1
|
Azimi A, Soveizi M, Salmanipour A, Mozafarybazargany M, Ghaffari Jolfayi A, Maleki M, Kalayinia S. Identification of a novel likely pathogenic TPM1 variant linked to hypertrophic cardiomyopathy in a family with sudden cardiac death. ESC Heart Fail 2024. [PMID: 38874371 DOI: 10.1002/ehf2.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/19/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
AIMS Hypertrophic cardiomyopathy (HCM) is an autosomal dominant genetic cardiac disorder characterized by unexplained left ventricular hypertrophy. It can cause a wide spectrum of clinical manifestations, ranging from asymptomatic to heart failure and sudden cardiac death (SCD). Approximately half of HCM cases are caused by variants in sarcomeric proteins, including α-tropomyosin (TPM1). In this study, we aimed to characterize the clinical and molecular phenotype of HCM in an Iranian pedigree with SCD. METHODS AND RESULTS The proband and available family members underwent comprehensive clinical evaluations, including echocardiography, cardiac magnetic resonance (CMR) imaging and electrocardiography (ECG). Whole-exome sequencing (WES) was performed in all available family members to identify the causal variant, which was validated, and segregation analysis was conducted via Sanger sequencing. WES identified a novel missense variant, c.761A>G:p.D254G (NM_001018005.2), in the TPM1 gene, in the proband, his father and one of his sisters. Bioinformatic analysis predicted it to be likely pathogenic. Clinical features in affected individuals were consistent with HCM. CONCLUSIONS The identification of a novel TPM1 variant in a family with HCM and SCD underscores the critical role of genetic screening in at-risk families. Early detection of pathogenic variants can facilitate timely intervention and management, potentially reducing the risk of SCD in individuals with HCM.
Collapse
Affiliation(s)
- Amir Azimi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Soveizi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Salmanipour
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Amir Ghaffari Jolfayi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Braga M, Shiga MAS, Silva PES, Yamanaka AHU, Souza VH, Grava S, Simão ANC, Neves JSF, de Lima Neto QA, Zacarias JMV, Visentainer JEL. Association between polymorphisms in TLR3, TICAM1 and IFNA1 genes and covid-19 severity in Southern Brazil. Expert Rev Mol Diagn 2024; 24:525-531. [PMID: 38864429 DOI: 10.1080/14737159.2024.2367466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/01/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND A distinct phenotype in Coronavirus disease 2019 (Covid-19) was observed in severe patients, consisting of a highly impaired interferon (IFN) type I response, an exacerbated inflammatory response. OBJECTIVE The aim of the present study was to investigate a possible association of single nucleotide polymorphisms (SNPs), in five genes related to the immune response, rs3775291 in TLR3; rs2292151 in TICAM1; rs1758566 in IFNA1; rs1800629 in TNF, and rs1800795 in IL6 with the severity of Covid-19. METHODS A cross-sectional study was performed, with non-severe and severe/critical patients diagnosed with Covid-19, by two public hospitals in Brazil. In total, 300 patients were genotyped for the SNPs, 150 with the non-severe form of the disease and 150 with severe/critical form. RESULTS The T/T genotype of TLR3 in recessive model shows 58% of protection against severe/critical Covid-19; as well as the genotypes G/A+A/A of TICAM1 in dominant model with 60% of protection, and in a codominant model G/A with 57% and A/A with 71% of protection against severe/critical Covid-19. Comparing severe and critical cases, the T/C genotype of IFNA1 in the codominant model and TC+C/C in the dominant model showed twice the risk of critical Covid-19. CONCLUSION We can conclude that rs3775291, rs2292151 and rs1758566 can influence the COVID-19 severity.
Collapse
Affiliation(s)
- Matheus Braga
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | | | | | | | - Victor Hugo Souza
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | - Sergio Grava
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | - Andréa Name Colado Simão
- Department of Pathology, Clinical Analysis and Toxicology, State University of Londrina, Londrina, Paraná, Brazil
| | | | | | | | | |
Collapse
|
3
|
Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BLM, Chang M, Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, Jain PK. PAM-free diagnostics with diverse type V CRISPR-Cas systems. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306194. [PMID: 38746294 PMCID: PMC11092703 DOI: 10.1101/2024.05.02.24306194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.
Collapse
|
4
|
Kuznetsova KG, Vašíček J, Skiadopoulou D, Molnes J, Udler M, Johansson S, Njølstad PR, Manning A, Vaudel M. Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes. PLoS One 2024; 19:e0300350. [PMID: 38635808 PMCID: PMC11025945 DOI: 10.1371/journal.pone.0300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/23/2024] [Indexed: 04/20/2024] Open
Abstract
Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Like for other rare diseases, multiple genes have been linked to monogenic diabetes with different measures of pathogenicity, but the information on the genes and variants is not unified among different resources, making it challenging to process them informatically. We have developed an automated pipeline for collecting and harmonizing data on genetic variants linked to monogenic diabetes. Furthermore, we have translated variant genetic sequences into protein sequences accounting for all protein isoforms and their variants. This allows researchers to consolidate information on variant genes and proteins linked to monogenic diabetes and facilitates their study using proteomics or structural biology. Our open and flexible implementation using Jupyter notebooks enables tailoring and modifying the pipeline and its application to other rare diseases.
Collapse
Affiliation(s)
- Ksenia G. Kuznetsova
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jakub Vašíček
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Dafni Skiadopoulou
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Miriam Udler
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Alisa Manning
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
5
|
Uribe-Carretero E, Rey V, Fuentes JM, Tamargo-Gómez I. Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases. BIOLOGY 2024; 13:34. [PMID: 38248465 PMCID: PMC10813815 DOI: 10.3390/biology13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field.
Collapse
Affiliation(s)
- Elisabet Uribe-Carretero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Verónica Rey
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jose Manuel Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| |
Collapse
|
6
|
Jeon S, Park C, Kim J, Lee JH, Joe SY, Ko YK, Gim JA. Comparing variants related to chronic diseases from genome-wide association study (GWAS) and the cancer genome atlas (TCGA). BMC Med Genomics 2023; 16:332. [PMID: 38114957 PMCID: PMC10729405 DOI: 10.1186/s12920-023-01758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Several genome-wide association studies (GWAS) have been performed to identify variants related to chronic diseases. Somatic variants in cancer tissues are associated with cancer development and prognosis. Expression quantitative trait loci (eQTL) and methylation QTL (mQTL) analyses were performed on chronic disease-related variants in TCGA dataset. METHODS MuTect2 calling variants for 33 cancers from TCGA and 296 GWAS variants provided by LocusZoom were used. At least one mutation was found in TCGA 22 cancers and LocusZoom 23 studies. Differentially expressed genes (DEGs) and differentially methylated regions (DMRs) from the three cancers (TCGA-COAD, TCGA-STAD, and TCGA-UCEC). Variants were mapped to the world map using population locations of the 1000 Genomes Project (1GP) populations. Decision tree analysis was performed on the discovered features and survival analysis was performed according to the cluster. RESULTS Based on the DEGs and DMRs with clinical data, the decision tree model classified seven and three nodes in TCGA-COAD and TCGA-STAD, respectively. A total of 11 variants were commonly detected from TCGA and LocusZoom, and eight variants were selected from the 1GP variants, and the distribution patterns were visualized on the world map. CONCLUSIONS Variants related to tumors and chronic diseases were selected, and their geological regional 1GP-based proportions are presented. The variant distribution patterns could provide clues for regional clinical trial designs and personalized medicine.
Collapse
Affiliation(s)
- Soohyun Jeon
- Department of Brain and Cognitive Engineering, Korea University, Seoul, 02841, South Korea
| | - Chaewon Park
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Jineui Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Jung Hoon Lee
- Department of Pharmacology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - Sung-Yune Joe
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, 08308, South Korea
| | - Jeong-An Gim
- Department of Medical Science, Soonchunhyang University, Asan, 31538, South Korea.
| |
Collapse
|
7
|
Pinto EM, Ribeiro EMSF, Wang J, Phillips AH, Kriwacki RW, Zambetti GP. Clinical and functional analysis of the germline TP53 p.K164E acetylation site variant. Cold Spring Harb Mol Case Stud 2023; 9:a006290. [PMID: 38050059 PMCID: PMC10815290 DOI: 10.1101/mcs.a006290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
TP53 plays a critical role as a tumor suppressor by controlling cell cycle progression, DNA repair, and apoptosis. Post-translational modifications such as acetylation of specific lysine residues in the DNA binding and carboxy-terminus regulatory domains modulate its tumor suppressor activities. In this study, we addressed the functional consequences of the germline TP53 p.K164E (NM_000546.5: c.490A>G) variant identified in a patient with early-onset breast cancer and a significant family history of cancer. K164 is a conserved residue located in the L2 loop of the p53 DNA binding domain that is post-translationally modified by acetylation. In silico, in vitro, and in vivo analyses demonstrated that the glutamate substitution at K164 marginally destabilizes the p53 protein structure but significantly impairs sequence-specific DNA binding, transactivation, and tumor cell growth inhibition. Although p.K164E is currently considered a variant of unknown significance by different clinical genetic testing laboratories, the clinical and laboratory-based findings presented here provide strong evidence to reclassify TP53 p.K164E as a likely pathogenic variant.
Collapse
Affiliation(s)
- Emilia Modolo Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
| | - Enilze M S F Ribeiro
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, Paraná, 81531-980, Brazil;
| | - Jinling Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
| |
Collapse
|
8
|
Pham HM, Nguyen DP, Ta TD, Le TP, Phan PH, Trinh HA, Tran TV, Luong TLA, Nguyen HM, Bui T, Tran TH, Ta TV, Tran V. In silico validation revealed the role of SCN5A mutations and their genotype-phenotype correlations in Brugada syndrome. Mol Genet Genomic Med 2023; 11:e2263. [PMID: 37547970 PMCID: PMC10724507 DOI: 10.1002/mgg3.2263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Brugada syndrome (BrS) is a rare genetic disease that causes sudden cardiac death (SCD) and arrhythmia. SCN5A pathogenic variants (about 30% of diagnosed patients) are responsible for BrS. AIMS Lack of knowledge regarding molecular characteristics and the correlation between genotype and phenotype interfere with the risk stratification and finding the optimal treatment in Vietnam. Therefore, we identified SCN5A variants and evaluated the genotype-phenotype correlation of BrS on 117 Vietnamese probands. MATERIALS AND METHODS The clinical characteristics and blood samples of BrS patients were collected. To determine SCN5A variants, Sanger sequencing was conducted, and subsequently, these variants were analyzed by bioinformatic tools. RESULTS In this cohort, the overall rate of detected variants in SCN5A was 25.6%, which could include both pathogenic and benign variants. In genetic testing, 21 SCN5A variants were identified, including eight novels and 15 published variants. Multiple bioinformatic tools were used to predict variant effect with c.551A>G, c.1890+14G>A, c.3338C>T, c.3578G>A, and c.5484C>T as benign, while other variants were predicted as disease-causing. The family history of SCD (risk ratio [RR] = 4.324, 95% CI: 2.290-8.269, p < 0.001), syncope (RR = 3.147, 95% CI: 1.668-5.982, p = 0.0004), and ventricular tachycardia/ventricular fibrillation (RR = 3.406, 95% CI: 1.722-5.400, p = 0.0035) presented a significantly higher risk in the SCN5A (+) group, consisting of individuals carrying any variant in the SCN5A gene, compared to SCN5A (-) individuals. CONCLUSION The results contribute to clarifying the impact of SCN5A variants on these phenotypes. Further follow-up studies need to be carried out to understand the functional effects of these SCN5A variants on the severity of BrS.
