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McGuire D, Markus H, Yang L, Xu J, Montgomery A, Berg A, Li Q, Carrel L, Liu DJ, Jiang B. Dissecting heritability, environmental risk, and air pollution causal effects using > 50 million individuals in MarketScan. Nat Commun 2024; 15:5357. [PMID: 38918381 PMCID: PMC11199552 DOI: 10.1038/s41467-024-49566-6] [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: 09/09/2021] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Large national-level electronic health record (EHR) datasets offer new opportunities for disentangling the role of genes and environment through deep phenotype information and approximate pedigree structures. Here we use the approximate geographical locations of patients as a proxy for spatially correlated community-level environmental risk factors. We develop a spatial mixed linear effect (SMILE) model that incorporates both genetics and environmental contribution. We extract EHR and geographical locations from 257,620 nuclear families and compile 1083 disease outcome measurements from the MarketScan dataset. We augment the EHR with publicly available environmental data, including levels of particulate matter 2.5 (PM2.5), nitrogen dioxide (NO2), climate, and sociodemographic data. We refine the estimates of genetic heritability and quantify community-level environmental contributions. We also use wind speed and direction as instrumental variables to assess the causal effects of air pollution. In total, we find PM2.5 or NO2 have statistically significant causal effects on 135 diseases, including respiratory, musculoskeletal, digestive, metabolic, and sleep disorders, where PM2.5 and NO2 tend to affect biologically distinct disease categories. These analyses showcase several robust strategies for jointly modeling genetic and environmental effects on disease risk using large EHR datasets and will benefit upcoming biobank studies in the era of precision medicine.
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Affiliation(s)
- Daniel McGuire
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Havell Markus
- MD/PhD Program, Penn State College of Medicine of Medicine, Hershey, PA, 17033, USA
- Bioinformatics and Genomics PhD Program, Penn State College of Medicine, Hershey, PA, 17033, USA
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Jingyu Xu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Austin Montgomery
- MD/PhD Program, Penn State College of Medicine of Medicine, Hershey, PA, 17033, USA
| | - Arthur Berg
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Qunhua Li
- Department of Statistics, Penn State University, University Park, PA, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA.
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA.
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2
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Jensen MR, Jelsig AM, Gerdes AM, Hölmich LR, Kainu KH, Lorentzen HF, Hansen MH, Bak M, Johansson PA, Hayward NK, Van Overeem Hansen T, Wadt KA. TINF2 is a major susceptibility gene in Danish patients with multiple primary melanoma. HGG ADVANCES 2023; 4:100225. [PMID: 37646013 PMCID: PMC10461021 DOI: 10.1016/j.xhgg.2023.100225] [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: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 09/01/2023] Open
Abstract
TINF2 encodes the TINF2 protein, which is a subunit in the shelterin complex critical for telomere regulation. Three recent studies have associated six truncating germline variants in TINF2 that have previously been associated with a cancer predisposition syndrome (CPS) caused by elongation of the telomeres. This has added TINF2 to the long telomere syndrome genes, together with other telomere maintenance genes such as ACD, POT1, TERF2IP, and TERT. We report a clinical study of 102 Danish patients with multiple primary melanoma (MPM) in which a germline truncating variant in TINF2 (p.(Arg265Ter)) was identified in four unrelated participants. The telomere lengths of three variant carriers were >90% percentile. In a routine diagnostic setting, the variant was identified in two more families, including an additional MPM patient and monozygotic twins with thyroid cancer and other cancer types. A total of 10 individuals from six independent families were confirmed carriers, all with cancer history, predominantly melanoma. Our findings suggest a major role of TINF2 in Danish patients with MPM. In addition to melanoma, other cancers in the six families include thyroid, renal, breast, and sarcoma, supporting a CPS in which melanoma, thyroid cancer, and sarcoma predominate. Further studies are needed to establish the full spectrum of associated cancer types and characterize lifetime cancer risk in carriers.
