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Fioretti T, Martora F, De Maggio I, Ambrosio A, Piscopo C, Vallone S, Amato F, Passaro D, Acquaviva F, Gaudiello F, Di Girolamo D, Maiolo V, Zarrilli F, Esposito S, Vitiello G, Auricchio L, Sammarco E, Brasi DD, Petillo R, Gambale A, Cattaneo F, Ammendola R, Nappa P, Esposito G. Comprehensive Molecular Analysis of Disease-Related Genes as First-Tier Test for Early Diagnosis, Classification, and Management of Patients Affected by Nonsyndromic Ichthyosis. Biomedicines 2024; 12:1112. [PMID: 38791074 PMCID: PMC11117922 DOI: 10.3390/biomedicines12051112] [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: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Inherited ichthyoses are a group of clinically and genetically heterogeneous rare disorders of skin keratinization with overlapping phenotypes. The clinical picture and family history are crucial to formulating the diagnostic hypothesis, but only the identification of the genetic defect allows the correct classification. In the attempt to molecularly classify 17 unrelated Italian patients referred with congenital nonsyndromic ichthyosis, we performed massively parallel sequencing of over 50 ichthyosis-related genes. Genetic data of 300 Italian unaffected subjects were also analyzed to evaluate frequencies of putative disease-causing alleles in our population. For all patients, we identified the molecular cause of the disease. Eight patients were affected by autosomal recessive congenital ichthyosis associated with ALOX12B, NIPAL4, and TGM1 mutations. Three patients had biallelic loss-of-function variants in FLG, whereas 6/11 males were affected by X-linked ichthyosis. Among the 24 different disease-causing alleles we identified, 8 carried novel variants, including a synonymous TGM1 variant that resulted in a splicing defect. Moreover, we generated a priority list of the ichthyosis-related genes that showed a significant number of rare and novel variants in our population. In conclusion, our comprehensive molecular analysis resulted in an effective first-tier test for the early classification of ichthyosis patients. It also expands the genetic, mutational, and phenotypic spectra of inherited ichthyosis and provides new insight into the current understanding of etiologies and epidemiology of this group of rare disorders.
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Affiliation(s)
- Tiziana Fioretti
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
| | - Fabrizio Martora
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Ilaria De Maggio
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Adelaide Ambrosio
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Sabrina Vallone
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Felice Amato
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Diego Passaro
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Fabio Acquaviva
- Medical Genetics Unit, Department of General and Emergency Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy; (F.A.); (D.D.B.)
| | - Francesca Gaudiello
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Daniela Di Girolamo
- Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy;
| | - Valeria Maiolo
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Federica Zarrilli
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Speranza Esposito
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Giuseppina Vitiello
- Medical Genetics Unit, Integrated Care Department of Laboratory and Transfusion Medicine, Federico II Hospital, 80131 Naples, Italy; (G.V.); (A.G.)
| | - Luigi Auricchio
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Elena Sammarco
- Pediatric Dermatology Unit, Department of Dermo-Immuno-Rheumatology Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy;
| | - Daniele De Brasi
- Medical Genetics Unit, Department of General and Emergency Paediatrics, AORN Santobono-Pausilipon, 80122 Naples, Italy; (F.A.); (D.D.B.)
| | - Roberta Petillo
- Medical and Laboratory Genetics Unit, AORN A. Cardarelli, 80131 Naples, Italy; (I.D.M.); (C.P.); (R.P.)
| | - Antonella Gambale
- Medical Genetics Unit, Integrated Care Department of Laboratory and Transfusion Medicine, Federico II Hospital, 80131 Naples, Italy; (G.V.); (A.G.)
| | - Fabio Cattaneo
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Rosario Ammendola
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
| | - Paola Nappa
- Section of Dermatology, Department of Clinical Medicine and Surgery, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.); (F.G.); (L.A.); (P.N.)
| | - Gabriella Esposito
- CEINGE Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy; (T.F.); (A.A.); (S.V.); (F.A.); (F.Z.); (S.E.)