Collapse
Affiliation(s)
- Hung Manh Pham
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Vietnam National Heart InstituteBach Mai HospitalHanoiVietnam
| | - Duy Phuong Nguyen
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Ho Chi Minh City Heart InstituteHo Chi MinhVietnam
| | - Thanh Dat Ta
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Thi Phuong Le
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Phong Hai Phan
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Vietnam National Heart InstituteBach Mai HospitalHanoiVietnam
| | | | - Tuan Viet Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Vietnam National Heart InstituteBach Mai HospitalHanoiVietnam
| | - Thi Lan Anh Luong
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Ha Minh Nguyen
- Hue Central HospitalHueVietnam
- Pham Ngoc Thanh UniversityHo Chi MinhVietnam
| | - The‐Hung Bui
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Center for Molecular Medicine, Clinical Genetics UnitKarolinska Institutet, Karolinska University HospitalStockholmSweden
| | - Thinh Huy Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Thanh Van Ta
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Van‐Khanh Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| |
Collapse
|
9
|
Brennenstuhl H, Schaaf CP. [Genomic newborn screening-research approaches, challenges, and opportunities]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023; 66:1232-1242. [PMID: 37831095 PMCID: PMC10622372 DOI: 10.1007/s00103-023-03777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
The application of high-throughput sequencing methods for population-based genomic newborn screening offers numerous opportunities for improving population health. The use of genome-based sequencing technology holds potential to enable the diagnosis of virtually any genetic disorder at an early stage and offers great flexibility when it comes to selection and expansion of target diseases. National and international efforts are therefore being made to investigate the ethical, legal, social, psychological, and technical aspects of genomic newborn screening. In addition to the many opportunities, there are numerous challenges and questions that remain to be answered: When and how should legal guardians be informed about such screening? Which diseases should be screened for? How should incidental findings or identification of a genetic predisposition be dealt with? Should data be stored long term and if so, how can this be done securely? Provided there is an appropriate regulatory framework and a transparent consent process, genomic newborn screening has the potential to fundamentally change the way in which we screen for congenital diseases. However, there is still much to be done. To achieve understanding and acceptance of genomic newborn screening amongst all stakeholders and thus to maximize its benefits for the population, a public discourse on the possibilities and limitations of genomic newborn screening is of critical importance. This article aims to provide an overview of the innovative technical developments in the field of human genetics, describe national and international approaches, and discuss challenges and opportunities of genomic newborn screening development.
Collapse
Affiliation(s)
- Heiko Brennenstuhl
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland
| | - Christian P Schaaf
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland.
| |
Collapse
|
10
|
Núñez-Núñez ME, Lona-Reyes JC, López-Barragán B, Cruz-Osorio RM, Gutiérrez-Zepeda BM, Quintero-Ramos A, Becerra-Loaiza DS. Case Report: Characterization of known (c.607G>C) and novel (c.416C>G) ELANE mutations in two Mexican families with congenital neutropenia. Front Immunol 2023; 14:1194262. [PMID: 37795094 PMCID: PMC10547563 DOI: 10.3389/fimmu.2023.1194262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
The most common causes of congenital neutropenia are mutations in the ELANE (Elastase, Neutrophil Expressed) gene (19p13.3), mostly in exon 5 and the distal portion of exon 4, which result in different clinical phenotypes of neutropenia. Here, we report two pathogenic mutations in ELANE, namely, c.607G>C (p.Gly203Arg) and a novel variant c.416C>G (p.Pro139Arg), found in two Mexican families ascertained via patients with congenital neutropenia who responded positively to the granulocyte colony-stimulating factor (G-CSF) treatment. These findings highlight the usefulness of identifying variants in patients with inborn errors of immunity for early clinical management and the need to rule out mosaicism in noncarrier parents with more than one case in the family.
Collapse
Affiliation(s)
- María Enriqueta Núñez-Núñez
- Departamento de Alergia e Inmunología Clínica Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Juan Carlos Lona-Reyes
- Departamento de Infectología, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Brenda López-Barragán
- Departamento de Pediatría, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Rosa Margarita Cruz-Osorio
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Hemato-Oncología Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Bricia Melissa Gutiérrez-Zepeda
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Antonio Quintero-Ramos
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Investigación Biomédica 02, Hospital de Especialidades, Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Denisse Stephania Becerra-Loaiza
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| |
Collapse
|
11
|
Lim HD, Lee SM, Yun YJ, Lee DH, Lee JH, Oh SH, Lee SY. WFS1 autosomal dominant variants linked with hearing loss: update on structural analysis and cochlear implant outcome. BMC Med Genomics 2023; 16:79. [PMID: 37041640 PMCID: PMC10088283 DOI: 10.1186/s12920-023-01506-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/02/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Wolfram syndrome type 1 gene (WFS1), which encodes a transmembrane structural protein (wolframin), is essential for several biological processes, including proper inner ear function. Unlike the recessively inherited Wolfram syndrome, WFS1 heterozygous variants cause DFNA6/14/38 and wolfram-like syndrome, characterized by autosomal dominant nonsyndromic hearing loss, optic atrophy, and diabetes mellitus. Here, we identified two WFS1 heterozygous variants in three DFNA6/14/38 families using exome sequencing. We reveal the pathogenicity of the WFS1 variants based on three-dimensional (3D) modeling and structural analysis. Furthermore, we present cochlear implantation (CI) outcomes in WFS1-associated DFNA6/14/38 and suggest a genotype-phenotype correlation based on our results and a systematic review. METHODS We performed molecular genetic test and evaluated clinical phenotypes of three WFS1-associated DFNA6/14/38 families. A putative WFS1-NCS1 interaction model was generated, and the impacts of WFS1 variants on stability were predicted by comparing intramolecular interactions. A total of 62 WFS1 variants associated with DFNA6/14/38 were included in a systematic review. RESULTS One variant is a known mutational hotspot variant in the endoplasmic reticulum (ER)-luminal domain WFS1(NM_006005.3) (c.2051 C > T:p.Ala684Val), and the other is a novel frameshift variant in transmembrane domain 6 (c.1544_1545insA:p.Phe515LeufsTer28). The two variants were pathogenic, based on the ACMG/AMP guidelines. Three-dimensional modeling and structural analysis show that non-polar, hydrophobic substitution of Ala684 (p.Ala684Val) destabilizes the alpha helix and contributes to the loss of WFS1-NCS1 interaction. Also, the p.Phe515LeufsTer28 variant truncates transmembrane domain 7-9 and the ER-luminal domain, possibly impairing membrane localization and C-terminal signal transduction. The systematic review demonstrates favorable outcomes of CI. Remarkably, p.Ala684Val in WFS1 is associated with early-onset severe-to-profound deafness, revealing a strong candidate variant for CI. CONCLUSIONS We expanded the genotypic spectrum of WFS1 heterozygous variants underlying DFNA6/14/38 and revealed the pathogenicity of mutant WFS1, providing a theoretical basis for WFS1-NCS1 interactions. We presented a range of phenotypic traits for WFS1 heterozygous variants and demonstrated favorable functional CI outcomes, proposing p.Ala684Val a strong potential marker for CI candidates.
Collapse
Affiliation(s)
- Hui Dong Lim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ye Jin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dae Hee Lee
- CTCELLS, Inc, 21, Yuseong-daero, 1205beon-gil, Yuseong-gu, Daejeon, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| |
Collapse
|
12
|
Luchini C, Mattiolo P, Basturk O, Mafficini A, Ozcan K, Lawlor RT, Hong SM, Brosens LA, Marchegiani G, Pea A, Manfrin E, Sciacca G, Zampieri F, Polati R, De Robertis R, Milella M, D'Onofrio M, Malleo G, Salvia R, Adsay V, Scarpa A. Acinar Cystic Transformation of the Pancreas: Histomorphology and Molecular Analysis to Unravel its Heterogeneous Nature. Am J Surg Pathol 2023; 47:379-386. [PMID: 36649476 DOI: 10.1097/pas.0000000000002017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acinar cystic transformation (ACT) of the pancreas, previously called acinar cell cystadenoma, is a poorly understood and rare entity among pancreatic cystic lesions. This study aims to clarify its real nature. This research cohort included 25 patients with pancreatic ACT, representing the largest series in the literature. We describe their clinicopathological features and molecular profile using next-generation sequencing. ACT arose more often in women (F/M≃2:1), in the body-tail region, with a mean size of ~4 cm. At the latest follow-up, all patients were alive and disease free. Histologically, a typical acinar epithelium lined all cysts, intermingled with ductal-like epithelium in 11/25 (44%) cases. All the cases lacked any evidence of malignancy. Three ACT showed peculiar features: 1 showed an extensive and diffuse microcystic pattern, and the other 2 harbored foci of low-grade pancreatic intraepithelial neoplasia (PanIN) in the ductal-like epithelium. Next-generation sequencing revealed the presence of 2 pathogenic/likely pathogenic mutations in 2 different cases, 1 with ductal-like epithelium and 1 with PanIN, and affecting KRAS (c.34G>C, p.G12R) and SMO (c.1685G>A, p.R562Q) genes, respectively. The other case with PanIN was not available for sequencing. Overall, our findings support that ACT is a benign entity, potentially arising from heterogeneous conditions/background, including: (1) acinar microcysts, (2) malformations, (3) obstructive/inflammatory setting, (4) genetic predisposition, (5) possible neoplastic origin. Although all indications are that ACT is benign, the potential occurrence of driver mutations suggests discussing a potential role of long-term surveillance for these patients.
Collapse
Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, NY
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Kerem Ozcan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, NY
| | - Rita T Lawlor
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, and Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Antonio Pea
- Department of Surgery, The Pancreas Institute
| | - Erminia Manfrin
- Department of Diagnostics and Public Health, Section of Pathology
| | - Giuseppe Sciacca
- Department of Diagnostics and Public Health, Section of Pathology
| | | | - Rita Polati
- Department of Diagnostics and Public Health, Section of Pathology
| | | | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Mirko D'Onofrio
- Department of Diagnostics and Public Health, Section of Radiology
| | | | | | - Volkan Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| |
Collapse
|
13
|
Quan X, Cai W, Xi C, Wang C, Yan L. AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine. Database (Oxford) 2023; 2023:7059703. [PMID: 36856726 PMCID: PMC9976745 DOI: 10.1093/database/baad006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 03/02/2023]
Abstract
The development of high-throughput molecular testing techniques has enabled the large-scale exploration of the underlying molecular causes of diseases and the development of targeted treatment for specific genetic alterations. However, knowledge to interpret the impact of genetic variants on disease or treatment is distributed in different databases, scientific literature studies and clinical guidelines. AIMedGraph was designed to comprehensively collect and interrogate standardized information about genes, genetic alterations and their therapeutic and diagnostic relevance and build a multi-relational, evidence-based knowledge graph. Graph database Neo4j was used to represent precision medicine knowledge as nodes and edges in AIMedGraph. Entities in the current release include 30 340 diseases/phenotypes, 26 140 genes, 187 541 genetic variants, 2821 drugs, 15 125 clinical trials and 797 911 supporting literature studies. Edges in this release cover 621 731 drug interactions, 9279 drug susceptibility impacts, 6330 pharmacogenomics effects, 30 339 variant pathogenicity and 1485 drug adverse reactions. The knowledge graph technique enables hidden knowledge inference and provides insight into potential disease or drug molecular mechanisms. Database URL: http://aimedgraph.tongshugene.net:8201.
Collapse
Affiliation(s)
- Xueping Quan
- Correspondence may also be addressed to Xueping Quan. Tel: +8621-58886662;
| | - Weijing Cai
- Department of Innovative Technology, Shanghai Tongshu Biotechnology Research Institute, No26 and 28, 377 Lane of Shanlian Road, Baoshan District, Shanghai 200444, China
| | - Chenghang Xi
- Department of Artificial Intelligence, Shanghai Tongshu Biotechnology Research Institute, No26 and 28, 377 Lane of Shanlian Road, Baoshan District, Shanghai 200444, China
| | - Chunxiao Wang
- Department of Innovative Technology, Shanghai Tongshu Biotechnology Research Institute, No26 and 28, 377 Lane of Shanlian Road, Baoshan District, Shanghai 200444, China
| | | |
Collapse
|
14
|
Lahiri S, Reys B, Wunder J, Pirzadeh-Miller S. Genetic variants with discordant classifications: An assessment of genetic counselor attitudes and practices. J Genet Couns 2023; 32:100-110. [PMID: 35978490 DOI: 10.1002/jgc4.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/11/2022]
Abstract
Discordant variant classifications (DVCs) can impact patient care and pose challenges for clinicians. A survey-based study was conducted to examine genetic counselor (GC) attitudes and practices related to DVCs. Most GCs (202/229, 88%) in the study provide direct patient care across clinical specialties; review patients' genetic test results to determine if reported genetic variants have DVCs (176/202, 88%); and inform patients of known DVCs that impact medical management (165/202, 82%). DVC review, which takes 41 min (range: 5-240) on average per week, is typically prompted by the identification of a variant of uncertain significance (VUS) (160/176, 90%) and is primarily conducted using public databases (176/176, 100%). While most GCs felt it would not be ethical to knowingly provide different medical management recommendations to patients with the same genetic variant (152/229, 66%), they also stated they would rely on the variant classification on the test report (141/229, 61%) and/or the patient's personal/family history (188/229, 82%) to determine which classification to follow if a DVC is identified. Both factors are patient-specific and, inherently, could lead to differing recommendations. When posed with a hypothetical scenario in which two patients have the same genetic variant, but test reports show a DVC (pathogenic vs VUS), most GCs (179/229, 78.2%) stated they would make the same recommendation for both patients regardless of management guidelines. One-third (52/179, 29.1%) cited patient-specific factors, such as personal/family history, would impact their recommendations. Disagreements about whether the pathogenic or VUS classification should be used to make medical management recommendations were noted. Differing practices and opinions on how to manage patients with DVCs, as well as the fact that most GCs (209/229, 91.3%) have consulted with colleagues on this matter, highlight the need for more professional guidance to ensure equitable patient care.
