, intron retention, and usage of de novo and cryptic splice sites. Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. Partial/complete splicing effect and quantitative contribution of different isoforms were assessed, leading to variant classification according to Evidence-based Network for the Interpretation of Mutant Alleles (ENIGMA) consortium guidelines. Two variants could be classified as pathogenic and two as likely benign, while due to a partial splicing effect, six variants remained of uncertain significance. The association with an undefined tumor risk justifies caution in recommending aggressive risk-reduction treatments, but prevents the possibility of receiving personalized therapies with potential beneficial effect. This indicates the need for applying additional approaches for the analysis of variants resistant to classification by gene transcript analyses.
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12
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Imperatore V, Pinto AM, Gelli E, Trevisson E, Morbidoni V, Frullanti E, Hadjistilianou T, De Francesco S, Toti P, Gusson E, Roversi G, Accogli A, Capra V, Mencarelli MA, Renieri A, Ariani F. Parent-of-origin effect of hypomorphic pathogenic variants and somatic mosaicism impact on phenotypic expression of retinoblastoma. Eur J Hum Genet 2018; 26:1026-1037. [PMID: 29662154 DOI: 10.1038/s41431-017-0054-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/27/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Retinoblastoma is the most common eye cancer in children. Numerous families have been described displaying reduced penetrance and expressivity. An extensive molecular characterization of seven families led us to characterize the two main mechanisms impacting on phenotypic expression, as follows: (i) mosaicism of amorphic pathogenic variants; and (ii) parent-of-origin-effect of hypomorphic pathogenic variants. Somatic mosaicism for RB1 splicing variants (c.1960+5G>C and c.2106+2T>C), leading to a complete loss of function was demonstrated by high-depth NGS in two families. In both cases, the healthy carrier parent (one with retinoma) showed a variant frequency lower than that expected for a heterozygous individual, indicating a 56-60% mosaicism level. Previous evidences of a ~3-fold excess of RB1 maternal canonical transcript led us to hypothesize that this differential allelic expression could influence phenotypic outcome in families at risk for RB onset. Accordingly, in five families, we identified a higher tumor risk associated with paternally inherited hypomorphic pathogenic variants, namely a deletion resulting in the loss of 37 amino acids at the N-terminus (c.608-16_608del), an exonic substitution with a "leaky" splicing effect (c.1331A>G), a partially deleterious substitution (c.1981C>T) and a truncating C-terminal variant (c.2663+2T>C). The identification of these mechanisms changes the genetic/prenatal counseling and the clinical management of families, indicating a higher recurrence risk when the hypomorphic pathogenic variant is inherited from the father, and suggesting the need for second tumor surveillance in unaffected carriers at risk of developing adult-onset cancer such as osteosarcoma or leiomyosarcoma.
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Affiliation(s)
| | - Anna Maria Pinto
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Gelli
- Medical Genetics, University of Siena, Siena, Italy
| | - Eva Trevisson
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | - Valeria Morbidoni
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | | | - Theodora Hadjistilianou
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Sonia De Francesco
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Paolo Toti
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Elena Gusson
- Unit of Ophthalmology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Gaia Roversi
- Department of Medicine and Surgery, University Milan-Bicocca; Ospedale San Gerardo, ASST Monza, Monza, Italy
| | | | | | - Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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13
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Daga S, Baldassarri M, Lo Rizzo C, Fallerini C, Imperatore V, Longo I, Frullanti E, Landucci E, Massella L, Pecoraro C, Garosi G, Ariani F, Mencarelli MA, Mari F, Renieri A, Pinto AM. Urine-derived podocytes-lineage cells: A promising tool for precision medicine in Alport Syndrome. Hum Mutat 2017; 39:302-314. [PMID: 29098738 DOI: 10.1002/humu.23364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 11/11/2022]
Abstract
Alport Syndrome (ATS) is a rare genetic disorder caused by collagen IV genes mutations, leading to glomerular basement membrane damage up to end-stage renal disease. Podocytes, the main component of the glomerular structure, are the only cells able to produce all the three collagens IV alpha chains associated with ATS and thus, they are key players in ATS pathogenesis. However, podocytes-targeted therapeutic strategies have been hampered by the difficulty of non-invasively isolating them and transcripts-based diagnostic approaches are complicated by the inaccessibility of other COL4 chains-expressing cells. We firstly isolated podocyte-lineage cells from ATS patients' urine samples, in a non-invasive way. RT-PCR analysis revealed COL4A3, COL4A4, and COL4A5 expression. Transcripts analysis on RNA extracted from patient's urine derived podocyte-lineage cells allowed defining the pathogenic role of intronic variants, namely one mutation in COL4A3 (c.3882+5G>A), three mutations in COL4A4 (c.1623+2T>A, c.3699_3706+1del, c.2545+143T>A), and one mutation in COL4A5 (c.3454+2T>C). Therefore, our cellular model represents a novel tool, essential to unequivocally prove the effect of spliceogenic intronic variants on transcripts expressed exclusively at a glomerular level. This process is a key step for providing the patient with a definite molecular diagnosis and with a proper recurrence risk. The established system also opens up the possibility of testing personalized therapeutic approaches on disease-relevant cells.