- Department of Molecular Medicine and Medical Biotechnologies, School of Medicine, University of Naples “Federico II”, 80131 Naples, Italy; (D.P.); (V.M.); (F.C.); (R.A.)
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2
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Kwak SH, Srinivasan S, Chen L, Todd J, Mercader JM, Jensen ET, Divers J, Mottl AK, Pihoker C, Gandica RG, Laffel LM, Isganaitis E, Haymond MW, Levitsky LL, Pollin TI, Florez JC, Flannick J. Genetic architecture and biology of youth-onset type 2 diabetes. Nat Metab 2024; 6:226-237. [PMID: 38278947 PMCID: PMC10896722 DOI: 10.1038/s42255-023-00970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
The prevalence of youth-onset type 2 diabetes (T2D) and childhood obesity has been rising steadily1, producing a growing public health concern1 that disproportionately affects minority groups2. The genetic basis of youth-onset T2D and its relationship to other forms of diabetes are unclear3. Here we report a detailed genetic characterization of youth-onset T2D by analysing exome sequences and common variant associations for 3,005 individuals with youth-onset T2D and 9,777 adult control participants matched for ancestry, including both males and females. We identify monogenic diabetes variants in 2.4% of individuals and three exome-wide significant (P < 2.6 × 10-6) gene-level associations (HNF1A, MC4R, ATXN2L). Furthermore, we report rare variant association enrichments within 25 gene sets related to obesity, monogenic diabetes and β-cell function. Many youth-onset T2D associations are shared with adult-onset T2D, but genetic risk factors of all frequencies-and rare variants in particular-are enriched within youth-onset T2D cases (5.0-fold increase in the rare variant and 3.4-fold increase in common variant genetic liability relative to adult-onset cases). The clinical presentation of participants with youth-onset T2D is influenced in part by the frequency of genetic risk factors within each individual. These findings portray youth-onset T2D as a heterogeneous disease situated on a spectrum between monogenic diabetes and adult-onset T2D.
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Affiliation(s)
- Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shylaja Srinivasan
- Division of Pediatric Endocrinology, University of California at San Francisco, San Francisco, CA, USA
| | - Ling Chen
- Center for Genomic Medicine, and Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jennifer Todd
- Division of Pediatric Endocrinology, Department of Pediatrics, University of Vermont, Burlington, VT, USA
| | - Josep M Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, and Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elizabeth T Jensen
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jasmin Divers
- Department of Foundations of Medicine, NYU Langone Health, New York, NY, USA
| | - Amy K Mottl
- Division of Nephrology and Hypertension, University of North Carolina, Chapel Hill, NC, USA
| | - Catherine Pihoker
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Rachelle G Gandica
- Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Lori M Laffel
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | | | - Morey W Haymond
- Department of Pediatrics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Lynne L Levitsky
- Pediatric Endocrine Division, Department of Pediatrics, Massachusetts General Hospital for Children and Harvard Medical School, Boston, MA, USA
| | - Toni I Pollin
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, and Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
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3