Collapse
Affiliation(s)
- Sayoni Lahiri
- Cancer Genetics Program, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Brian Reys
- Cancer Genetics Program, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Julia Wunder
- Oncology-Abstraction, Tempus Labs, Inc., Chicago, Illinois, USA
| | | |
Collapse
|
15
|
Next-generation sequencing of postmortem molecular markers to support for medicolegal autopsy. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
16
|
Rodríguez-López R, Gimeno-Ferrer F, do Santos DA, Ferrer-Bolufer I, Luján CG, Alcalá OZ, García-Banacloy A, Cogollos VB, Juan CS. Reviewed and updated Algorithm for Genetic Characterization of Syndromic Obesity Phenotypes. Curr Genomics 2022; 23:147-162. [PMID: 36777005 PMCID: PMC9878830 DOI: 10.2174/1389202923666220426093436] [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: 10/26/2021] [Revised: 11/30/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Individuals with a phenotype of early-onset severe obesity associated with intellectual disability can have molecular diagnoses ranging from monogenic to complex genetic traits. Severe overweight is the major sign of a syndromic physical appearance and predicting the influence of a single gene and/or polygenic risk profile is extremely complicated among the majority of the cases. At present, considering rare monogenic bases as the principal etiology for the majority of obesity cases associated with intellectual disability is scientifically poor. The diversity of the molecular bases responsible for the two entities makes the appliance of the current routinely powerful genomics diagnostic tools essential. Objective: Clinical investigation of these difficult-to-diagnose patients requires pediatricians and neurologists to use optimized descriptions of signs and symptoms to improve genotype correlations. Methods: The use of modern integrated bioinformatics strategies which are conducted by experienced multidisciplinary clinical teams. Evaluation of the phenotype of the patient's family is also of importance. Results: The next step involves discarding the monogenic canonical obesity syndromes and considering infrequent unique molecular cases, and/or then polygenic bases. Adequate management of the application of the new technique and its diagnostic phases is essential for achieving good cost/efficiency balances. Conclusion: With the current clinical management, it is necessary to consider the potential coincidence of risk mutations for obesity in patients with genetic alterations that induce intellectual disability. In this review, we describe an updated algorithm for the molecular characterization and diagnosis of patients with a syndromic obesity phenotype.
Collapse
Affiliation(s)
- Raquel Rodríguez-López
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain;,Address correspondence to this author at the Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Avenida de las Tres Cruces no. 2 46014, Valencia, Spain; Tel: 0034 963 131 800 – 437317; Fax: 0034 963 131 979; E-mail:
| | - Fátima Gimeno-Ferrer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - David Albuquerque do Santos
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Irene Ferrer-Bolufer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Carola Guzmán Luján
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Otilia Zomeño Alcalá
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Amor García-Banacloy
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | | | - Carlos Sánchez Juan
- Endocrinology Service, General Hospital Consortium of Valencia, Valencia, Spain
| |
Collapse
|
17
|
AIMP2-DX2 provides therapeutic interface to control KRAS-driven tumorigenesis. Nat Commun 2022; 13:2572. [PMID: 35546148 PMCID: PMC9095880 DOI: 10.1038/s41467-022-30149-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2022] [Indexed: 12/11/2022] Open
Abstract
Recent development of the chemical inhibitors specific to oncogenic KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog) mutants revives much interest to control KRAS-driven cancers. Here, we report that AIMP2-DX2, a variant of the tumor suppressor AIMP2 (aminoacyl-tRNA synthetase-interacting multi-functional protein 2), acts as a cancer-specific regulator of KRAS stability, augmenting KRAS-driven tumorigenesis. AIMP2-DX2 specifically binds to the hypervariable region and G-domain of KRAS in the cytosol prior to farnesylation. Then, AIMP2-DX2 competitively blocks the access of Smurf2 (SMAD Ubiquitination Regulatory Factor 2) to KRAS, thus preventing ubiquitin-mediated degradation. Moreover, AIMP2-DX2 levels are positively correlated with KRAS levels in colon and lung cancer cell lines and tissues. We also identified a small molecule that specifically bound to the KRAS-binding region of AIMP2-DX2 and inhibited the interaction between these two factors. Treatment with this compound reduces the cellular levels of KRAS, leading to the suppression of KRAS-dependent cancer cell growth in vitro and in vivo. These results suggest the interface of AIMP2-DX2 and KRAS as a route to control KRAS-driven cancers. Direct targeting of oncogenic KRAS activity is a challenge. Here the authors report that a splice variant of AIMP2, AIMP2-DX2, enhances KRAS stability by blocking ubiquitin-mediated degradation of KRAS via the E3 ligase, Smurf2, and identify a chemical that can hinder AIMP2-DX2 from interacting with KRAS.
Collapse
|
18
|
Bletsis P, Metzger R, Nelson JA, Gasparini J, Alsayed M, Milas M. A novel missense CASR gene mutation resulting in familial hypocalciuric hypercalcemia. AACE Clin Case Rep 2022; 8:194-198. [PMID: 36189134 PMCID: PMC9508602 DOI: 10.1016/j.aace.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/20/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022] Open
Abstract
Background/Objective Familial hypocalciuric hypercalcemia (FHH) is an uncommon cause of hypercalcemia; however, it is important to consider and rule out in patients with suspected primary hyperparathyroidism (PHPT), ideally, before proceeding with surgery. Herein, we present a patient where this process identified a calcium-sensing receptor gene (CASR) sequence variant currently labeled as a variant of unknown significance (VUS), yet the patient’s family pedigree suggests that it is in fact a pathogenic CASR sequence variant. Case Report A 35-year-old woman was referred to the Endocrine Surgery clinic for evaluation of “recurrent PHPT” and need for reoperative parathyroidectomy. Before referral, she was treated with subtotal parathyroidectomy for the presumed diagnosis of PHPT-related symptomatic hypercalcemia. Postoperatively, she had persistent symptoms. Upon referral, additional relevant information was elicited that suspected FHH instead of PHPT, including a family history of hypercalcemia with CASR VUS in multiple family members and hypocalciuria in the patient. She underwent genetic testing revealing a missense CASR VUS in exon 3 c.392C>A (p.Ala110Asp), the same as in her mother. Medical management instead of reoperation was advised for the diagnosis of FHH. Discussion To our knowledge, this CASR sequence variation has not been previously reported in the literature. Reporting newly discovered sequence variations with the context of a family’s medical history is important because it allows for the recognition of new pathogenic variants. This expands the registry of already known sequence variations and their associated clinical pathology for future patients undergoing genetic testing. Conclusion This CASR variant represents a novel pathogenic sequence variation causing FHH.
Collapse
|
19
|
Ahmed Z, Renart EG, Zeeshan S. Investigating underlying human immunity genes, implicated diseases and their relationship to COVID-19. Per Med 2022; 19:229-250. [PMID: 35261286 PMCID: PMC8919975 DOI: 10.2217/pme-2021-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Aim: A human immunogenetics variation study was conducted in samples collected from diverse COVID-19 populations. Materials & methods: Whole-genome and whole-exome sequencing (WGS/WES), data processing, analysis and visualization pipeline were applied to identify variants associated with genes of interest. Results: A total of 2886 mutations were found across the entire set of 13 genomes. Functional annotation of the gene variants revealed mutation type and protein change. Many variants were found to be biologically implicated in COVID-19. The involvement of these genes was also found in multiple other diseases. Conclusion: The analysis determined that ACE2, TMPRSS4, TMPRSS2, SLC6A20 and FYCOI had functional implications and TMPRSS4 was the gene most altered in virally infected patients. The quest to establish an understanding of the genetics underlying COVID-19 is a central focus of life sciences today. COVID-19 is triggered by SARS-CoV-2, a single-stranded RNA respiratory virus. Several clinical-genomics studies have emerged positing different human gene mutations occurring due to COVID-19. A global analysis of these genes was conducted targeting major components of the immune system to identify possible variations likely to be involved in COVID-19 predisposition. Gene-variant analysis was performed on whole-genome sequencing samples collected from diverse populations. ACE2, TMPRSS4, TMPRSS2, SLC6A20 and FYCOI were found to have functional implications and TMPRSS4 may have a role in the severity of clinical manifestations of COVID-19.
Collapse
Affiliation(s)
- Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy & Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ 08901, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical & Health Sciences, 125 Paterson Street, New Brunswick, NJ 08901, USA
| | - Eduard Gibert Renart
- Rutgers Institute for Health, Health Care Policy & Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ 08901, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ 08901, USA
| |
Collapse
|
20
|
Wu T, Cui L, Mou Y, Guo W, Liu D, Qiu J, Xu C, Zhou J, Han F, Sun Y. A newly identified mutation (c.2029 C > T) in SLC26A4 gene is associated with enlarged vestibular aqueducts in a Chinese family. BMC Med Genomics 2022; 15:49. [PMID: 35249537 PMCID: PMC8898487 DOI: 10.1186/s12920-022-01200-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background The enlarged vestibular aqueduct (EVA), associated with mutations in the SLC26A4 gene, characterized by non-syndromic hearing loss, is an autosomal recessive disorder. Here, we intended to investigate genetic causes of hearing loss in a Han Chinese man. Method First, whole-exome sequencing was performed to identify the gene mutations responsible for hearing loss in the proband. Sanger sequencing was used to verify the candidate mutations detected in the family. Next, we collected blood samples and clinical data from the three-generation pedigree. Finally, SLC26A4 mRNA and protein expression levels were detected by qPCR and western blotting. Result The proband suffered from bilateral progressive sensorineural hearing loss with EVA. The sequence analysis of SLC26A4 revealed that the proband and his sister both harbored a compound heterozygous mutation of c.2168A > G/c.2029C > T, inherited from their father and mother respectively. c.2029C > T mutation has not been recorded in the relevant literature previously. Relative mRNA levels of the SLC26A4 gene in individuals carrying a compound heterozygous mutation were significantly lower compared to a heterozygous mutation. SLC26A4 protein levels of 293t cells which transfected with recombinant plasmids [GV219-SLC26A4-mut (c.2029C > T) and GV219-SLC26A4-mut (c.2168A > G/c.2029C > T)] were significantly lower than normal control recombinant plasmids (GV219-SLC26A4-wt). Conclusion This study found a novel heterozygous mutation c.2029 (exon17) C > T compound with c.2168 (exon19) A > G in the SLC26A4 gene in a patient with EVA. The c.2029 (exon17) C > T mutation is proved to be pathogenic. This finding broadens the spectrum of variants in SLC26A4 gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01200-4.
Collapse
|
21
|
Alimohamed MZ, Westers H, Vos YJ, Van der Velde KJ, Sijmons RH, Van der Zwaag PA, Sikkema-Raddatz B, Jongbloed JDH. Validation of New Gene Variant Classification Methods: a Field-Test in Diagnostic Cardiogenetics. Front Genet 2022; 13:824510. [PMID: 35299955 PMCID: PMC8921548 DOI: 10.3389/fgene.2022.824510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: In the molecular genetic diagnostics of Mendelian disorders, solutions are needed for the major challenge of dealing with the large number of variants of uncertain significance (VUSs) identified using next-generation sequencing (NGS). Recently, promising approaches using constraint metrics to calculate case excess scores (CE), etiological fractions (EF), and gnomAD-derived constraint scores have been reported that estimate the likelihood of rare variants in specific genes or regions that are pathogenic. Our objective is to study the usability of these constraint data into variant interpretation in a diagnostic setting, using our cardiomyopathy cohort.Methods and Results: Patients (N = 2002) referred for clinical genetic diagnostics underwent NGS testing of 55–61 genes associated with cardiomyopathies. Previously classified likely pathogenic (LP) and pathogenic (P) variants were used to validate the use of data from CE, EF, and gnomAD constraint analyses for (re)classification of associated variant types in specific cardiomyopathy subtype-related genes. The classifications corroborated in 94% (354/378) of cases. Next, we reclassified 23 unique VUSs to LP, increasing the diagnostic yield by 1.2%. In addition, 106 unique VUSs (5.3% of patients) were prioritized for co-segregation or functional analyses.Conclusions: Our analysis confirms that the use of constraint metrics data can improve variant interpretation, and we, therefore, recommend using constraint scores on other cohorts and disorders and its inclusion in variant interpretation protocols.
