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Ross JE, Mohan S, Zhang J, Sullivan MJ, Bury L, Lee K, Futchi I, Frantz A, McDougal D, Perez Botero J, Cattaneo M, Cooper N, Downes K, Gresele P, Keenan C, Lee AI, Megy K, Morange PE, Morgan NV, Schulze H, Zimowski K, Freson K, Lambert MP. Evaluating the clinical validity of genes related to hemostasis and thrombosis using the Clinical Genome Resource gene curation framework. J Thromb Haemost 2024; 22:645-665. [PMID: 38016518 PMCID: PMC10922649 DOI: 10.1016/j.jtha.2023.11.011] [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: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Inherited bleeding, thrombotic, and platelet disorders (BTPDs) are a heterogeneous set of diseases, many of which are very rare globally. Over the past 5 decades, the genetic basis of some of these disorders has been identified, and recently, high-throughput sequencing has become the primary means of identifying disease-causing genetic variants. OBJECTIVES Knowledge of the clinical validity of a gene-disease relationship is essential to provide an accurate diagnosis based on results of diagnostic gene panel tests and inform the construction of such panels. The Scientific and Standardization Committee for Genetics in Thrombosis and Hemostasis undertook a curation process for selecting 96 TIER1 genes for BTPDs. The purpose of the process was to evaluate the evidence supporting each gene-disease relationship and provide an expert-reviewed classification for the clinical validity of genes associated with BTPDs. METHODS The Clinical Genome Resource (ClinGen) Hemostasis/Thrombosis Gene Curation Expert Panel assessed the strength of evidence for TIER1 genes using the semiquantitative ClinGen gene-disease clinical validity framework. ClinGen Lumping and Splitting guidelines were used to determine the appropriate disease entity or entities for each gene, and 101 gene-disease relationships were identified for curation. RESULTS The final outcome included 68 Definitive (67%), 26 Moderate (26%), and 7 Limited (7%) classifications. The summary of each curation is available on the ClinGen website. CONCLUSION Expert-reviewed assignment of gene-disease relationships by the ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel facilitates accurate molecular diagnoses of BTPDs by clinicians and diagnostic laboratories. These curation efforts can allow genetic testing to focus on genes with a validated role in disease.
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Affiliation(s)
- Justyne E Ross
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Zhang
- KingMed Diagnostics, Guangzhou, Guangdong, China
| | - Mia J Sullivan
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA
| | - Loredana Bury
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isabella Futchi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annabelle Frantz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dara McDougal
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Juliana Perez Botero
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA; Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marco Cattaneo
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Nichola Cooper
- Centre for Haematology, Imperial College London, London, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Catriona Keenan
- Haemostasis Molecular Diagnostic Laboratory, National Coagulation Centre, St James's Hospital, Dublin, Ireland
| | - Alfred I Lee
- Section of Hematology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Pierre-Emmanuel Morange
- INSERM, INRAE, C2VN, Aix Marseille University, Marseille, France; Hematology Laboratory, La Timone Hospital, APHM, Marseille, France
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Harald Schulze
- Institute of Experimental Biomedicine, Julius-Maximilians-University Wuerzburg, Wuerzburg, Germany
| | - Karen Zimowski
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
| | - Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Schedel M, Leach SM, Strand MJ, Danhorn T, MacBeth M, Faino AV, Lynch AM, Winn VD, Munoz LL, Forsberg SM, Schwartz DA, Gelfand EW, Hauk PJ. Molecular networks in atopic mothers impact the risk of infant atopy. Allergy 2023; 78:244-257. [PMID: 35993851 DOI: 10.1111/all.15490] [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: 03/07/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The prevalence of atopic diseases has increased with atopic dermatitis (AD) as the earliest manifestation. We assessed if molecular risk factors in atopic mothers influence their infants' susceptibility to an atopic disease. METHODS Pregnant women and their infants with (n = 174, high-risk) or without (n = 126, low-risk) parental atopy were enrolled in a prospective birth cohort. Global differentially methylated regions (DMRs) were determined in atopic (n = 92) and non-atopic (n = 82) mothers. Principal component analysis was used to predict atopy risk in children dependent on maternal atopy. Genome-wide transcriptomic analyses were performed in paired atopic (n = 20) and non-atopic (n = 15) mothers and cord blood. Integrative genomic analyses were conducted to define methylation-gene expression relationships. RESULTS Atopic dermatitis was more prevalent in high-risk compared to low-risk children by age 2. Differential methylation analyses identified 165 DMRs distinguishing atopic from non-atopic mothers. Inclusion of DMRs in addition to maternal atopy significantly increased the odds ratio to develop AD in children from 2.56 to 4.26. In atopic compared to non-atopic mothers, 139 differentially expressed genes (DEGs) were identified significantly enriched of genes within the interferon signaling pathway. Expression quantitative trait methylation analyses dependent on maternal atopy identified 29 DEGs controlled by 136 trans-acting methylation marks, some located near transcription factors. Differential expression for the same nine genes, including MX1 and IFI6 within the interferon pathway, was identified in atopic and non-atopic mothers and high-risk and low-risk children. CONCLUSION These data suggest that in utero epigenetic and transcriptomic mechanisms predominantly involving the interferon pathway may impact and predict the development of infant atopy.