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Bloch C, Jais JP, Gil M, Boubaya M, Lepelletier Y, Bader-Meunier B, Mahlaoui N, Garcelon N, Lambotte O, Launay D, Larroche C, Lazaro E, Liffermann F, Lortholary O, Michel M, Michot JM, Morel P, Cheminant M, Suarez F, Terriou L, Urbanski G, Viallard JF, Alcais A, Fischer A, de Saint Basile G, Hermine O. Severe adult hemophagocytic lymphohistiocytosis (HLHa) correlates with HLH-related gene variants. J Allergy Clin Immunol 2024; 153:256-264. [PMID: 37678575 DOI: 10.1016/j.jaci.2023.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/14/2023] [Accepted: 07/14/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND The contribution of genetic factors to the severity of adult hemophagocytic lymphohistiocytosis (HLHa) remains unclear. OBJECTIVE We sought to assess a potential link between HLHa outcomes and HLH-related gene variants. METHODS Clinical characteristics of 130 HLHa patients (age ≥ 18 years and HScore ≥ 169) and genotype of 8 HLH-related genes (LYST, PRF1, UNC13-D, STX11, STXBP2, RAB27A, XIAP, and SAP) were collected. A total of 34 variants found in only 6 genes were selected on the basis of their frequency and criteria predicted to impair protein function. Severity was defined by refractory disease to HLH treatment, death, or transfer to an intensive care unit. RESULTS HLHa-associated diseases (ADs) were neoplasia (n = 49 [37.7%]), autoimmune/inflammatory disease (n = 33 [25.4%]), or idiopathic when no AD was identified (n = 48 [36.9%]). Infectious events occurred in 76 (58.5%) patients and were equally distributed in all ADs. Severe and refractory HLHa were observed in 80 (61.5%) and 64 (49.2%) patients, respectively. HScore, age, sex ratio, AD, and infectious events showed no significant association with HLHa severity. Variants were identified in 71 alleles and were present in 56 (43.1%) patients. They were distributed as follows: 44 (34.4%), 9 (6.9%), and 3 (2.3%) patients carrying 1, 2, and 3 variant alleles, respectively. In a logistic regression model, only the number of variants was significantly associated with HLHa severity (1 vs 0: 3.86 [1.73-9.14], P = .0008; 2-3 vs 0: 29.4 [3.62-3810], P = .0002) and refractoriness (1 vs 0: 2.47 [1.17-5.34], P = .018; 2-3 vs 0: 13.2 [2.91-126.8], P = .0003). CONCLUSIONS HLH-related gene variants may be key components to the severity and refractoriness of HLHa.
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Affiliation(s)
- Coralie Bloch
- Clinical Research Unit, Avicenne University Hospital, AP-HP, Bobigny, France; Paris 13 University, Sorbonne Paris Cité, Paris, France; Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR1163/CNRS URL 8254, Paris, France; French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France.
| | - Jean Philippe Jais
- Imagine Institute, Université Paris Cité, Paris, France; Biostatistic Unit, Necker University Hospital, AP-HP, Paris, France; Human Genetics of Infectious Diseases: Complex Predisposition, INSERM UMR1163, Paris, France
| | - Marine Gil
- Imagine Institute, Université Paris Cité, Paris, France
| | - Marouane Boubaya
- Clinical Research Unit, Avicenne University Hospital, AP-HP, Bobigny, France
| | - Yves Lepelletier
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR1163/CNRS URL 8254, Paris, France; Imagine Institute, Université Paris Cité, Paris, France
| | - Brigitte Bader-Meunier
- Imagine Institute, Université Paris Cité, Paris, France; Department of Pediatric Immunology and Rheumatology, Necker University Hospital, AP-HP, Paris, France
| | - Nizar Mahlaoui
- French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Department of Pediatric Immunology and Rheumatology, Necker University Hospital, AP-HP, Paris, France
| | | | - Olivier Lambotte
- University Paris Saclay, AP-HP, Hôpital Bicêtre, IMVAHB UMR1184, INSERM, CEA, Le Kremlin Bicêtre, France
| | - David Launay
- Université de Lille, CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France; INSERM INFINITE U1286, Lille, France
| | - Claire Larroche
- Internal Medicine Unit, Avicenne Hospital, AP-HP, Bobigny, France
| | - Estibaliz Lazaro
- Internal Medicine Department, Bordeaux Hospital University, Bordeaux, France; CNRS-UMR 5164 Immuno ConcEpT, Bordeaux, France
| | - Francois Liffermann
- Service de medecine interne-hematologie, Centre hospitalier de Dax, Dax, France
| | - Olivier Lortholary
- French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Service de Maladies Infectieuses et Tropicales, Centre d'Infectiologie Necker Pasteur, Hôpital Universitaire Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Marc Michel
- Department of Internal Medicine, Centre de Référence maladies rares sur les Cytopénies Auto-Immunes de l'adulte, Hôpitaux Universitaires Henri Mondor, AP-HP, Université Paris-Est Créteil, Créteil, France
| | - Jean-Marie Michot