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Affiliation(s)
- Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Caterina Lo Rizzo
- Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | | | - Ilaria Longo
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | | | - Laura Massella
- Division of Nephrology and Dialysis, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carmine Pecoraro
- Pediatric Nephrology Unit, Santobono-Pausilipon Hospital, Naples, Italy
| | - Guido Garosi
- Nephrology, Dialysis and Transplantation Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Anna Maria Pinto
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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14
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Alhenc-Gelas M, Plu-Bureau G, Hugon-Rodin J, Picard V, Horellou MH. Thrombotic risk according to SERPINC1 genotype in a large cohort of subjects with antithrombin inherited deficiency. Thromb Haemost 2017; 117:1040-1051. [PMID: 28300866 DOI: 10.1160/th16-08-0635] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/23/2017] [Indexed: 12/24/2022]
Abstract
Inherited quantitative (type I) or qualitative (type II) antithrombin deficiency (ATD) due to mutations in the SERPINC1 gene is a well-known risk factor for venous thromboembolism. ATD may also increase risk for arterial thrombosis. Few studies have investigated risk for thrombosis according to mutations. We addressed this topic in a large retrospective cohort study of 540 heterozygous carriers of SERPINC1 mutations and compared risk for first venous or arterial thrombosis associated with carrying of different type II or type I mutations. No clear difference in risk for first venous thrombotic event was observed among type I (missense or null), type IIRS or type IIPE mutation carriers except for a few variants that displayed lower risk [all events, adjusted relative risk: Cambridge II: 0.42 (95 %CI 0.25-0.70), Dublin: 0.35 (95 %CI 0.13-0.99)]. IIHBS mutation carrying was associated with a clearly lower risk than type I mutation carrying [0.28 (95 %CI 0.20-0.40)]. These differences in risk were observed for both all venous thrombotic events and pulmonary embolism associated with deep venous thrombosis. The HBS group was also heterogeneous, with AT Budapest 3 carriers displaying a non-significantly different risk [0.61 (95 %CI 0.31-1.20)] compared to type I mutation carriers. We also studied risk for arterial thrombosis and found no significant influence of mutation type. Altogether, our findings suggest a place for SERPINC1 genotyping in the diagnosis of ATD.
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Affiliation(s)
- Martine Alhenc-Gelas
- M. Alhenc-Gelas, Laboratoire d'Hématologie, HEGP, 20 Rue Leblanc, 75015 Paris, France, Tel: +33 156093901, Fax: +33 156093393, E-mail:
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15
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Carstens N, Williams S, Goolam S, Carmichael T, Cheung MS, Büchmann-Møller S, Sultan M, Staedtler F, Zou C, Swart P, Rice DS, Lacoste A, Paes K, Ramsay M. Novel mutation in the CHST6 gene causes macular corneal dystrophy in a black South African family. BMC MEDICAL GENETICS 2016; 17:47. [PMID: 27439461 PMCID: PMC4955246 DOI: 10.1186/s12881-016-0308-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 06/23/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Macular corneal dystrophy (MCD) is a rare autosomal recessive disorder that is characterized by progressive corneal opacity that starts in early childhood and ultimately progresses to blindness in early adulthood. The aim of this study was to identify the cause of MCD in a black South African family with two affected sisters. METHODS A multigenerational South African Sotho-speaking family with type I MCD was studied using whole exome sequencing. Variant filtering to identify the MCD-causal mutation included the disease inheritance pattern, variant minor allele frequency and potential functional impact. RESULTS Ophthalmologic evaluation of the cases revealed a typical MCD phenotype and none of the other family members were affected. An average of 127 713 variants per individual was identified following exome sequencing and approximately 1.2 % were not present in any of the investigated public databases. Variant filtering identified a homozygous E71Q mutation in CHST6, a known MCD-causing gene encoding corneal N-acetyl glucosamine-6-O-sulfotransferase. This E71Q mutation results in a non-conservative amino acid change in a highly conserved functional domain of the human CHST6 that is essential for enzyme activity. CONCLUSION We identified a novel E71Q mutation in CHST6 as the MCD-causal mutation in a black South African family with type I MCD. This is the first description of MCD in a black Sub-Saharan African family and therefore contributes valuable insights into the genetic aetiology of this disease, while improving genetic counselling for this and potentially other MCD families.