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Affiliation(s)
- Michaela Schedel
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Pulmonary Medicine, University Medicine Essen-Ruhrlandklinik, Essen, Germany.,Department of Pulmonary Medicine, University Medicine Essen, University Hospital, Essen, Germany
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment & Health, National Jewish Health, Denver, Colorado, USA
| | - Matthew J Strand
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA.,Department of Pharmacology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Morgan MacBeth
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Anna V Faino
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA.,Biostatistics, Epidemiology and Research Core, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Anne M Lynch
- Department of Ophthalmology, School of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Obstetrics and Gynecology, Stanford University, Stanford, California, USA
| | - Lindsay L Munoz
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Shannon M Forsberg
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Thoracic Oncology, University of Colorado Cancer Center, University of Colorado, Aurora, Colorado, USA
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Erwin W Gelfand
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Pia J Hauk
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Section Allergy/Immunology, Children's Hospital Colorado, University of Colorado, Aurora, Colorado, USA
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A Novel Likely Pathogenic Variant in the BLOC1S5 Gene Associated with Hermansky-Pudlak Syndrome Type 11 and an Overview of Human BLOC-1 Deficiencies. Cells 2021; 10:cells10102630. [PMID: 34685610 PMCID: PMC8533863 DOI: 10.3390/cells10102630] [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: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/26/2021] [Indexed: 01/18/2023] Open
Abstract
Hermansky-Pudlak syndrome (HPS) is a heterogeneous disorder combining oculocutaneous albinism (OCA) and a platelet function disorder of varying severity as its most prominent features. The genes associated with HPS encode for different BLOC- (biogenesis of lysosome-related organelles complex) complexes and for the AP-3 (adaptor protein-3) complex, respectively. These proteins are involved in maturation, trafficking, and the function of lysosome-related organelles (LROs) such as melanosomes and platelet δ-granules. Some patients with different types of HPS can develop additional complications and symptoms like pulmonary fibrosis, granulomatous colitis, and immunodeficiency. A new type of HPS has recently been identified associated with genetic alterations in the BLOC1S5 gene, which encodes the subunit Muted of the BLOC-1 complex. Our aim was to unravel the genetic defect in two siblings with a suspected HPS diagnosis (because of OCA and bleeding symptoms) using next generation sequencing (NGS). Platelet functional analysis revealed reduced platelet aggregation after stimulation with ADP and a severe secretion defect in platelet δ-granules. NGS identified a novel homozygous essential splice site variant in the BLOC1S5 gene present in both affected siblings who are descendants of a consanguine marriage. The patients exhibited no additional symptoms. Our study confirms that pathogenic variants of BLOC1S5 cause the recently described HPS type 11.
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Liu T, Yuan Y, Bai D, Yao X, Zhang T, Huang Q, Qi Z, Yang L, Yang X, Li W, Wei A. The first Hermansky-Pudlak syndrome type 9 patient with two novel variants in Chinese population. J Dermatol 2021; 48:676-680. [PMID: 33543539 DOI: 10.1111/1346-8138.15762] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/20/2020] [Accepted: 12/27/2020] [Indexed: 12/27/2022]
Abstract
Hermansky-Pudlak syndrome 9 (HPS-9) is a recessive disorder caused by BLOC1S6 gene. There are only four variants identified from four HPS-9 patients so far. Here, we reported the first HPS-9 patient in a Chinese population. He had brownish-yellow hair, white skin, brown irises with visual acuity, photophobia and nystagmus. Two novel variants, c.148G>T (p.Glu50*) and c.351dupT (p.Ile118Tyrfs*10) in BLOC1S6 gene were identified by whole-exome sequencing (WES). Absence of platelet dense granules was found by whole-mount platelet electron microscopy and Western blotting assays showed the destabilized BLOC-1 subunits. He had recurrent bruising and was found to have abnormal brain waves by electroencephalogram, but did not develop thrombopenia, immunodeficiency or other symptoms reported in other HPS-9 patients. This is the first case report of BLOC-1 mutation in a Chinese population and our findings expand the mutational spectrum of HPS genes.
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Affiliation(s)
- Teng Liu
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,Shunyi Women and Children's Hospital of Beijing Children's Hospital, Beijing, China
| | - Yefeng Yuan
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Genetics and Birth Defects Control Center, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Dayong Bai
- Department of Ophthalmology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xingfeng Yao
- Department of Pathology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tianjiao Zhang
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qiaorong Huang
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhan Qi
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Genetics and Birth Defects Control Center, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiumin Yang
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- Shunyi Women and Children's Hospital of Beijing Children's Hospital, Beijing, China.,Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Genetics and Birth Defects Control Center, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Aihua Wei
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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