Collapse
Affiliation(s)
- Mohamed Z. Alimohamed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
- Department of Research and Training, Shree Hindu Mandal Hospital, Dar-es-salaam, Tanzania
- Tanzania Human Genetics Organization, Groningen, Netherlands
- *Correspondence: Mohamed Z. Alimohamed, ; Jan D. H. Jongbloed,
| | - Helga Westers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Yvonne J. Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - K. Joeri Van der Velde
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rolf H. Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paul A. Van der Zwaag
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jan D. H. Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- *Correspondence: Mohamed Z. Alimohamed, ; Jan D. H. Jongbloed,
| |
Collapse
|
22
|
Lou J, Chen H, Huang S, Chen P, Yu Y, Chen F. Update on risk factors and biomarkers of sudden unexplained cardiac death. J Forensic Leg Med 2022; 87:102332. [DOI: 10.1016/j.jflm.2022.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023]
|
23
|
Complement activation and regulation in preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome. Am J Obstet Gynecol 2022; 226:S1059-S1070. [PMID: 32986992 DOI: 10.1016/j.ajog.2020.09.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022]
Abstract
The complement system is critical to human health owing to its central role in host defense and innate immunity. During pregnancy, the complement system must be appropriately regulated to allow for immunologic tolerance to the developing fetus and placenta. Although some degree of complement activation can be seen in normal pregnancy, the fetus seems to be protected in part through the placental expression of complement regulatory proteins, which inhibit complement activation at different steps along the complement activation cascade. In women who develop preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome, there is a shift toward increased complement activation and decreased complement regulation. There is an increase in placental deposition of C5b-9, which is the terminal effector of classical, lectin, and alternative complement pathways. C5b-9 deposition stimulates trophoblasts to secrete soluble fms-like tyrosine kinase-1, which sequesters vascular endothelial growth factor and placental growth factor. Pathogenic mutations or deletions in complement regulatory genes, which predispose to increased complement activation, have been detected in women with preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome. Before the disease, biomarkers of alternative complement pathway activation are increased; during active disease, biomarkers of terminal complement pathway activation are increased. Urinary excretion of C5b-9 is associated with preeclampsia with severe features and distinguishes it from other hypertensive disorders of pregnancy. Taken together, existing data link preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome with increased activation of the terminal complement pathway that, in some cases, may be influenced by genetic alterations in complement regulators. These findings suggest that the inhibition of the terminal complement pathway, possibly through C5 blockade, may be an effective strategy to treat preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome, but this strategy warrants further evaluation in clinical trials.
Collapse
|
24
|
Zouk H, Yu W, Oza A, Hawley M, Vijay Kumar PK, Koch C, Mahanta LM, Harley JB, Jarvik GP, Karlson EW, Leppig KA, Myers MF, Prows CA, Williams MS, Weiss ST, Lebo MS, Rehm HL. Reanalysis of eMERGE phase III sequence variants in 10,500 participants and infrastructure to support the automated return of knowledge updates. Genet Med 2022; 24:454-462. [PMID: 34906510 PMCID: PMC10128874 DOI: 10.1016/j.gim.2021.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The clinical genomics knowledgebase is dynamic with variant classifications changing as newly identified cases, additional population data, and other evidence become available. This is a challenge for the clinical laboratory because of limited resource availability for variant reassessment. METHODS Throughout the Electronic Medical Records and Genomics phase III program, clinical sites associated with the Mass General Brigham/Broad sequencing center received automated, real-time notifications when reported variants were reclassified. In this study, we summarized the nature of these reclassifications and described the proactive reassessment framework we used for the Electronic Medical Records and Genomics program data set to identify variants most likely to undergo reclassification. RESULTS Reanalysis of 1855 variants led to the reclassification of 2% (n = 45) of variants, affecting 0.6% (n = 67) of participants. Of these reclassifications, 78% (n = 35) were high-impact changes affecting reportability, with 8 variants downgraded from likely pathogenic/pathogenic to variants of uncertain significance (VUS) and 27 variants upgraded from VUS to likely pathogenic/pathogenic. Most upgraded variants (67%) were initially classified as VUS-Favor Pathogenic, highlighting the benefit of VUS subcategorization. The most common reason for reclassification was new published case data and/or functional evidence. CONCLUSION Our results highlight the importance of periodic sequence variant reevaluation and the need for automated approaches to advance routine implementation of variant reevaluations in clinical practice.
Collapse
Affiliation(s)
- Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Prathik K Vijay Kumar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - John B Harley
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH; US Department of Veteran Affairs Medical Center, Cincinnati, OH
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Scott T Weiss
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
| |
Collapse
|
25
|
Abstract
Junctophilins (JPHs) comprise a family of structural proteins that connect the plasma membrane to intracellular organelles such as the endo/sarcoplasmic reticulum. Tethering of these membrane structures results in the formation of highly organized subcellular junctions that play important signaling roles in all excitable cell types. There are four JPH isoforms, expressed primarily in muscle and neuronal cell types. Each JPH protein consists of 6 'membrane occupation and recognition nexus' (MORN) motifs, a joining region connecting these to another set of 2 MORN motifs, a putative alpha-helical region, a divergent region exhibiting low homology between JPH isoforms, and a carboxy-terminal transmembrane region anchoring into the ER/SR membrane. JPH isoforms play essential roles in developing and maintaining subcellular membrane junctions. Conversely, inherited mutations in JPH2 cause hypertrophic or dilated cardiomyopathy, while trinucleotide expansions in the JPH3 gene cause Huntington Disease-Like 2. Loss of JPH1 protein levels can cause skeletal myopathy, while loss of cardiac JPH2 levels causes heart failure and atrial fibrillation, among other disease. This review will provide a comprehensive overview of the JPH gene family, phylogeny, and evolutionary analysis of JPH genes and other MORN domain proteins. JPH biogenesis, membrane tethering, and binding partners will be discussed, as well as functional roles of JPH isoforms in excitable cells. Finally, potential roles of JPH isoform deficits in human disease pathogenesis will be reviewed.
Collapse
Affiliation(s)
- Stephan E Lehnart
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Department of Cardiology and Pneumology, Georg-August University Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Germany
| | - Xander H T Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States; Departments of Molecular Physiology and Biophysics, Medicine (Cardiology), Pediatrics (Cardiology), Neuroscience, and Center for Space Medicine, Baylor College of Medicine, Houston, Texas, United States
| |
Collapse
|
26
|
Mason AB, Lynn ML, Baldo AP, Deranek AE, Tardiff JC, Schwartz SD. Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament. JCI Insight 2021; 6:154350. [PMID: 34699384 PMCID: PMC8675185 DOI: 10.1172/jci.insight.154350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Point mutations within sarcomeric proteins have been associated with altered function and cardiomyopathy development. Difficulties remain, however, in establishing the pathogenic potential of individual mutations, often limiting the use of genotype in management of affected families. To directly address this challenge, we utilized our all-atom computational model of the human full cardiac thin filament (CTF) to predict how sequence substitutions in CTF proteins might affect structure and dynamics on an atomistic level. Utilizing molecular dynamics calculations, we simulated 21 well-defined genetic pathogenic cardiac troponin T and tropomyosin variants to establish a baseline of pathogenic changes induced in computational observables. Computational results were verified via differential scanning calorimetry on a subset of variants to develop an experimental correlation. Calculations were performed on 9 independent variants of unknown significance (VUS), and results were compared with pathogenic variants to identify high-resolution pathogenic signatures. Results for VUS were compared with the baseline set to determine induced structural and dynamic changes, and potential variant reclassifications were proposed. This unbiased, high-resolution computational methodology can provide unique structural and dynamic information that can be incorporated into existing analyses to facilitate classification both for de novo variants and those where established approaches have provided conflicting information.
Collapse
Affiliation(s)
| | - Melissa L Lynn
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | | | - Andrea E Deranek
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | - Jil C Tardiff
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | | |
Collapse
|
27
|
Moon IS, Grant AR, Sagi V, Rehm HL, Stankovic KM. TMPRSS3 Gene Variants With Implications for Auditory Treatment and Counseling. Front Genet 2021; 12:780874. [PMID: 34868270 PMCID: PMC8641783 DOI: 10.3389/fgene.2021.780874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
Objective: To identify and report novel variants in the TMPRSS3 gene and their clinical manifestations related to hearing loss as well as intervention outcomes. This information will be helpful for genetic counseling and treatment planning for these patients. Methods: Literature review of previously reported TMPRSS3 variants was conducted. Reported variants and associated clinical information was compiled. Additionally, cohort data from 18 patients, and their families, with a positive result for TMPRSS3-associated hearing loss were analyzed. Genetic testing included sequencing and copy number variation (CNV) analysis of TMPRSS3 and the Laboratory for Molecular Medicine’s OtoGenome-v1, -v2, or -v3 panels. Clinical data regarding patient hearing rehabilitation was interpreted along with their genetic testing results and in the context of previously reported cochlear implant outcomes in individuals with TMPRSS3 variants. Results: There have been 87 previously reported TMPRSS3 variants associated with non-syndromic hearing loss in more than 20 ancestral groups worldwide. Here we report occurrences of known variants as well as one novel variant: deletion of Exons 1–5 and 13 identified from our cohort of 18 patients. The hearing impairment in many of these families was consistent with that of previously reported patients with TMPRSS3 variants (i.e., typical down-sloping audiogram). Four patients from our cohort underwent cochlear implantation. Conclusion: Bi-allelic variants of TMPRSS3 are associated with down-sloping hearing loss regardless of ancestry. The outcome following cochlear implantation in patients with variants of TMPRSS3 is excellent. Therefore, cochlear implantation is strongly recommended for hearing rehabilitation in these patients.
Collapse
Affiliation(s)
- In Seok Moon
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Andrew R Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,New York Medical College, Valhalla, NY, United States
| | - Varun Sagi
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States.,University of Minnesota Medical School, Minneapolis, MN, United States
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Center for Genomic Medicine and Departments of Pathology and Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Konstantina M Stankovic
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States.,Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States
| |
Collapse
|
28
|
Umair M, Farooq Khan M, Aldrees M, Nashabat M, Alhamoudi KM, Bilal M, Alyafee Y, Al Tuwaijri A, Aldarwish M, Al-Rumayyan A, Alkhalaf H, Wadaan MAM, Alfadhel M. Mutated VWA8 Is Associated With Developmental Delay, Microcephaly, and Scoliosis and Plays a Novel Role in Early Development and Skeletal Morphogenesis in Zebrafish. Front Cell Dev Biol 2021; 9:736960. [PMID: 34660594 PMCID: PMC8517341 DOI: 10.3389/fcell.2021.736960] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/26/2021] [Indexed: 11/21/2022] Open
Abstract
Von Willebrand A domain-containing protein 8 (VWA8), also named KIAA0564, is a poorly characterized, mitochondrial matrix-targeted protein having a putative ATPase activity. VWA8 is comprising of ATPase-associated domains and a VWFA domain associated with ATPase activity inside the cell. In the present study, we describe a large consanguineous family of Saudi origin segregating a complex developmental syndrome in an autosomal recessive fashion. All the affected individuals exhibited severe developmental disorders. DNA from three patients was subjected to whole-exome sequencing followed by Sanger sequencing. VWA8 knock-down zebrafish morpholinos were used to study the phenotypic effect of this gene on zebrafish development. A homozygous missense variant [c.947A > G; p.(Asp316Gly)] was identified in exon 8 of the VWA8 gene, which perfectly segregated with the disease phenotype. Using zebrafish morpholino, we observed delayed development at an early stage, lack of movement, light sensitivity, severe skeletal deformity such as scoliosis, and facial dysmorphism. This is the first homozygous variant identified in the VWA8 gene underlying global developmental delay, microcephaly, scoliosis, limbs, and cardiovascular malformations in humans. We provide genetic and molecular evidence using zebrafish morpholino for a homozygous variant in the VWA8 gene, associated with such a complex developmental syndrome in humans.