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Affiliation(s)
- Nadia Carstens
- />Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
| | - Susan Williams
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Saadiah Goolam
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Trevor Carmichael
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ming Sin Cheung
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stine Büchmann-Møller
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Marc Sultan
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Frank Staedtler
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Chao Zou
- />Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Peter Swart
- />Division of Anatomical Pathology, National Health Laboratory Services and University of the Witwatersrand, Johannesburg, South Africa
| | - Dennis S. Rice
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Arnaud Lacoste
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Kim Paes
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Michèle Ramsay
- />Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
- />Division of Human Genetics, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
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16
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Mohamed S, Hamad MH, Kondkar AA, Abu-Amero KK. A novel mutation in ornithine transcarbamylase gene causing mild intermittent hyperammonemia. Saudi Med J 2016; 36:1229-32. [PMID: 26446336 PMCID: PMC4621731 DOI: 10.15537/smj.2015.10.12127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We report a 3-year-old Saudi boy with recurrent episodes of vomiting, poor feeding, and altered mental status accompanied by an intermittent mild hyperammonemia, and a large elevation of urinary orotic acid. Sanger sequencing of the ornithine transcarbamylase (OTC) gene revealed a novel hemizygous deletion at the fourth nucleotide of intron 4 (c.386+4delT) in the proband and his asymptomatic mother. This novel mutation in the OTC gene is responsible for the late-onset phenotype of OTC deficiency.
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Affiliation(s)
- Sarar Mohamed
- Department of Pediatrics (39), College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia. E-mail.
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17
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Shah K, Ali RH, Ansar M, Lee K, Chishti MS, Abbe I, Li B, Smith JD, Nickerson DA, Shendure J, Coucke PJ, Steyaert W, Bamshad MJ, Santos-Cortez RLP, Leal SM, Ahmad W. Mitral regurgitation as a phenotypic manifestation of nonphotosensitive trichothiodystrophy due to a splice variant in MPLKIP. BMC MEDICAL GENETICS 2016; 17:13. [PMID: 26880286 PMCID: PMC4754937 DOI: 10.1186/s12881-016-0275-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
Abstract
Background Nonphotosensitive trichothiodystrophy (TTDN) is a rare autosomal recessive disorder of neuroectodermal origin. The condition is marked by hair abnormalities, intellectual impairment, nail dystrophies and susceptibility to infections but with no UV sensitivity. Methods We identified three consanguineous Pakistani families with varied TTDN features and used homozygosity mapping, linkage analysis, and Sanger and exome sequencing in order to identify pathogenic variants. Haplotype analysis was performed and haplotype age estimated. A splicing assay was used to validate the effect of the MPLKIP splice variant on expression. Results Affected individuals from all families exhibit several TTDN features along with a heart-specific feature, i.e. mitral regurgitation. Exome sequencing in the probands from families ED168 and ED241 identified a homozygous splice mutation c.339 + 1G > A within MPLKIP. The same splice variant co-segregates with TTDN in a third family ED210. The MPLKIP splice variant was not found in public databases, e.g. the Exome Aggregation Consortium, and in unrelated Pakistani controls. Functional analysis of the splice variant confirmed intron retention, which leads to protein truncation and loss of a phosphorylation site. Haplotype analysis identified a 585.1-kb haplotype which includes the MPLKIP variant, supporting the existence of a founder haplotype that is estimated to be 25,900 years old. Conclusion This study extends the allelic and phenotypic spectra of MPLKIP-related TTDN, to include a splice variant that causes cardiomyopathy as part of the TTDN phenotype.