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Affiliation(s)
- Marlene Richter Jensen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne Marie Jelsig
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisbet Rosenkrantz Hölmich
- Department of Plastic and Reconstructive Surgery, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kati Hannele Kainu
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Dermatology and Allergology, Herlev and Gentofte Hospital, 2900 Gentofte, Denmark
| | | | | | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | - Thomas Van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin A.W. Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Whole exome sequencing of 28 families of Danish descent reveals novel candidate genes and pathways in developmental dysplasia of the hip. Mol Genet Genomics 2023; 298:329-342. [PMID: 36454308 PMCID: PMC9938029 DOI: 10.1007/s00438-022-01980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022]
Abstract
Developmental dysplasia of the hip (DDH) is a common condition involving instability of the hip with multifactorial etiology. Early diagnosis and treatment are critical as undetected DDH is an important cause of long-term hip complications. Better diagnostics may be achieved through genetic methods, especially for patients with positive family history. Several candidate genes have been reported but the exact molecular etiology of the disease is yet unknown. In the present study, we performed whole exome sequencing of DDH patients from 28 families with at least two affected first-degree relatives. Four genes previously not associated with DDH (METTL21B, DIS3L2, PPP6R2, and TM4SF19) were identified with the same variants shared among affected family members, in more than two families. Among known association genes, we found damaging variants in DACH1, MYH10, NOTCH2, TBX4, EVC2, OTOG, and SHC3. Mutational burden analysis across the families identified 322 candidate genes, and enriched pathways include the extracellular matrix, cytoskeleton, ion-binding, and detection of mechanical stimulus. Taken altogether, our data suggest a polygenic mode of inheritance for DDH, and we propose that an impaired transduction of the mechanical stimulus is involved in the etiopathological mechanism. Our findings refine our current understanding of candidate causal genes in DDH, and provide a foundation for downstream functional studies.
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Disease Status at Diagnosis in Danish Children with α 1 -antitrypsin Deficiency. J Pediatr Gastroenterol Nutr 2022; 75:629-634. [PMID: 36070551 DOI: 10.1097/mpg.0000000000003604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES The aim of this cross-sectional study was to assess the state of disease at the time of diagnosis in Danish children with α 1 -antitrypsin deficiency as Denmark has a high prevalence of ZZ-homozygosity. METHODS Children either heterozygous, compound heterozygous, or homozygous for Z- and S-variants in the SERPINA1 -gene were included. Clinical characteristics, SERPINA1 -genotype, and blood serum (S) concentrations were recorded concurrently with genetic testing. Serum liver marker concentrations were compared using T tests and Wilcoxon-Mann-Whitney tests. Generalized estimating equation (GEE) linear regression models, both univariable and multivariable adjusted for age and sex, were applied to identify correlations with serum α 1 -antitrypsin (S-AAT). The relationship between S-AAT concentration and genotype was assessed using logistic regression with GEE. RESULTS The study included 183 of 225 children genetically tested for alpha-1-antitrypsin deficiency (AATD). Of these, 36.6% were homozygous for the Z-variant. Of the heterozygotes, 89.7% had a ZM genotype and the remaining had either an MS genotype or were compound heterozygous. At diagnosis, ZZ-homozygous children had higher serum concentrations of liver enzymes and conjugated bilirubin, but lower concentrations of S-AAT compared with heterozygotes. Serum concentrations of conjugated bilirubin and liver enzymes were negatively associated with S-AAT. Children under 6 months of age had higher total S-bilirubin concentrations than children over 6 months of age. CONCLUSIONS A low S-AAT concentration is a strong indicator of homozygosity, and homozygous children have higher enzymatic and cholestatic parameters compared with heterozygous children at diagnosis. This underlines the importance of measuring the S-AAT concentration in children with prolonged neonatal jaundice.