Collapse
Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Muhammad Farooq Khan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Aldrees
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Marwan Nashabat
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Kheloud M Alhamoudi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Manar Aldarwish
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al-Rumayyan
- Pediatric Neurology Division, Department of Pediatrics, Ministry of National Guard-Health Affairs (MNGHA), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hamad Alkhalaf
- Department of Pediatrics, Ministry of National Guard-Health Affairs (MNGHA), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammad A M Wadaan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Genetics and Precision Medicine Department (GPM), Ministry of National Guard Health Affairs (MNG-HA), King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Riyadh, Saudi Arabia
| |
Collapse
|
29
|
Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, Lv C, Wang R, Ning B, Roberts R, Tong W, Liu Z, Shi T. X-CNV: genome-wide prediction of the pathogenicity of copy number variations. Genome Med 2021; 13:132. [PMID: 34407882 PMCID: PMC8375180 DOI: 10.1186/s13073-021-00945-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/30/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but with limited success. Results We have developed a novel computational framework X-CNV (www.unimd.org/XCNV), to predict the pathogenicity of CNVs by integrating more than 30 informative features such as allele frequency (AF), CNV length, CNV type, and some deleterious scores. Notably, over 14 million CNVs across various ethnic groups, covering nearly 93% of the human genome, were unified to calculate the AF. X-CNV, which yielded area under curve (AUC) values of 0.96 and 0.94 in training and validation sets, was demonstrated to outperform other available tools in terms of CNV pathogenicity prediction. A meta-voting prediction (MVP) score was developed to quantitively measure the pathogenic effect, which is based on the probabilistic value generated from the XGBoost algorithm. The proposed MVP score demonstrated a high discriminative power in determining pathogenetic CNVs for inherited traits/diseases in different ethnic groups. Conclusions The ability of the X-CNV framework to quantitatively prioritize functional, deleterious, and disease-causing CNV on a genome-wide basis outperformed current CNV-annotation tools and will have broad utility in population genetics, disease-association studies, and diagnostic screening. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00945-4.
Collapse
Affiliation(s)
- Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jian Ouyang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Riquan Zhang
- School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Yiran Tao
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dongsheng Yuan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chengkai Lv
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Ruiyuan Wang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Ruth Roberts
- ApconiX Ltd, Alderley Park, Alderley Edge, SK10 4TG, UK.,University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China. .,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China. .,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
| |
Collapse
|
30
|
Unraveling the genetic complexities of combined retinal dystrophy and hearing impairment. Hum Genet 2021; 141:785-803. [PMID: 34148116 PMCID: PMC9035000 DOI: 10.1007/s00439-021-02303-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022]
Abstract
Usher syndrome, the most prevalent cause of combined hereditary vision and hearing impairment, is clinically and genetically heterogeneous. Moreover, several conditions with phenotypes overlapping Usher syndrome have been described. This makes the molecular diagnosis of hereditary deaf–blindness challenging. Here, we performed exome sequencing and analysis on 7 Mexican and 52 Iranian probands with combined retinal degeneration and hearing impairment (without intellectual disability). Clinical assessment involved ophthalmological examination and hearing loss questionnaire. Usher syndrome, most frequently due to biallelic variants in MYO7A (USH1B in 16 probands), USH2A (17 probands), and ADGRV1 (USH2C in 7 probands), was diagnosed in 44 of 59 (75%) unrelated probands. Almost half of the identified variants were novel. Nine of 59 (15%) probands displayed other genetic entities with dual sensory impairment, including Alström syndrome (3 patients), cone-rod dystrophy and hearing loss 1 (2 probands), and Heimler syndrome (1 patient). Unexpected findings included one proband each with Scheie syndrome, coenzyme Q10 deficiency, and pseudoxanthoma elasticum. In four probands, including three Usher cases, dual sensory impairment was either modified/aggravated or caused by variants in distinct genes associated with retinal degeneration and/or hearing loss. The overall diagnostic yield of whole exome analysis in our deaf–blind cohort was 92%. Two (3%) probands were partially solved and only 3 (5%) remained without any molecular diagnosis. In many cases, the molecular diagnosis is important to guide genetic counseling, to support prognostic outcomes and decisions with currently available and evolving treatment modalities.
Collapse
|
31
|
Hamadou WS, Mani R, Bouali N, Besbes S, Bourdon V, El Abed R, Ben Youssef Y, Mari V, Gesta P, Dreyfus H, Bonadona V, Dugast C, Zattara H, Faivre L, Noguchi T, Khélif A, Sobol H, Soua Z. Mutational analysis of apoptotic genes in familial aggregation of hematological malignancies. Bull Cancer 2021; 108:798-805. [PMID: 34140154 DOI: 10.1016/j.bulcan.2021.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Apoptosis deregulation have been associated to tumorigenesis process and was highlighted as a prominent hallmark of cancer. Several mutations have been reported in several forms of Blood cancer. However, it has never been investigated in familial aggregations of hematological malignancies. METHODS In this study, we performed a mutational analysis by sequencing the entire coding regions in four key apoptotic genes FAS, FASLG, CASP8 and CASP10 in 92 independent families belonging to French and Tunisian populations and diagnosed with several forms of familial hematological malignancies. RESULTS We report 15 genetic variations among which 7 were previously reported in several form of cancers and have a potential effect on gene expression. Particularly, the CASP8 variants p.Asp302His and p.Lys337Lys were detected in 15% and 10% of our group of patients respectively and were previously reported in association to breast cancer and to breast cancer susceptibility. DISCUSSION In this study, we do not report the underlining deleterious mutations in familial hematological malignancies, but we describe some variants with potential risk of developing blood cancer. To gain further insights on the association between apoptosis pathway deregulation and familial hematological malignancies, more apoptotic genes should be investigated.
Collapse
Affiliation(s)
- Walid Sabri Hamadou
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; Hail university, biology department, Hail, Saudi Arabia.
| | - Rahma Mani
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Nouha Bouali
- Hail university, biology department, Hail, Saudi Arabia
| | - Sawsen Besbes
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Violaine Bourdon
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Rym El Abed
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Yosra Ben Youssef
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Véronique Mari
- Centre de lutte contre le cancer, centre Antoine-Lacassagne, service d'oncologie génétique, Nice, France
| | - Paul Gesta
- Centre hospitalier, service d'oncologie génétique, Niort, France
| | | | - Valérie Bonadona
- Centre Léon-Bérard, unité de génétique épidémiologique, Lyon, France
| | | | - Hélène Zattara
- Hôpital de la Timone, département de génétique, Marseille, France
| | | | - Tetsuro Noguchi
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Abderrahim Khélif
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Hagay Sobol
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Zohra Soua
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| |
Collapse
|
32
|
McInnes G, Sharo AG, Koleske ML, Brown JEH, Norstad M, Adhikari AN, Wang S, Brenner SE, Halpern J, Koenig BA, Magnus DC, Gallagher RC, Giacomini KM, Altman RB. Opportunities and challenges for the computational interpretation of rare variation in clinically important genes. Am J Hum Genet 2021; 108:535-548. [PMID: 33798442 PMCID: PMC8059338 DOI: 10.1016/j.ajhg.2021.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome sequencing is enabling precision medicine-tailoring treatment to the unique constellation of variants in an individual's genome. The impact of recurrent pathogenic variants is often understood, however there is a long tail of rare genetic variants that are uncharacterized. The problem of uncharacterized rare variation is especially acute when it occurs in genes of known clinical importance with functionally consequential variants and associated mechanisms. Variants of uncertain significance (VUSs) in these genes are discovered at a rate that outpaces current ability to classify them with databases of previous cases, experimental evaluation, and computational predictors. Clinicians are thus left without guidance about the significance of variants that may have actionable consequences. Computational prediction of the impact of rare genetic variation is increasingly becoming an important capability. In this paper, we review the technical and ethical challenges of interpreting the function of rare variants in two settings: inborn errors of metabolism in newborns and pharmacogenomics. We propose a framework for a genomic learning healthcare system with an initial focus on early-onset treatable disease in newborns and actionable pharmacogenomics. We argue that (1) a genomic learning healthcare system must allow for continuous collection and assessment of rare variants, (2) emerging machine learning methods will enable algorithms to predict the clinical impact of rare variants on protein function, and (3) ethical considerations must inform the construction and deployment of all rare-variation triage strategies, particularly with respect to health disparities arising from unbalanced ancestry representation.
Collapse
Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA
| | - Andrew G Sharo
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia E H Brown
- Program in Bioethics, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Health & Aging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Norstad
- Program in Bioethics, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Health & Aging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aashish N Adhikari
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Illumina, Inc., Foster City, CA 94404, USA
| | - Sheng Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Steven E Brenner
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jodi Halpern
- UCSF-UCB Joint Medical Program, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Barbara A Koenig
- Program in Bioethics, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Health & Aging, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Social & Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Humanities & Social Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David C Magnus
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Renata C Gallagher
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Russ B Altman
- Departments of Bioengineering & Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
33
|
Spectrum of MYO7A Mutations in an Indigenous South African Population Further Elucidates the Nonsyndromic Autosomal Recessive Phenotype of DFNB2 to Include Both Homozygous and Compound Heterozygous Mutations. Genes (Basel) 2021; 12:genes12020274. [PMID: 33671976 PMCID: PMC7919343 DOI: 10.3390/genes12020274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022] Open
Abstract
MYO7A gene encodes unconventional myosin VIIA, which, when mutated, causes a phenotypic spectrum ranging from recessive hearing loss DFNB2 to deaf-blindness, Usher Type 1B (USH1B). MYO7A mutations are reported in nine DFNB2 families to date, none from sub-Saharan Africa.In DNA, from a cohort of 94 individuals representing 92 families from the Limpopo province of South Africa, eight MYO7A variations were detected among 10 individuals. Family studies identified homozygous and compound heterozygous mutations in 17 individuals out of 32 available family members. Four mutations were novel, p.Gly329Asp, p.Arg373His, p.Tyr1780Ser, and p.Pro2126Leufs*5. Two variations, p.Ser617Pro and p.Thr381Met, previously listed as of uncertain significance (ClinVar), were confirmed to be pathogenic. The identified mutations are predicted to interfere with the conformational properties of myosin VIIA through interruption or abrogation of multiple interactions between the mutant and neighbouring residues. Specifically, p.Pro2126Leufs*5, is predicted to abolish the critical site for the interactions between the tail and the motor domain essential for the autoregulation, leaving a non-functional, unregulated protein that causes hearing loss. We have identified MYO7A as a possible key deafness gene among indigenous sub-Saharan Africans. The spectrum of MYO7A mutations in this South African population points to DFNB2 as a specific entity that may occur in a homozygous or in a compound heterozygous state.
Collapse
|
34
|
Demir S, Yalçıntepe S, Atlı Eİ, Sanrı A, Yıldırım R, Tütüncüler F, Çelik M, Atlı E, Özemri Sağ Ş, Eker D, Temel Ş, Gürkan H. Targeted High-Throughput Sequencing Analysis Results of Osteogenesis Imperfecta Patients from Different Regions of Turkey. Genet Test Mol Biomarkers 2021; 25:59-67. [PMID: 33470886 DOI: 10.1089/gtmb.2020.0169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objective: Osteogenesis imperfecta (OI) includes a group of disorders characterized by susceptibility to bone fractures with different severities. The increasing number of genes that may underlie the disorder, along with the broad phenotypic spectrum that overlaps with other skeletal diseases, provided a compelling case for the use of high-throughput sequencing (HTS) technology as an aid to OI diagnoses. The aim of this analysis was to present the data from our 5-year targeted HTS results, that includes the reporting of 9 novel and 24 known mutations, found in OI patients, from 5 different regions of Turkey. Materials and Methods: We performed a retrospective cross-sectional study, reporting the HTS results of 43 patients (23 female and 20 male; mean age: 9.5 years), directed to our center with a suspicion of OI between February 2015 and May 2020. Genetic analyses were also performed for 24 asymptomatic parents to aid the segregation analyses. We utilized an HTS panel targeting the coding regions of 57 genes associated with a reduction, increase, or abnormal development of bone mineralization. In addition, we sequenced the entire coding region of the IFITM5 gene through HTS. Results: Thirty-nine patients had at least one pathogenic/likely pathogenic variation (90.69%) in the COL1A1 (56.41%), COL1A2 (20.51%), FKBP10 (7.7%), P3H1 (5.13%), IFITM5 (5.13%), CTRAP (2.56%), or TMEM38B (2.56%) genes. Nine of the determined pathogenic/likely pathogenic variations were novel. The recurrent pathogenic mutations were c.1081C>T (p.Arg361Ter) (3/43), c.1405C>T (p.Arg469Ter) (2/43), and c.3749del (p.Gly1250AlafsTer81) in COL1A1 gene, along with c.-14C>T variation in the 5'UTR of the IFITM5 gene (2/43) and the c.890_897dup variation in the FKBP10 gene (2/43). Three out of 43 patients were carrying at least one additional variant of unknown significance, highlighting the importance of a multigene panel approach and segregation analyses. Conclusion: We suggest that a targeted HTS panel is a feasible tool for genetic diagnosis of OI in patients.