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Affiliation(s)
- Khadim Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Raja Hussain Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.,Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.,Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Muhammad Salman Chishti
- Department of Biochemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, 21300, Pakistan
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Paul J Coucke
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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18
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Havranek O, Kleiblova P, Hojny J, Lhota F, Soucek P, Trneny M, Kleibl Z. Association of Germline CHEK2 Gene Variants with Risk and Prognosis of Non-Hodgkin Lymphoma. PLoS One 2015; 10:e0140819. [PMID: 26506619 PMCID: PMC4624763 DOI: 10.1371/journal.pone.0140819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/29/2015] [Indexed: 01/09/2023] Open
Abstract
The checkpoint kinase 2 gene (CHEK2) codes for the CHK2 protein, an important mediator of the DNA damage response pathway. The CHEK2 gene has been recognized as a multi-cancer susceptibility gene; however, its role in non-Hodgkin lymphoma (NHL) remains unclear. We performed mutation analysis of the entire CHEK2 coding sequence in 340 NHL patients using denaturing high-performance liquid chromatography (DHPLC) and multiplex ligation-dependent probe amplification (MLPA). Identified hereditary variants were genotyped in 445 non-cancer controls. The influence of CHEK2 variants on disease risk was statistically evaluated. Identified CHEK2 germline variants included four truncating mutations (found in five patients and no control; P = 0.02) and nine missense variants (found in 21 patients and 12 controls; P = 0.02). Carriers of non-synonymous variants had an increased risk of NHL development [odds ratio (OR) 2.86; 95% confidence interval (CI) 1.42–5.79] and an unfavorable prognosis [hazard ratio (HR) of progression-free survival (PFS) 2.1; 95% CI 1.12–4.05]. In contrast, the most frequent intronic variant c.319+43dupA (identified in 22% of patients and 31% of controls) was associated with a decreased NHL risk (OR = 0.62; 95% CI 0.45–0.86), but its positive prognostic effect was limited to NHL patients with diffuse large B-cell lymphoma (DLBCL) treated by conventional chemotherapy without rituximab (HR-PFS 0.4; 94% CI 0.17–0.74). Our results show that germ-line CHEK2 mutations affecting protein coding sequence confer a moderately-increased risk of NHL, they are associated with an unfavorable NHL prognosis, and they may represent a valuable predictive biomarker for patients with DLBCL.
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Affiliation(s)
- Ondrej Havranek
- First Department of Medicine–Department of Hematology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
- * E-mail: (OH); (ZK)
| | - Petra Kleiblova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jan Hojny
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Filip Lhota
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Pavel Soucek
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Marek Trneny
- First Department of Medicine–Department of Hematology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- * E-mail: (OH); (ZK)
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19
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Alhenc-Gelas M, Plu-Bureau G, Horellou MH, Rauch A, Suchon P. PROS1 genotype phenotype relationships in a large cohort of adults with suspicion of inherited quantitative protein S deficiency. Thromb Haemost 2015; 115:570-9. [PMID: 26466767 DOI: 10.1160/th15-05-0391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/08/2015] [Indexed: 11/05/2022]
Abstract
Inherited protein S deficiency (PSD) is an established risk factor for venous thromboembolism (VTE). However, data are conflicting concerning risk of VTE associated with decreased free PS level (FPS) and information on PROS1 genotype-phenotype relationship is sparse. In a retrospective cohort of 579 patients with inherited type I/III deficiency suspicion, PROS1 genotyping was performed and the effect of genotype on FPS and on VTE risk was investigated. We found 116 (including 65 novel) detrimental mutations (DM) in 222 (type I/III in 194, type II in 28), PS Heerlen in 74, possibly non DM in 38 and no mutation in 245 subjects. Among DMs, type I/IIIDMs only were found in subjects with FPS< 30 %. Prevalence of type I/III DM decreased with increasing FPS level. Risk of VT associated with FPS level and genotype was studied in the 467 subjects with personal or family history of thrombosis. Only type I/IIIDM carriers presented with an increased risk of VTE [1.41 (95 %CI (1.05-1.89)] compared to subjects with no mutation. Among the group of type I/IIIDM heterozygotes and subjects with no mutation, the optimal FPS cut-off point for identifying subjects at increased VTE risk was searched for. We found that only subjects with FPS< 30 % and type I/IIIDM presented with an increased risk [1.48 (95 %CI 1.08-2.04)]. Our findings confirm the value of a cut-off FPS level for identifying subjects at increased VTE risk far below the lower limit of the normal range and suggest a place for PROS1 genotyping in PSD diagnosis strategy.