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Dornbos P, Koesterer R, Ruttenburg A, Nguyen T, Cole JB, Leong A, Meigs JB, Florez JC, Rotter JI, Udler MS, Flannick J. A combined polygenic score of 21,293 rare and 22 common variants improves diabetes diagnosis based on hemoglobin A1C levels. Nat Genet 2022; 54:1609-1614. [PMID: 36280733 PMCID: PMC9995082 DOI: 10.1038/s41588-022-01200-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Polygenic scores (PGSs) combine the effects of common genetic variants1,2 to predict risk or treatment strategies for complex diseases3-7. Adding rare variation to PGSs has largely unknown benefits and is methodically challenging. Here, we developed a method for constructing rare variant PGSs and applied it to calculate genetically modified hemoglobin A1C thresholds for type 2 diabetes (T2D) diagnosis7-10. The resultant rare variant PGS is highly polygenic (21,293 variants across 154 genes), depends on ultra-rare variants (72.7% observed in fewer than three people) and identifies significantly more undiagnosed T2D cases than expected by chance (odds ratio = 2.71; P = 1.51 × 10-6). A PGS combining common and rare variants is expected to identify 4.9 million misdiagnosed T2D cases in the United States-nearly 1.5-fold more than the common variant PGS alone. These results provide a method for constructing complex trait PGSs from rare variants and suggest that rare variants will augment common variants in precision medicine approaches for common disease.
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Affiliation(s)
- Peter Dornbos
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ryan Koesterer
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Andrew Ruttenburg
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Trang Nguyen
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Joanne B Cole
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron Leong
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Miriam S Udler
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA.
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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6
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Deaton AM, Dubey A, Ward LD, Dornbos P, Flannick J, Yee E, Ticau S, Noetzli L, Parker MM, Hoffing RA, Willis C, Plekan ME, Holleman AM, Hinkle G, Fitzgerald K, Vaishnaw AK, Nioi P. Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity. Nat Commun 2022; 13:4319. [PMID: 35896531 PMCID: PMC9329324 DOI: 10.1038/s41467-022-31757-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/01/2022] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI (WHRadjBMI), a surrogate for abdominal fat that is causally linked to type 2 diabetes and coronary heart disease. Predicted loss of function (pLOF) variants in INHBE associate with lower WHRadjBMI and this association replicates in data from AMP-T2D-GENES. INHBE encodes a secreted protein, the hepatokine activin E. In vitro characterization of the most common INHBE pLOF variant in our study, indicates an in-frame deletion resulting in a 90% reduction in secreted protein levels. We detect associations with lower WHRadjBMI for variants in ACVR1C, encoding an activin receptor, further highlighting the involvement of activins in regulating fat distribution. These findings highlight activin E as a potential therapeutic target for abdominal obesity, a phenotype linked to cardiometabolic disease.
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Affiliation(s)
| | | | | | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Elaine Yee
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Paul Nioi
- Alnylam Pharmaceuticals, Cambridge, MA, USA
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7
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Sørensen AT, Rombach J, Gether U, Madsen KL. The Scaffold Protein PICK1 as a Target in Chronic Pain. Cells 2022; 11:cells11081255. [PMID: 35455935 PMCID: PMC9031029 DOI: 10.3390/cells11081255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Well-tolerated and effective drugs for treating chronic pain conditions are urgently needed. Most chronic pain patients are not effectively relieved from their pain and suffer from debilitating drug side effects. This has not only drastic negative consequences for the patients’ quality of life, but also constitute an enormous burden on society. It is therefore of great interest to explore new potent targets for effective pain treatment with fewer side effects and without addiction liability. A critical component of chronic pain conditions is central sensitization, which involves the reorganization and strengthening of synaptic transmission within nociceptive pathways. Such changes are considered as maladaptive and depend on changes in the surface expression and signaling of AMPA-type glutamate receptors (AMPARs). The PDZ-domain scaffold protein PICK1 binds the AMPARs and has been suggested to play a key role in these maladaptive changes. In the present paper, we review the regulation of AMPARs by PICK1 and its relation to pain pathology. Moreover, we highlight other pain-relevant PICK1 interactions, and we evaluate various compounds that target PICK1 and have been successfully tested in pain models. Finally, we evaluate the potential on-target side effects of interfering with the action of PICK1 action in CNS and beyond. We conclude that PICK1 constitutes a valid drug target for the treatment of inflammatory and neuropathic pain conditions without the side effects and abuse liability associated with current pain medication.