- Gustave Roussy, University Paris Saclay, Drug Development Department, Villejuif, France
| | - Pierre Morel
- Service d'Hématologie Clinique, Hôpital Schaffner de Lens, Lens Cedex, France
| | - Morgane Cheminant
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR1163/CNRS URL 8254, Paris, France; French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Clinical Hematology, Necker University Hospital, AP-HP, Paris, France
| | - Felipe Suarez
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR1163/CNRS URL 8254, Paris, France; French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Clinical Hematology, Necker University Hospital, AP-HP, Paris, France
| | - Louis Terriou
- Université de Lille, CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France; INSERM INFINITE U1286, Lille, France
| | - Geoffrey Urbanski
- Department of Internal Medicine and Clinical Immunology, University Hospital, Angers, France; MitoLab Team, MITOVASC Institute, UMR CNRS 6015, INSERM U1083, University of Angers, Angers, France
| | | | - Alexandre Alcais
- Imagine Institute, Université Paris Cité, Paris, France; Biostatistic Unit, Necker University Hospital, AP-HP, Paris, France; Human Genetics of Infectious Diseases: Complex Predisposition, INSERM UMR1163, Paris, France
| | - Alain Fischer
- French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Department of Pediatric Immunology and Rheumatology, Necker University Hospital, AP-HP, Paris, France; Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR1163, Paris, France; Necker University Hospital, AP-HP, Paris, France; College de France, Paris, France
| | - Geneviève de Saint Basile
- French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR1163, Paris, France
| | - Olivier Hermine
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR1163/CNRS URL 8254, Paris, France; French National Center for Primary Immunodeficiencies, Necker University Hospital, AP-HP, Paris, France; Imagine Institute, Université Paris Cité, Paris, France; Clinical Hematology, Necker University Hospital, AP-HP, Paris, France.
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4
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Kwak SH, Srinivasan S, Chen L, Todd J, Mercader J, Jensen E, Divers J, Mottl A, Pihoker C, Gandica R, Laffel L, Isganaitis E, Haymond M, Levitsky L, Pollin T, Florez J, Flannick J. Insights from rare variants into the genetic architecture and biology of youth-onset type 2 diabetes. RESEARCH SQUARE 2023:rs.3.rs-2886343. [PMID: 37292813 PMCID: PMC10246295 DOI: 10.21203/rs.3.rs-2886343/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Youth-onset type 2 diabetes (T2D) is a growing public health concern. Its genetic basis and relationship to other forms of diabetes are largely unknown. To gain insight into the genetic architecture and biology of youth-onset T2D, we analyzed exome sequences of 3,005 youth-onset T2D cases and 9,777 ancestry matched adult controls. We identified (a) monogenic diabetes variants in 2.1% of individuals; (b) two exome-wide significant (P < 4.3×10-7) common coding variant associations (in WFS1 and SLC30A8); (c) three exome-wide significant (P < 2.5×10-6) rare variant gene-level associations (HNF1A, MC4R, ATX2NL); and (d) rare variant association enrichments within 25 gene sets broadly related to obesity, monogenic diabetes, and β-cell function. Many association signals were shared between youth-onset and adult-onset T2D but had larger effects for youth-onset T2D risk (1.18-fold increase for common variants and 2.86-fold increase for rare variants). Both common and rare variant associations contributed more to youth-onset T2D liability variance than they did to adult-onset T2D, but the relative increase was larger for rare variant associations (5.0-fold) than for common variant associations (3.4-fold). Youth-onset T2D cases showed phenotypic differences depending on whether their genetic risk was driven by common variants (primarily related to insulin resistance) or rare variants (primarily related to β-cell dysfunction). These data paint a picture of youth-onset T2D as a disease genetically similar to both monogenic diabetes and adult-onset T2D, in which genetic heterogeneity might be used to sub-classify patients for different treatment strategies.