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Affiliation(s)
- Martine Alhenc-Gelas
- M. Alhenc-Gelas, Laboratoire d'Hématologie, HEGP, 20 Rue Leblanc, 75015 Paris, France, Tel.: +33 156093901, Fax: +33 156093393, E-mail:
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20
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Martorell L, Corrales I, Ramirez L, Parra R, Raya A, Barquinero J, Vidal F. Molecular characterization of ten
F8
splicing mutations in RNA isolated from patient's leucocytes: assessment of
in silico
prediction tools accuracy. Haemophilia 2015; 21:249-257. [DOI: 10.1111/hae.12562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Affiliation(s)
- L. Martorell
- Gene and Cell Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
- Control of Stem Cell Potency Institute for Bioengineering of Catalonia (IBEC)Barcelona Spain
- Molecular Diagnosis and Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
| | - I. Corrales
- Molecular Diagnosis and Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
- Congenital Coagulopathies Laboratory Blood and Tissue Bank (BST)Barcelona Spain
| | - L. Ramirez
- Molecular Diagnosis and Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
- Congenital Coagulopathies Laboratory Blood and Tissue Bank (BST)Barcelona Spain
| | - R. Parra
- Congenital Coagulopathies Laboratory Blood and Tissue Bank (BST)Barcelona Spain
- Haemophilia Unit Vall d'Hebron University HospitalBarcelona Spain
| | - A. Raya
- Control of Stem Cell Potency Institute for Bioengineering of Catalonia (IBEC)Barcelona Spain
- Catalan Institution for Research and Advanced Studies (ICREA)Barcelona Spain
- Center of Regenerative Medicine in Barcelona (CMRB)Barcelona Spain
- Networking Center of Biomedical Research in Bioengineering Biomaterials and Nanomedicine (CIBER‐BBN) Barcelona Spain
| | - J. Barquinero
- Gene and Cell Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
| | - F. Vidal
- Molecular Diagnosis and Therapy Vall d'Hebron Research Institute Universitat Autònoma de Barcelona (VHIR‐UAB)Barcelona Spain
- Congenital Coagulopathies Laboratory Blood and Tissue Bank (BST)Barcelona Spain
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21
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Bullich G, Trujillano D, Santín S, Ossowski S, Mendizábal S, Fraga G, Madrid Á, Ariceta G, Ballarín J, Torra R, Estivill X, Ars E. Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity. Eur J Hum Genet 2014; 23:1192-9. [PMID: 25407002 PMCID: PMC4538209 DOI: 10.1038/ejhg.2014.252] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/14/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023] Open
Abstract
Genetic diagnosis of steroid-resistant nephrotic syndrome (SRNS) using Sanger sequencing is complicated by the high genetic heterogeneity and phenotypic variability of this disease. We aimed to improve the genetic diagnosis of SRNS by simultaneously sequencing 26 glomerular genes using massive parallel sequencing and to study whether mutations in multiple genes increase disease severity. High-throughput mutation analysis was performed in 50 SRNS and/or focal segmental glomerulosclerosis (FSGS) patients, a validation cohort of 25 patients with known pathogenic mutations, and a discovery cohort of 25 uncharacterized patients with probable genetic etiology. In the validation cohort, we identified the 42 previously known pathogenic mutations across NPHS1, NPHS2, WT1, TRPC6, and INF2 genes. In the discovery cohort, disease-causing mutations in SRNS/FSGS genes were found in nine patients. We detected three patients with mutations in an SRNS/FSGS gene and COL4A3. Two of them were familial cases and presented a more severe phenotype than family members with mutation in only one gene. In conclusion, our results show that massive parallel sequencing is feasible and robust for genetic diagnosis of SRNS/FSGS. Our results indicate that patients carrying mutations in an SRNS/FSGS gene and also in COL4A3 gene have increased disease severity.