Collapse
Affiliation(s)
- Selma Demir
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Sinem Yalçıntepe
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Emine İkbal Atlı
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Aslıhan Sanrı
- Department of Pediatrics, Samsun Ondokuz Mayıs Üniversitesi, Samsun, Turkey
| | - Ruken Yıldırım
- Department of Pediatric Endocrinology, Diyarbakır Hospital of Pediatric Diseases, Diyarbakır, Turkey
| | - Filiz Tütüncüler
- Department of Pediatric Endocrinology and Trakya University Faculty of Medicine, Edirne, Turkey
| | - Mehmet Çelik
- Department of Endocrinology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Engin Atlı
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Şebnem Özemri Sağ
- Department of Medical Genetics, Faculty of Medicine, Uludağ University, Bursa, Turkey
| | - Damla Eker
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Şehime Temel
- Department of Medical Genetics, Faculty of Medicine, Uludağ University, Bursa, Turkey
| | - Hakan Gürkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| |
Collapse
|
35
|
Souissi A, Ben Said M, Ben Ayed I, Elloumi I, Bouzid A, Mosrati MA, Hasnaoui M, Belcadhi M, Idriss N, Kamoun H, Gharbi N, Gibriel AA, Tlili A, Masmoudi S. Novel pathogenic mutations and further evidence for clinical relevance of genes and variants causing hearing impairment in Tunisian population. J Adv Res 2021; 31:13-24. [PMID: 34194829 PMCID: PMC8240103 DOI: 10.1016/j.jare.2021.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Hearing impairment (HI) is characterized by complex genetic heterogeneity. The evolution of next generation sequencing, including targeted enrichment panels, has revolutionized HI diagnosis. Objectives In this study, we investigated genetic causes in 22 individuals with non-GJB2 HI. Methods We customized a HaloplexHS kit to include 30 genes known to be associated with autosomal recessive nonsyndromic HI (ARNSHI) and Usher syndrome in North Africa. Results In accordance with the ACMG/AMP guidelines, we report 11 pathogenic variants; as follows; five novel variants including three missense (ESRRB-Tyr295Cys, MYO15A-Phe2089Leu and MYO7A-Tyr560Cys) and two nonsense (USH1C-Gln122Ter and CIB2-Arg104Ter) mutations; two previously reported mutations (OTOF-Glu57Ter and PNPT1-Glu475Gly), but first time identified among Tunisian families; and four other identified mutations namely WHRN-Gly808AspfsX11, SLC22A4-Cys113Tyr and two MYO7A compound heterozygous splice site variants that were previously described in Tunisia. Pathogenic variants in WHRN and CIB2 genes, in patients with convincing phenotype ruling out retinitis pigmentosa, provide strong evidence supporting their association with ARNSHI. Moreover, we shed lights on the pathogenic implication of mutations in PNPT1 gene in auditory function providing new evidence for its association with ARNSHI. Lack of segregation of a previously identified causal mutation OTOA-Val603Phe further supports its classification as variant of unknown significance. Our study reports absence of otoacoustic emission in subjects using bilateral hearing aids for several years indicating the importance of screening genetic alteration in OTOF gene for proper management of those patients. Conclusion In conclusion, our findings do not only expand the spectrum of HI mutations in Tunisian patients, but also improve our knowledge about clinical relevance of HI causing genes and variants.
Collapse
Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mohamed Ali Mosrati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Malek Belcadhi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Nourhene Gharbi
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Abdullah A. Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy. The British University in Egypt (BUE) Cairo, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
- Corresponding author at: Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sidi Mansour road Km 6, BP “1177”, 3018 Sfax, Tunisia.
| |
Collapse
|
36
|
Amanat S, Gallego-Martinez A, Lopez-Escamez JA. Genetic Inheritance and Its Contribution to Tinnitus. Curr Top Behav Neurosci 2021; 51:29-47. [PMID: 32705497 DOI: 10.1007/7854_2020_155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tinnitus is the abnormal perception of sound that affects more than 15% of adult population around the globe. Severe tinnitus is considered a complex disorder that arises as result of the interaction of genetic and environmental factors, and it is associated with several comorbidities such as hearing loss, anxiety, and insomnia. We begin this review with an introduction to human molecular genetics and the role of genetic variation on the inheritance. There are some genetic reports on tinnitus heritability including concordance studies in twins and adoptees or aggregation in families providing some evidence for familial aggregation in patients with severe tinnitus and high concordance in monozygotic twins with bilateral tinnitus. So, sex differences in familial aggregation and heritability of bilateral tinnitus suggest a potential sexual dimorphism in tinnitus inheritance.Molecular genetic studies have been demonstrated to be a useful tool to understand the role of genetic variation in rare diseases and complex disorders. The reported associations in common variants in neurotrophic factors such as GDNF, BDNF, or potassium channels genes were underpowered, and the lack of replication questions these findings. Although candidate gene approaches have failed in replicating these genetic associations, the development of high throughput sequencing technology and the selection of extreme phenotypes are strategies that will allow the clinicians and researchers to combine genetic information with clinical data to implement a personalized diagnosis and therapy in patients with tinnitus.
Collapse
Affiliation(s)
- Sana Amanat
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain.
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, Granada, Spain.
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, Granada, Spain.
| |
Collapse
|
37
|
Jiang YL, Song C, Wang Y, Zhao J, Yang F, Gao Q, Leng X, Man Y, Jiang W. Clinical Utility of Exome Sequencing and Reinterpreting Genetic Test Results in Children and Adults With Epilepsy. Front Genet 2020; 11:591434. [PMID: 33391346 PMCID: PMC7775549 DOI: 10.3389/fgene.2020.591434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
The clinical utility of genetic testing for epilepsy has been enhanced with the advancement of next-generation sequencing (NGS) technology along with the rapid updating of publicly available databases. The aim of this study was to evaluate the diagnostic yield of NGS and assess the value of reinterpreting genetic test results in children and adults with epilepsy. We performed genetic testing on 200 patients, including 82 children and 118 adults. The results were classified into three categories: positive, inconclusive, or negative. The reinterpretation of inconclusive results was conducted in April 2020. Overall, we identified disease-causing variants in 12% of the patients in the original analysis, and 14.5% at reinterpretation. The diagnostic yield for adults with epilepsy was similar to that for children (11 vs. 19.5%, p = 0.145). After reinterpretation, 9 of the 86 patients who initially had inconclusive results obtained a clinically significant change in diagnosis. Among these nine revised cases, five obtained positive diagnoses, representing a diagnosis rate of 5.8% (5/86). Manual searches for additional evidence of pathogenicity for candidate variants and updated patient clinical information were the main reasons for diagnostic reclassification. This study emphasizes the diagnostic potential of combining NGS and reinterpretation of inconclusive genetic test reports in children and adults with epilepsy.
Collapse
Affiliation(s)
- Yong-Li Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Changgeng Song
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuanyuan Wang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingjing Zhao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Yang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiong Gao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiuxiu Leng
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yulin Man
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
38
|
Fernlund E, Kissopoulou A, Green H, Karlsson JE, Ellegård R, Årstrand HK, Jonasson J, Gunnarsson C. Hereditary Hypertrophic Cardiomyopathy in Children and Young Adults-The Value of Reevaluating and Expanding Gene Panel Analyses. Genes (Basel) 2020; 11:genes11121472. [PMID: 33302605 PMCID: PMC7764692 DOI: 10.3390/genes11121472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction: Sudden cardiac death (SCD) and early onset cardiomyopathy (CM) in the young will always lead to suspicion of an underlying genetic disorder. Incited by the rapid advances in genetic testing for disease we have revisited families, which previously tested “gene-negative” for familial predominantly pediatric CM, in hopes of finding a causative gene variant. Methods: 10 different families with non-syndromic pediatric CM or hypertrophic cardiomyopathy (HCM) with severe disease progression and/or heredity for HCM/CM related SCD with “gene-negative” results were included. The index patient underwent genetic testing with a recently updated gene panel for CM and SCD. In case of failure to detect a pathogenic variant in a relevant gene, the index patient and both parents underwent clinical (i.e., partial) exome sequencing (trio-exome) in order to catch pathogenic variants linked to the disease in genes that were not included in the CM panel. Results: The mean age at clinical presentation of the 10 index cases was 12.5 years (boys 13.4 years, n = 8; girls 9 years, n = 2) and the family history burden was 33 HCM/CM cases including 9 HCM-related SCD and one heart transplantation. In 5 (50%) families we identified a genetic variant classified as pathogenic or likely pathogenic, in accordance with the American College of Medical Genetics and Genomics (ACMG) criteria, in MYH7 (n = 2), RBM20, ALPK3, and PGM1, respectively, and genetic variants of unknown significance (VUS) segregating with the disease in an additional 3 (30%) families, in MYBPC3, ABCC9, and FLNC, respectively. Conclusion: Our results show the importance of renewed thorough clinical assessment and the necessity to challenge previous genetic test results with more comprehensive updated gene panels or exome sequencing if the initial test failed to identify a causative gene for early onset CM or SCD in children. In pediatric cardiomyopathy cases when the gene panel still fails to detect a causative variant, a trio exome sequencing strategy might resolve some unexplained cases, especially if a multisystemic condition is clinically missed.
Collapse
Affiliation(s)
- Eva Fernlund
- Crown Princess Victoria Children’s Hospital, and Department of Biomedical and Clinical Sciences, Department of Pediatrics, Linköping University, 581 83 Linköping, Sweden;
- Department of Clinical Sciences Lund, Pediatric Heart Center, Skåne University Hospital, Lund University, 221 00 Lund, Sweden
| | - Antheia Kissopoulou
- Department of Internal Medicine, County Council of Jönköping, Department of Health, Medicine and Caring Sciences, Linköping University, 581 83 Linköping, Sweden;
- Correspondence:
| | - Henrik Green
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden;
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, 111 64 Stockholm, Sweden
| | - Jan-Erik Karlsson
- Department of Internal Medicine, County Council of Jönköping, Department of Health, Medicine and Caring Sciences, Linköping University, 581 83 Linköping, Sweden;
| | - Rada Ellegård
- Department of Clinical Genetics, and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (R.E.); (H.K.Å.); (J.J.); (C.G.)
| | - Hanna Klang Årstrand
- Department of Clinical Genetics, and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (R.E.); (H.K.Å.); (J.J.); (C.G.)
| | - Jon Jonasson
- Department of Clinical Genetics, and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (R.E.); (H.K.Å.); (J.J.); (C.G.)
| | - Cecilia Gunnarsson
- Department of Clinical Genetics, and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (R.E.); (H.K.Å.); (J.J.); (C.G.)