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Affiliation(s)
| | | | - Ling Chen
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jason Flannick
- Broad Institute of MIT and Harvard/Boston Children's Hospital/Harvard Medical School
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5
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Nickchi P, Karunarathna C, Graham J. An exploration of linkage fine-mapping on sequences from case-control studies. Genet Epidemiol 2023; 47:78-94. [PMID: 36047334 PMCID: PMC10087369 DOI: 10.1002/gepi.22502] [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: 12/09/2021] [Revised: 05/30/2022] [Accepted: 08/09/2022] [Indexed: 02/01/2023]
Abstract
Linkage analysis maps genetic loci for a heritable trait by identifying genomic regions with excess relatedness among individuals with similar trait values. Analysis may be conducted on related individuals from families, or on samples of unrelated individuals from a population. For allelically heterogeneous traits, population-based linkage analysis can be more powerful than genotypic-association analysis. Here, we focus on linkage analysis in a population sample, but use sequences rather than individuals as our unit of observation. Earlier investigations of sequence-based linkage mapping relied on known sequence relatedness, whereas we infer relatedness from the sequence data. We propose two ways to associate similarity in relatedness of sequences with similarity in their trait values and compare the resulting linkage methods to two genotypic-association methods. We also introduce a procedure to label case sequences as potential carriers or noncarriers of causal variants after an association has been found. This post hoc labeling of case sequences is based on inferred relatedness to other case sequences. Our simulation results indicate that methods based on sequence relatedness improve localization and perform as well as genotypic-association methods for detecting rare causal variants. Sequence-based linkage analysis therefore has potential to fine-map allelically heterogeneous disease traits.
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Affiliation(s)
- Payman Nickchi
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Charith Karunarathna
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jinko Graham
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
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6
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Jang SK, Evans L, Fialkowski A, Arnett DK, Ashley-Koch AE, Barnes KC, Becker DM, Bis JC, Blangero J, Bleecker ER, Boorgula MP, Bowden DW, Brody JA, Cade BE, Jenkins BWC, Carson AP, Chavan S, Cupples LA, Custer B, Damrauer SM, David SP, de Andrade M, Dinardo CL, Fingerlin TE, Fornage M, Freedman BI, Garrett ME, Gharib SA, Glahn DC, Haessler J, Heckbert SR, Hokanson JE, Hou L, Hwang SJ, Hyman MC, Judy R, Justice AE, Kaplan RC, Kardia SLR, Kelly S, Kim W, Kooperberg C, Levy D, Lloyd-Jones DM, Loos RJF, Manichaikul AW, Gladwin MT, Martin LW, Nouraie M, Melander O, Meyers DA, Montgomery CG, North KE, Oelsner EC, Palmer ND, Payton M, Peljto AL, Peyser PA, Preuss M, Psaty BM, Qiao D, Rader DJ, Rafaels N, Redline S, Reed RM, Reiner AP, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Silverman EK, Smith NL, Smith JG, Smith AV, Smith JA, Tang W, Taylor KD, Telen MJ, Vasan RS, Gordeuk VR, Wang Z, Wiggins KL, Yanek LR, Yang IV, Young KA, Young KL, Zhang Y, Liu DJ, Keller MC, Vrieze S. Rare genetic variants explain missing heritability in smoking. Nat Hum Behav 2022; 6:1577-1586. [PMID: 35927319 PMCID: PMC9985486 DOI: 10.1038/s41562-022-01408-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Common genetic variants explain less variation in complex phenotypes than inferred from family-based studies, and there is a debate on the source of this 'missing heritability'. We investigated the contribution of rare genetic variants to tobacco use with whole-genome sequences from up to 26,257 unrelated individuals of European ancestries and 11,743 individuals of African ancestries. Across four smoking traits, single-nucleotide-polymorphism-based heritability ([Formula: see text]) was estimated from 0.13 to 0.28 (s.e., 0.10-0.13) in European ancestries, with 35-74% of it attributable to rare variants with minor allele frequencies between 0.01% and 1%. These heritability estimates are 1.5-4 times higher than past estimates based on common variants alone and accounted for 60% to 100% of our pedigree-based estimates of narrow-sense heritability ([Formula: see text], 0.18-0.34). In the African ancestry samples, [Formula: see text] was estimated from 0.03 to 0.33 (s.e., 0.09-0.14) across the four smoking traits. These results suggest that rare variants are important contributors to the heritability of smoking.