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Affiliation(s)
- Gemma Bullich
- 1] Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain [2] Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Daniel Trujillano
- 1] Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain [2] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [3] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain [4] CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Catalonia, Spain
| | - Sheila Santín
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Stephan Ossowski
- 1] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [2] Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain
| | - Santiago Mendizábal
- Pediatric Nephrology Department, Hospital Universitario La Fe, Valencia, Spain
| | - Gloria Fraga
- Pediatric Nephrology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Álvaro Madrid
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Gema Ariceta
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - José Ballarín
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Roser Torra
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Xavier Estivill
- 1] Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain [2] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [3] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain [4] CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Catalonia, Spain
| | - Elisabet Ars
- 1] Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain [2] Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
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22
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Bernier R, Golzio C, Xiong B, Stessman HA, Coe BP, Penn O, Witherspoon K, Gerdts J, Baker C, Vulto-van Silfhout AT, Schuurs-Hoeijmakers JH, Fichera M, Bosco P, Buono S, Alberti A, Failla P, Peeters H, Steyaert J, Vissers LELM, Francescatto L, Mefford HC, Rosenfeld JA, Bakken T, O'Roak BJ, Pawlus M, Moon R, Shendure J, Amaral DG, Lein E, Rankin J, Romano C, de Vries BBA, Katsanis N, Eichler EE. Disruptive CHD8 mutations define a subtype of autism early in development. Cell 2014; 158:263-276. [PMID: 24998929 DOI: 10.1016/j.cell.2014.06.017] [Citation(s) in RCA: 520] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/01/2014] [Accepted: 06/05/2014] [Indexed: 11/28/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous disease in which efforts to define subtypes behaviorally have met with limited success. Hypothesizing that genetically based subtype identification may prove more productive, we resequenced the ASD-associated gene CHD8 in 3,730 children with developmental delay or ASD. We identified a total of 15 independent mutations; no truncating events were identified in 8,792 controls, including 2,289 unaffected siblings. In addition to a high likelihood of an ASD diagnosis among patients bearing CHD8 mutations, characteristics enriched in this group included macrocephaly, distinct faces, and gastrointestinal complaints. chd8 disruption in zebrafish recapitulates features of the human phenotype, including increased head size as a result of expansion of the forebrain/midbrain and impairment of gastrointestinal motility due to a reduction in postmitotic enteric neurons. Our findings indicate that CHD8 disruptions define a distinct ASD subtype and reveal unexpected comorbidities between brain development and enteric innervation.
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Affiliation(s)
- Raphael Bernier
- Department of Psychiatry, University of Washington, Seattle, WA 98195, USA
| | - Christelle Golzio
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA
| | - Bo Xiong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Holly A Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kali Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jennifer Gerdts
- Department of Psychiatry, University of Washington, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | - Marco Fichera
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy; Medical Genetics, University of Catania, Catania 95123, Italy
| | - Paolo Bosco
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy
| | - Serafino Buono
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy
| | - Antonino Alberti
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy
| | - Pinella Failla
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy
| | - Hilde Peeters
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium; Leuven Autism Research (LAuRes), 3000 Leuven, Belgium
| | - Jean Steyaert
- Leuven Autism Research (LAuRes), 3000 Leuven, Belgium; Department of Child and Adolescent Psychiatry, KU Leuven, 3000 Leuven, Belgium; Department of Clinical Genetics, Academic Hospital Maastricht, and Research Institute Growth & Development (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ludmila Francescatto
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jill A Rosenfeld
- Signature Genomics Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Brian J O'Roak
- Molecular & Medical Genetics, Oregon Health & Science University (OHSU), Portland, OR 97208, USA
| | - Matthew Pawlus
- Department of Pharmacology, University of Washington, Seattle, WA 98109, USA
| | - Randall Moon
- Department of Pharmacology, University of Washington, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - David G Amaral
- Autism Phenome Project, MIND Institute, University of California-Davis, Sacramento, CA 95817, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Julia Rankin
- Peninsula Clinical Genetics Service, Exeter EX1 2ED, UK
| | - Corrado Romano
- I.R.C.C.S. Associazione Oasi Maria Santissima, Troina 94018, Italy
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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23
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Aissat A, de Becdelièvre A, Golmard L, Vasseur C, Costa C, Chaoui A, Martin N, Costes B, Goossens M, Girodon E, Fanen P, Hinzpeter A. Combined computational-experimental analyses of CFTR exon strength uncover predictability of exon-skipping level. Hum Mutat 2013; 34:873-81. [PMID: 23420618 DOI: 10.1002/humu.22300] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 02/08/2013] [Indexed: 01/24/2023]
Abstract
With the increased number of identified nucleotide sequence variations in genes, the current challenge is to classify them as disease causing or neutral. These variants of unknown clinical significance can alter multiple processes, from gene transcription to RNA splicing or protein function. Using an approach combining several in silico tools, we identified some exons presenting weaker splicing motifs than other exons in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. These exons exhibit higher rates of basal skipping than exons harboring no identifiable weak splicing signals using minigene assays. We then screened 19 described mutations in three different exons, and identified exon-skipping substitutions. These substitutions induced higher skipping levels in exons having one or more weak splicing motifs. Indeed, this level remained under 2% for exons with strong splicing motifs and could reach 40% for exons having at least one weak motif. Further analysis revealed a functional exon splicing enhancer within exon 3 that was associated with the SR protein SF2/ASF and whose disruption induced exon skipping. Exon skipping was confirmed in vivo in two nasal epithelial cell brushing samples. Our approach, which point out exons with some splicing signals weaknesses, will help spot splicing mutations of clinical relevance.