- Centre for Rare Diseases in South East Region of Sweden, Linköping University, 581 83 Linköping, Sweden
| |
Collapse
|
39
|
Subaran RL, Stewart WCL. FREQMAX provides an alternative approach for determining high-resolution allele frequency thresholds in carrier screening. Hum Mutat 2020; 41:2078-2086. [PMID: 33032373 DOI: 10.1002/humu.24123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 11/08/2022]
Abstract
As whole-genome data become available for increasing numbers of individuals across diverse populations, the list of genomic variants of unknown significance (VOUS) continues to grow. One powerful tool in VOUS interpretation is determining whether an allele is too common to be considered pathogenic. As genetic and epidemiological parameters vary across disease models, so too does the pathogenic allele frequency threshold for each disease gene. One threshold-setting approach is the maximum credible allele frequency (MCAF) method. However, estimating some of the input values MCAF requires, especially those involving heterogeneity, can present nontrivial statistical challenges. Here, we introduce FREQMAX, our alternative approach for determining allele frequency thresholds in carrier screening. FREQMAX makes efficient use of the data available for well-studied traits and exhibits flexibility for traits where information may be less complete. For cystic fibrosis, more alleles are excluded as benign by FREQMAX than by MCAF. For less-comprehensively characterized traits like ciliary dyskinesia and Smith-Lemli-Opitz syndrome, FREQMAX is able to set the allele frequency threshold without requiring a priori estimates of maximum genetic and allelic contributions. Furthermore, though we describe FREQMAX in the context of carrier screening, its classical population genetics framework also provides context for adaptation to other trait models.
Collapse
Affiliation(s)
- Ryan L Subaran
- Bioinformatics R&D, Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - William C L Stewart
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| |
Collapse
|
40
|
Nefzi M, Wahabi I, Hadj Fredj S, Othmani R, Dabboubi R, Boussetta K, Fanen P, Messaoud T. Association analysis of the surfactant protein-C gene to childhood asthma. J Asthma 2020; 59:1-11. [PMID: 32962475 DOI: 10.1080/02770903.2020.1827419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
OBJECTIVES This study aims to describe the molecular variability in the SFTPC gene in a childhood chronic respiratory disease, asthma, in the Tunisian population and to identify the implications based on a case-control study of p.Thr138Asn (T138N) and p.Ser186Asn (S186N) variants. METHODS We used direct sequencing for the genotyping of the SFTPC gene within 101 asthmatic children. The study of T138N and S186N variants in 110 controls is conducted by the PCR-RFLP technique. RESULTS The molecular study revealed 26 variants including 24 intronic variations and 2 exonic variations (T138N and S186N) with respective frequencies of 16.8% and 18.3%. We conducted a case-control study of the two identified exonic variations. A different genotypic and allelic distribution between the two groups was noted. Only the T138N polymorphism showed a significant association with asthma disease (p < 1 0 -3). Statistical analysis elaborated four haplotypes with the following frequencies in patients vs controls: 138Thr-186Ser (79.5% vs 57.6%), 138Thr-186Asn (3.7% vs 7.8%), 138Asn-186Thr (2.2% vs 20.2%) and 138Asn-186Asn (14.6% vs 14.4%). A significant difference (p < 1 0 -3) was highlighted in haplotype distribution. The 138Asn-186Ser (OR [95%CI] = 0.14[0.04-0.54], p = 0.004, R2=0.93) and 138Thr-186Asn (OR [95%CI] = 0.35[0.12-0.54], p = 0.047, R2=0.88) haplotypes showed a negative association with asthma which may constitute a protective factor against the disease. CONCLUSION In Tunisia, this work constitutes the first report interested in the SFTPC gene and highlights the genetic variability of the SFTPC gene in asthma. Therefore, the case-controls analysis may be useful in the study of surfactant proteins dysfunction in chronic respiratory disease at an early age.
Collapse
Affiliation(s)
- Malek Nefzi
- Biochemistry Laboratory (LR00SP03), Children's Hospital, Tunis, Tunisia
| | - Imen Wahabi
- Biochemistry Laboratory (LR00SP03), Children's Hospital, Tunis, Tunisia
| | | | - Rym Othmani
- Biochemistry Laboratory (LR00SP03), Children's Hospital, Tunis, Tunisia
| | - Rym Dabboubi
- Biochemistry Laboratory (LR00SP03), Children's Hospital, Tunis, Tunisia
| | | | - Pascale Fanen
- Genetic Department, AP-HP, Henri Mondor Hospital, Creteil, France
| | - Taieb Messaoud
- Biochemistry Laboratory (LR00SP03), Children's Hospital, Tunis, Tunisia
| |
Collapse
|
41
|
Beyond medically actionable results: an analytical pipeline for decreasing the burden of returning all clinically significant secondary findings. Hum Genet 2020; 140:493-504. [PMID: 32892247 DOI: 10.1007/s00439-020-02220-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Genomic sequencing advances have increased the potential to identify secondary findings (SFs). Current guidelines recommend the analysis of 59 medically actionable genes; however, patient preferences indicate interest in learning a broader group of SFs. We aimed to develop an analytical pipeline for the efficient analysis and return of all clinically significant SFs. We developed a pipeline consisting of comprehensive gene lists for five categories of SFs and filtration parameters for prioritization of variants in each category. We applied the pipeline to 42 exomes to assess feasibility and efficiency. Comprehensive lists of clinically significant SF genes were curated for each category: (1) 90 medically actionable genes and 28 pharmacogenomic variants; (2) 17 common disease risk variants; (3) 3166 Mendelian disease genes, (4) 7 early onset neurodegenerative disorder genes; (5) 688 carrier status results. Analysis of 42 exomes using our pipeline resulted in a significant decrease (> 98%) in variants compared to the raw analysis (13,036.56 ± 59.72 raw variants/exome vs 161.32 ± 7.68 filtered variants/exome), and aided in time and costs savings for the overall analysis process. Our pipeline represents a critical step in overcoming the analytic challenge associated with returning all clinically relevant SFs to allow for its routine implementation in clinical practice.
Collapse
|
42
|
Elbehi AM, Anu RI, Ekine-Afolabi B, Cash E. Emerging role of immune checkpoint inhibitors and predictive biomarkers in head and neck cancers. Oral Oncol 2020; 109:104977. [PMID: 32853912 DOI: 10.1016/j.oraloncology.2020.104977] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
Head and neck cancers are a group of diverse and heterogeneous tumors, among which squamous cell carcinoma of the head and neck (SCCHN) is the most prevalent. Current treatment modalities have limited efficacy; therefore, new therapies are being actively developed and evaluated. The introduction of immune checkpoint inhibitors (ICIs) has led to a paradigm shift in the management of difficult-to-treat malignancies. In this review, we summarize recent advances in the development of immunotherapies, which are aimed at the functional restoration of the immune system to counteract immune-evasion strategies of cancer cells, and related biomarkers. Monotherapies with ICIs, which primarily target the programmed cell death-1 (PD-1) pathway, have shown promising results in clinical trials of patients with recurrent and metastatic SCCHN. Combinations of ICIs with conventional or virus therapies often have synergistic therapeutic effects, without increased toxicity. As only a small subset of patients respond to immunotherapy, biomarkers are essential for the prediction of treatment response and better selection of patients for ICIs. PD-1 ligand (PD-L1) expression is correlated with response but has several limitations as a predictive marker, as its expression is dynamic and heterogeneous, and the cut-off needs further confirmation. Therefore, tumor mutation burden, gene expression signatures, microsatellite instability, tumor-infiltrating lymphocytes, viral antigens, and the oral microbiota are being investigated as predictive biomarkers. Finally, we delineate other challenges and future prospects for improving patient outcomes, including the major challenge of identifying and validating predictive biomarkers that need to be addressed in future studies.
Collapse
Affiliation(s)
- Attia M Elbehi
- School of Care and Health Sciences, University of South Wales, Wales, United Kingdom; Cancer Biology and Therapeutics: High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, USA.
| | - R I Anu
- Cancer Biology and Therapeutics: High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, USA; Department of Clinical Biochemistry, MVR Cancer Center and Research Institute, Kerala, India
| | - Bene Ekine-Afolabi
- Cancer Biology and Therapeutics: High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, USA; Founder & CEO, ZEAB Therapeutic, London, United Kingdom
| | - Elizabeth Cash
- Cancer Biology and Therapeutics: High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, USA; Department of Otolaryngology and Communicative Disorders, University of Louisville School of Medicine, Louisville, KY, USA
| |
Collapse
|
43
|
Michelson DJ, Clark RD. Optimizing Genetic Diagnosis of Neurodevelopmental Disorders in the Clinical Setting. Clin Lab Med 2020; 40:231-256. [PMID: 32718497 DOI: 10.1016/j.cll.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in medical genetics has changed the practice of medicine in general and child neurology in particular. A genetic diagnosis has become critically important in determining optimal management of many neurodevelopmental disorders, making genetic testing a routine consideration of patient care in outpatient and inpatient settings. Today's child neurologists should be familiar with various genetic testing modalities and their appropriate use. Molecular genetic testing of children with unexplained developmental delays and/or congenital anomalies has a 20% to 30% chance of identifying a causative etiology. Newer methods have made genetic testing more widely available and sensitive but also more likely to produce ambiguous results.
Collapse
Affiliation(s)
- David Joshua Michelson
- Division of Child Neurology, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA.
| | - Robin Dawn Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA
| |
Collapse
|
44
|
Shickh S, Gutierrez Salazar M, Zakoor KR, Lázaro C, Gu J, Goltz J, Kleinman D, Noor A, Khalouei S, Mighton C, Reble E, Kodida R, Bombard Y, DiTroia S, Baxter S, Watkins N, Care M, Adler A, Horsburgh S, Morar O, Murphy J, Nevay DL, Szybowska M, Aronson M, Panchal S, Godoy R, Holter S, Randall Armel S, Semotiuk K, Elser C, Kim RH, Chitayat D, So J, Faghfoury H, Silver J, Morel CF, Lerner-Ellis J. Exome and genome sequencing in adults with undiagnosed disease: a prospective cohort study. J Med Genet 2020; 58:275-283. [PMID: 32581083 DOI: 10.1136/jmedgenet-2020-106936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Exome and genome sequencing have been demonstrated to increase diagnostic yield in paediatric populations, improving treatment options and providing risk information for relatives. There are limited studies examining the clinical utility of these tests in adults, who currently have limited access to this technology. METHODS Patients from adult and cancer genetics clinics across Toronto, Ontario, Canada were recruited into a prospective cohort study evaluating the diagnostic utility of exome and genome sequencing in adults. Eligible patients were ≥18 years of age and suspected of having a hereditary disorder but had received previous uninformative genetic test results. In total, we examined the diagnostic utility of exome and genome sequencing in 47 probands and 34 of their relatives who consented to participate and underwent exome or genome sequencing. RESULTS Overall, 17% (8/47) of probands had a pathogenic or likely pathogenic variant identified in a gene associated with their primary indication for testing. The diagnostic yield for patients with a cancer history was similar to the yield for patients with a non-cancer history (4/18 (22%) vs 4/29 (14%)). An additional 24 probands (51%) had an inconclusive result. Secondary findings were identified in 10 patients (21%); three had medically actionable results. CONCLUSIONS This study lends evidence to the diagnostic utility of exome or genome sequencing in an undiagnosed adult population. The significant increase in diagnostic yield warrants the use of this technology. The identification and communication of secondary findings may provide added value when using this testing modality as a first-line test.
Collapse
Affiliation(s)
- Salma Shickh
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Mariana Gutierrez Salazar
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Kathleen-Rose Zakoor
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Conxi Lázaro
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet, Barcelona, Spain.,Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - Jessica Gu
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Genetics, Medcan Clinic, Toronto, Ontario, Canada
| | - Jamie Goltz
- University of Guelph, Guelph, Ontario, Canada
| | - Dakota Kleinman
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Abdul Noor
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Sam Khalouei
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Chloe Mighton
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rita Kodida
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Broad Institute, Cambridge, Massachusetts, USA
| | - Samantha Baxter
- Center for Mendelian Genomics, Broad Institute, Cambridge, Massachusetts, USA
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Arnon Adler
- Department of Cardiology, Peter Munk Cardiac Centre, Toronto General Hospital, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sheri Horsburgh
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Oana Morar
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Clinical Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Jillian Murphy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Dayna-Lynn Nevay
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Marta Szybowska
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Seema Panchal
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Ruth Godoy
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Lifelabs, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Familial Breast and Ovarian Cancer Clinic, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Christine Elser
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Raymond H Kim
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Joyce So
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Faghfoury
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Josh Silver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Chantal F Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| |
Collapse
|
45
|
Quiat D, Witkowski L, Zouk H, Daly KP, Roberts AE. Retrospective Analysis of Clinical Genetic Testing in Pediatric Primary Dilated Cardiomyopathy: Testing Outcomes and the Effects of Variant Reclassification. J Am Heart Assoc 2020; 9:e016195. [PMID: 32458740 PMCID: PMC7428992 DOI: 10.1161/jaha.120.016195] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022]
Abstract
Background Genetic testing in pediatric primary dilated cardiomyopathy (DCM) patients has identified numerous disease-causing variants, but few studies have evaluated genetic testing outcomes in this population in the context of patient and familial clinical data or assessed the clinical implications of temporal changes in genetic testing results. Methods and Results We performed a retrospective analysis of all patients with primary DCM who presented to our institution between 2008 and 2018. Variants identified by genetic testing were reevaluated for pathogenicity on the basis of current guidelines for variant classification. A total of 73 patients with primary DCM presented to our institution and 63 (86%) were probands that underwent cardiomyopathy-specific gene testing. A disease-causing variant was identified in 19 of 63 (30%) of cases, with at least 9/19 (47%) variants occurring de novo. Positive family history was not associated with identification of a causal variant. Reclassification of variants resulted in the downgrading of a large proportion of variants of uncertain significance and did not identify any new disease-causing variants. Conclusions Clinical genetic testing identifies a causal variant in one third of pediatric patients with primary DCM. Variant reevaluation significantly decreased the number of variants of uncertain significance, but a large burden of variants of uncertain significance remain. These results highlight the need for periodic reanalysis of genetic testing results, additional investigation of genotype-phenotype correlations in DCM through large, multicenter genetic studies, and development of improved tools for functional characterization of variants of uncertain significance.