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Affiliation(s)
- Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Luke Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Ecology & Evolution, University of Colorado Boulder, Boulder, CO, USA
| | | | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KY, USA
| | | | - Kathleen C Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | | | - Meher Preethi Boorgula
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda W Campbell Jenkins
- Jackson Heart Study Graduate Training and Education Center, Jackson State University School of Public Health, Jackson, MS, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sameer Chavan
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Sean P David
- Department of Family Medicine, Prtizker School of Medicine, University of Chicago, Chicago, IL, USA
- NorthShore University HealthSystem, Evanston, IL, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Tasha E Fingerlin
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes Environment and Health, National Jewish Health, Denver, CO, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E Garrett
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hosptial and Harvard Medical School, Boston, MA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew C Hyman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health System, Danville, PA, USA
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Shannon Kelly
- Department of Pediatrics, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mark T Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | | | - Courtney G Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Division of General Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marinelle Payton
- Department of Epidemiology and Biostatistics, Jackson Heart Study Graduate Training and Education Center, Jackson State University School of Public Health, Jackson, MS, USA
| | - Anna L Peljto
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas Rafaels
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert M Reed
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - J Gustav Smith
- Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ramachandran S Vasan
- Sections of Preventive Medicine and Epidemiology and Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Victor R Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Zhe Wang
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
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7
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Chen W, Coombes BJ, Larson NB. Recent advances and challenges of rare variant association analysis in the biobank sequencing era. Front Genet 2022; 13:1014947. [PMID: 36276986 PMCID: PMC9582646 DOI: 10.3389/fgene.2022.1014947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
Causal variants for rare genetic diseases are often rare in the general population. Rare variants may also contribute to common complex traits and can have much larger per-allele effect sizes than common variants, although power to detect these associations can be limited. Sequencing costs have steadily declined with technological advancements, making it feasible to adopt whole-exome and whole-genome profiling for large biobank-scale sample sizes. These large amounts of sequencing data provide both opportunities and challenges for rare-variant association analysis. Herein, we review the basic concepts of rare-variant analysis methods, the current state-of-the-art methods in utilizing variant annotations or external controls to improve the statistical power, and particular challenges facing rare variant analysis such as accounting for population structure, extremely unbalanced case-control design. We also review recent advances and challenges in rare variant analysis for familial sequencing data and for more complex phenotypes such as survival data. Finally, we discuss other potential directions for further methodology investigation.
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Affiliation(s)
- Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
| | - Brandon J. Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
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8
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Dattani S, Howard DM, Lewis CM, Sham PC. Clarifying the causes of consistent and inconsistent findings in genetics. Genet Epidemiol 2022; 46:372-389. [PMID: 35652173 PMCID: PMC9544854 DOI: 10.1002/gepi.22459] [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] [Received: 02/04/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022]
Abstract
As research in genetics has advanced, some findings have been unexpected or shown to be inconsistent between studies or datasets. The reasons these inconsistencies arise are complex. Results from genetic studies can be affected by various factors including statistical power, linkage disequilibrium, quality control, confounding and selection bias, as well as real differences from interactions and effect modifiers, which may be informative about the mechanisms of traits and disease. Statistical artefacts can manifest as differences between results but they can also conceal underlying differences, which implies that their critical examination is important for understanding the underpinnings of traits. In this review, we examine these factors and outline how they can be identified and conceptualised with structural causal models. We explain the consequences they have on genetic estimates, such as genetic associations, polygenic scores, family‐ and genome‐wide heritability, and describe methods to address them to aid in the estimation of true effects of genetic variation. Clarifying these factors can help researchers anticipate when results are likely to diverge and aid researchers' understanding of causal relationships between genes and complex traits.
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Affiliation(s)
- Saloni Dattani
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Psychiatry, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - David M Howard
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Cathryn M Lewis
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Pak C Sham
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, and Centre for Panoromic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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