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24
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Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations. PLoS One 2013; 8:e57173. [PMID: 23451180 PMCID: PMC3579815 DOI: 10.1371/journal.pone.0057173] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022] Open
Abstract
Several unclassified variants (UVs) have been identified in splicing regions of disease-associated genes and their characterization as pathogenic mutations or benign polymorphisms is crucial for the understanding of their role in disease development. In this study, 24 UVs located at BRCA1 and BRCA2 splice sites were characterized by transcripts analysis. These results were used to evaluate the ability of nine bioinformatics programs in predicting genetic variants causing aberrant splicing (spliceogenic variants) and the nature of aberrant transcripts. Eleven variants in BRCA1 and 8 in BRCA2, including 8 not previously characterized at transcript level, were ascertained to affect mRNA splicing. Of these, 16 led to the synthesis of aberrant transcripts containing premature termination codons (PTCs), 2 to the up-regulation of naturally occurring alternative transcripts containing PTCs, and one to an in-frame deletion within the region coding for the DNA binding domain of BRCA2, causing the loss of the ability to bind the partner protein DSS1 and ssDNA. For each computational program, we evaluated the rate of non-informative analyses, i.e. those that did not recognize the natural splice sites in the wild-type sequence, and the rate of false positive predictions, i.e., variants incorrectly classified as spliceogenic, as a measure of their specificity, under conditions setting sensitivity of predictions to 100%. The programs that performed better were Human Splicing Finder and Automated Splice Site Analyses, both exhibiting 100% informativeness and specificity. For 10 mutations the activation of cryptic splice sites was observed, but we were unable to derive simple criteria to select, among the different cryptic sites predicted by the bioinformatics analyses, those actually used. Consistent with previous reports, our study provides evidences that in silico tools can be used for selecting splice site variants for in vitro analyses. However, the latter remain mandatory for the characterization of the nature of aberrant transcripts.
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25
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Ravenscroft G, Thompson EM, Todd EJ, Yau KS, Kresoje N, Sivadorai P, Friend K, Riley K, Manton ND, Blumbergs P, Fietz M, Duff RM, Davis MR, Allcock RJ, Laing NG. Whole exome sequencing in foetal akinesia expands the genotype-phenotype spectrum of GBE1 glycogen storage disease mutations. Neuromuscul Disord 2012; 23:165-9. [PMID: 23218673 DOI: 10.1016/j.nmd.2012.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 10/27/2022]
Abstract
The clinically and genetically heterogenous foetal akinesias have low rates of genetic diagnosis. Exome sequencing of two siblings with phenotypic lethal multiple pterygium syndrome identified compound heterozygozity for a known splice site mutation (c.691+2T>C) and a novel missense mutation (c.956A>G; p.His319Arg) in glycogen branching enzyme 1 (GBE1). GBE1 mutations cause glycogen storage disease IV (GSD IV), including a severe foetal akinesia sub-phenotype. Re-investigating the muscle pathology identified storage material, consistent with GSD IV, which was confirmed biochemically. This study highlights the power of exome sequencing in genetically heterogeneous diseases and adds multiple pterygium syndrome to the phenotypic spectrum of GBE1 mutation.
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Affiliation(s)
- Gianina Ravenscroft
- Western Australian Institute for Medical Research and the Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia.