Collapse
Affiliation(s)
- Daniel Quiat
- Department of CardiologyBoston Children’s HospitalBostonMA
- Harvard Medical SchoolBostonMA
| | - Leora Witkowski
- Laboratory for Molecular MedicinePartner’s HealthcareCambridgeMA
- Harvard Medical SchoolBostonMA
| | - Hana Zouk
- Laboratory for Molecular MedicinePartner’s HealthcareCambridgeMA
- Harvard Medical SchoolBostonMA
| | | | - Amy E. Roberts
- Department of CardiologyBoston Children’s HospitalBostonMA
- Department of PediatricsDivision of GeneticsBoston Children’s HospitalBostonMA
- Harvard Medical SchoolBostonMA
| |
Collapse
|
46
|
Abstract
PURPOSE OF REVIEW Intracranial atherosclerosis (ICAS) is the most common cause of stroke throughout the world. It also increases the risk of recurrent stroke and dementia. As a complex and multifactorial disease, ICAS is influenced by multiple genetic, biological, and environmental factors. This review summarizes the candidate gene and genome-wide studies aimed at discovering genetic risk factors of ICAS. RECENT FINDINGS Numerous studies have focused on the association between single-nucleotide polymorphisms (SNPs) of atherosclerosis-related genes and the risk of ICAS. Variants in adiponectin Q (ADIPOQ), ring finger protein 213 (RNF213), apolipoprotein E (APOE), phosphodiesterase 4D (PDE4D), methylenetetrahydrofolate reductase (MTHFR), lipoprotein lipase (LPL), α-adducin (ADD1) genes, angiotensin-converting enzyme (ACE), and other genes related to renin-angiotensin-aldosterone system have been associated with ICAS. We review the available evidences on the candidate genes and SNPs associated with genetic susceptibility to ICAS, and point out future developments of this field. Genetic discoveries could have clinical implications for intracranial atherosclerotic disease.
Collapse
Affiliation(s)
- Minghua Liu
- Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 W 168th Street, 6th floor, Suite 639, New York, NY, 10032, USA
| | - Jose Gutierrez
- Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 W 168th Street, 6th floor, Suite 639, New York, NY, 10032, USA.
| |
Collapse
|
47
|
Wilkins-Haug L. Genetic innovations and our understanding of stillbirth. Hum Genet 2020; 139:1161-1172. [PMID: 32318853 DOI: 10.1007/s00439-020-02146-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/27/2020] [Indexed: 12/11/2022]
Abstract
Stillbirth after 20 weeks gestation happens in 1 in 200 pregnancies and occurs more commonly than neonatal loss and sudden infant death syndrome (SIDs) combined. The stillbirth rate is several times greater in low as opposed to high-resource countries. However, among high-resource countries, although a lower overall stillbirth rate exists, there has been little change for several decades. Molecular genetic technologies are emerging as important contributors to our understanding of stillbirth. Initially, genetic etiologies included alterations in chromosome number or structure such as aneuploidy and microduplications and deletions. More recently, next-generation sequencing analysis in two genetic conditions, Smith Lemli Optiz Syndrome (SLOs) and the channelopathy disorders (such as long QT syndrome (LQTS)) provide examples into the association of pathogenic gene variants with stillbirth. Although these specific conditions individually account for only a small number of stillbirths, investigating these disorders provides a new and innovative approach for further understanding genetic contributors to adverse pregnancy outcomes. Our knowledge of the role of genetic disease as an etiology for stillbirth is elementary. Genomic interrogation of maternal-fetal genotypes, gene-gene, and genotype-environment interaction is lacking in stillbirth research. At the DNA sequence level, further investigation of variants of unknown significance is an opportunity for exploration of biologic pathways of importance to pregnancy loss. This review concentrates on SLO as an example of a single gene disorder with a high carrier but low affected liveborn proband rate. The channelopathy disorders are included as initial examples of genetic conditions with variable presentation including an association with sudden infant death syndrome. Highlighted are the challenges when numerous genes and variants are involved, and the task of assigning pathogenicity. The advantages and limitations of genetic evaluations are presented and avenues for further research considered.
Collapse
Affiliation(s)
- Louise Wilkins-Haug
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 01770, USA.
| |
Collapse
|
48
|
Bever YV, Brüggenwirth HT, Wolffenbuttel KP, Dessens AB, Groenenberg IAL, Knapen MFCM, De Baere E, Cools M, van Ravenswaaij-Arts CMA, Sikkema-Raddatz B, Claahsen-van der Grinten H, Kempers M, Rinne T, Hersmus R, Looijenga L, Hannema SE. Under-reported aspects of diagnosis and treatment addressed in the Dutch-Flemish guideline for comprehensive diagnostics in disorders/differences of sex development. J Med Genet 2020; 57:581-589. [PMID: 32303604 PMCID: PMC7476274 DOI: 10.1136/jmedgenet-2019-106354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/02/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022]
Abstract
We present key points from the updated Dutch-Flemish guideline on comprehensive diagnostics in disorders/differences of sex development (DSD) that have not been widely addressed in the current (inter)national literature. These points are of interest to physicians working in DSD (expert) centres and to professionals who come across persons with a DSD but have no (or limited) experience in this area. The Dutch-Flemish guideline is based on internationally accepted principles. Recent initiatives striving for uniform high-quality care across Europe, and beyond, such as the completed COST action 1303 and the European Reference Network for rare endocrine conditions (EndoERN), have generated several excellent papers covering nearly all aspects of DSD. The Dutch-Flemish guideline follows these international consensus papers and covers a number of other topics relevant to daily practice. For instance, although next-generation sequencing (NGS)-based molecular diagnostics are becoming the gold standard for genetic evaluation, it can be difficult to prove variant causality or relate the genotype to the clinical presentation. Network formation and centralisation are essential to promote functional studies that assess the effects of genetic variants and to the correct histological assessment of gonadal material from DSD patients, as well as allowing for maximisation of expertise and possible cost reductions. The Dutch-Flemish guidelines uniquely address three aspects of DSD. First, we propose an algorithm for counselling and diagnostic evaluation when a DSD is suspected prenatally, a clinical situation that is becoming more common. Referral to ultrasound sonographers and obstetricians who are part of a DSD team is increasingly important here. Second, we pay special attention to healthcare professionals not working within a DSD centre as they are often the first to diagnose or suspect a DSD, but are not regularly exposed to DSDs and may have limited experience. Their thoughtful communication to patients, carers and colleagues, and the accessibility of protocols for first-line management and efficient referral are essential. Careful communication in the prenatal to neonatal period and the adolescent to adult transition are equally important and relatively under-reported in the literature. Third, we discuss the timing of (NGS-based) molecular diagnostics in the initial workup of new patients and in people with a diagnosis made solely on clinical grounds or those who had earlier genetic testing that is not compatible with current state-of-the-art diagnostics.
Collapse
Affiliation(s)
- Yolande van Bever
- Department of Clinical Genetics and DSD Expert Center Erasmus Medical Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics and DSD Expert Center Erasmus Medical Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Katja P Wolffenbuttel
- Department of Pediatric Urology and DSD Expert Center Erasmus Medical Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Arianne B Dessens
- Department of Child and Adolescent Psychiatry and DSD Expert Center Erasmus Medical Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Irene A L Groenenberg
- Department of Obstetrics and Prenatal Medicine and DSD Expert Center Erasmus Medical Center, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Maarten F C M Knapen
- Department of Obstetrics and Prenatal Medicine and DSD Expert Center Erasmus Medical Center, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Elfride De Baere
- Center for Medical Genetics, University Hospital Ghent Center Medical Genetics, Ghent, Belgium
| | - Martine Cools
- Department of Internal Medicine and Paediatrics and Department of Pediatric Endocrinology, University Hospital Ghent, Ghent, Belgium
| | | | - Birgit Sikkema-Raddatz
- Department of Genetics and DSD team, University Medical Center Groningen, Groningen, The Netherlands
| | - Hedi Claahsen-van der Grinten
- Department of Pediatric Endocrinology and DSD Expert Center Radboud UMC, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Marlies Kempers
- Department of Clinical genetics and DSD Expert Center Radboud UMC, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Clinical genetics and DSD Expert Center Radboud UMC, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Remko Hersmus
- Department of Pathology, DSD Expert Center ErasmusMC, Erasmus MC-University Medical Centre, Rotterdam, The Netherlands
| | - Leendert Looijenga
- Department of Pathology, DSD Expert Center ErasmusMC, Erasmus MC-University Medical Centre, Rotterdam, The Netherlands.,Department of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sabine E Hannema
- Department of Pediatric Endocrinology and DSD Expert Center ErasmusMC, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands.,Department of Pediatrics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| |
Collapse
|
49
|
Lerner-Ellis J, Sopik V, Wong A, Lázaro C, Narod SA, Charames GS. Retesting of women who are negative for a BRCA1 and BRCA2 mutation using a 20-gene panel. J Med Genet 2019; 57:380-384. [PMID: 31784482 DOI: 10.1136/jmedgenet-2019-106403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 10/04/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND The value of retesting women who previously tested negative for a pathogenic variant (mutation) in BRCA1 and BRCA2 using an expanded panel of breast and ovarian cancer genes is unclear. METHODS We studied 110 BRCA1/2-negative women who were retested using a panel of 20 breast and/or ovarian cancer susceptibility genes at the Advanced Molecular Diagnostics Laboratory (AMDL) at Mount Sinai Hospital in Toronto between March 2017 and March 2019. All patients had previously tested negative for BRCA pathogenic variants at the AMDL between January 2012 and March 2018 and were subsequently referred for retesting by their physician. RESULTS Overall, six pathogenic variants in genes other than BRCA1 and BRCA2 were found (prevalence 5.5%). There were two pathogenic variants found in RAD51C, and one found in each of BRIP1, PALB2, PMS2 and PTEN. The prevalence of pathogenic variants was 6.5% for women affected with cancer (6 of 93), including 4.9% for women with breast cancer (4 of 82) and 22.2% for women with ovarian cancer (2 of 9). None of the 17 unaffected women had a clinically significant or pathogenic variant. There were 44 women (40%) for whom the result of the panel test was inconclusive due to the detection of a variant of uncertain significance. CONCLUSIONS Our findings indicate that the retesting of BRCA1/2-negative individuals with an expanded panel of 20 breast and ovarian cancer genes can produce clinically relevant results, with a yield of 5.5% for pathogenic variants in genes other than BRCA1 and BRCA2.
Collapse
Affiliation(s)
- Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada .,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Victoria Sopik
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Conxi Lázaro
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| |
Collapse
|
50
|
Liu M, Gutierrez J. Developing Novel Therapeutic Strategies Against Ring Finger Protein 213 Vasculopathy: Is It an Achievable Goal? J Am Heart Assoc 2019; 8:e014273. [PMID: 31590588 PMCID: PMC6818045 DOI: 10.1161/jaha.119.014273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
See Article Choi et al.
Collapse
Affiliation(s)
- Minghua Liu
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University Irving Medical CenterNew YorkNY
| | - Jose Gutierrez
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University Irving Medical CenterNew YorkNY
| |
Collapse
|