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26
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Ronchi D, Garone C, Bordoni A, Gutierrez Rios P, Calvo SE, Ripolone M, Ranieri M, Rizzuti M, Villa L, Magri F, Corti S, Bresolin N, Mootha VK, Moggio M, DiMauro S, Comi GP, Sciacco M. Next-generation sequencing reveals DGUOK mutations in adult patients with mitochondrial DNA multiple deletions. Brain 2012; 135:3404-15. [PMID: 23043144 DOI: 10.1093/brain/aws258] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The molecular diagnosis of mitochondrial disorders still remains elusive in a large proportion of patients, but advances in next generation sequencing are significantly improving our chances to detect mutations even in sporadic patients. Syndromes associated with mitochondrial DNA multiple deletions are caused by different molecular defects resulting in a wide spectrum of predominantly adult-onset clinical presentations, ranging from progressive external ophthalmoplegia to multi-systemic disorders of variable severity. The mutations underlying these conditions remain undisclosed in half of the affected subjects. We applied next-generation sequencing of known mitochondrial targets (MitoExome) to probands presenting with adult-onset mitochondrial myopathy and harbouring mitochondrial DNA multiple deletions in skeletal muscle. We identified autosomal recessive mutations in the DGUOK gene (encoding mitochondrial deoxyguanosine kinase), which has previously been associated with an infantile hepatocerebral form of mitochondrial DNA depletion. Mutations in DGUOK occurred in five independent subjects, representing 5.6% of our cohort of patients with mitochondrial DNA multiple deletions, and impaired both muscle DGUOK activity and protein stability. Clinical presentations were variable, including mitochondrial myopathy with or without progressive external ophthalmoplegia, recurrent rhabdomyolysis in a young female who had received a liver transplant at 9 months of age and adult-onset lower motor neuron syndrome with mild cognitive impairment. These findings reinforce the concept that mutations in genes involved in deoxyribonucleotide metabolism can cause diverse clinical phenotypes and suggest that DGUOK should be screened in patients harbouring mitochondrial DNA deletions in skeletal muscle.
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Affiliation(s)
- Dario Ronchi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy.
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27
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Jalkh N, Nassar-Slaba J, Chouery E, Salem N, Uhrchammer N, Golmard L, Stoppa-Lyonnet D, Bignon YJ, Mégarbané A. Prevalance of BRCA1 and BRCA2 mutations in familial breast cancer patients in Lebanon. Hered Cancer Clin Pract 2012; 10:7. [PMID: 22713736 PMCID: PMC3441239 DOI: 10.1186/1897-4287-10-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/19/2012] [Indexed: 12/27/2022] Open
Abstract
Breast cancer is the most prevalent malignancy in women in Western countries, currently accounting for one third of all female cancers. Familial aggregation is thought to account for 5–10 % of all BC cases, and germline mutations in BRCA1 and BRCA2 account for less of the half of these inherited cases. In Lebanon, breast cancer represents the principal death-causing malignancy among women, with 50 % of the cases diagnosed before the age of 50 years. In order to study BRCA1/2 mutation spectra in the Lebanese population, 72 unrelated patients with a reported family history of breast and/or ovarian cancers or with an early onset breast cancer were tested. Fluorescent direct sequencing of the entire coding region and intronic sequences flanking each exon was performed. A total of 38 BRCA1 and 40 BRCA2 sequence variants were found. Seventeen of them were novel. Seven confirmed deleterious mutations were identified in 9 subjects providing a frequency of mutations of 12.5 %. Fifteen variants were considered of unknown clinical significance according to BIC and UMD-BRCA1/BRCA2 databases. In conclusion, this study represents the first evaluation of the deleterious and unclassified genetic variants in the BRCA1/2 genes found in a Lebanese population with a relatively high risk of breast cancer.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale et laboratoire associé INSERM à l'Unité UMR_S910, Université Saint-Joseph, Beirut, Lebanon.
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28
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KLUKOWSKA A, LAGUNA P, WALESZKIEWICZ-MAJEWSKA B, PEREGUD-POGORZELSKI J, KAMIENSKA E, BIGNELL P, GIANGRANDE P. Successful immune tolerance induction in two boys with haemophilia B and inhibitory antibodies. Haemophilia 2012; 18:e67-9. [DOI: 10.1111/j.1365-2516.2012.02784.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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