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Vad OB, Yan Y, Denti F, Ahlberg G, Refsgaard L, Bomholtz SH, Santos JL, Rasmussen S, Haunsø S, Svendsen JH, Christophersen IE, Schmitt N, Olesen MS, Bentzen BH. Whole-Exome Sequencing Implicates Neuronal Calcium Channel with Familial Atrial Fibrillation. Front Genet 2022; 13:806429. [PMID: 35154276 PMCID: PMC8832975 DOI: 10.3389/fgene.2022.806429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atrial Fibrillation (AF) is the most prevalent sustained cardiac arrhythmia, responsible for considerable morbidity and mortality. The heterogenic and complex pathogenesis of AF remains poorly understood, which contributes to the current limitation in effective treatments. We aimed to identify rare genetic variants associated with AF in patients with familial AF. Methods and results: We performed whole exome sequencing in a large family with familial AF and identified a rare variant in the gene CACNA1A c.5053G > A which co-segregated with AF. The gene encodes for the protein variants CaV2.1-V1686M, and is important in neuronal function. Functional characterization of the CACNA1A, using patch-clamp recordings on transiently transfected mammalian cells, revealed a modest loss-of-function of CaV2.1-V1686M. Conclusion: We identified a rare loss-of-function variant associated with AF in a gene previously linked with neuronal function. The results allude to a novel link between dysfunction of an ion channel previously associated with neuronal functions and increased risk of developing AF.
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Affiliation(s)
- Oliver Bundgaard Vad
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Yannan Yan
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Federico Denti
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lena Refsgaard
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sofia Hammami Bomholtz
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joana Larupa Santos
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Disease Systems Biology Program, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesper Hastrup Svendsen
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Elizabeth Christophersen
- The Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway
| | - Nicole Schmitt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Salling Olesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- *Correspondence: Morten Salling Olesen,
| | - Bo Hjorth Bentzen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Andersen RC, Schmidt JH, Rombach J, Lycas MD, Christensen NR, Lund VK, Stapleton DS, Pedersen SS, Olsen MA, Stoklund M, Noes-Holt G, Nielsen TT, Keller MP, Jansen AM, Herlo R, Pietropaolo M, Simonsen JB, Kjærulff O, Holst B, Attie AD, Gether U, Madsen KL. Coding variants identified in diabetic patients alter PICK1 BAR domain function in insulin granule biogenesis. J Clin Invest 2022; 132:144904. [PMID: 35077398 PMCID: PMC8884907 DOI: 10.1172/jci144904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Bin/amphiphysin/Rvs (BAR) domains are positively charged crescent-shaped modules that mediate curvature of negatively charged lipid membranes during remodeling processes. The BAR domain proteins PICK1, ICA69, and the arfaptins have recently been demonstrated to coordinate the budding and formation of immature secretory granules (ISGs) at the trans-Golgi network. Here, we identify 4 coding variants in the PICK1 gene from a whole-exome screening of Danish patients with diabetes that each involve a change in positively charged residues in the PICK1 BAR domain. All 4 coding variants failed to rescue insulin content in INS-1E cells upon knock down of endogenous PICK1. Moreover, 2 variants showed dominant-negative properties. In vitro assays addressing BAR domain function suggested that the coding variants compromised BAR domain function but increased the capacity to cause fission of liposomes. Live confocal microscopy and super-resolution microscopy further revealed that PICK1 resides transiently on ISGs before egress via vesicular budding events. Interestingly, this egress of PICK1 was accelerated in the coding variants. We propose that PICK1 assists in or complements the removal of excess membrane and generic membrane trafficking proteins, and possibly also insulin, from ISGs during the maturation process; and that the coding variants may cause premature budding, possibly explaining their dominant-negative function.
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Affiliation(s)
- Rita C. Andersen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan H. Schmidt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joscha Rombach
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Lycas
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaj R. Christensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor K. Lund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Signe S. Pedersen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias A. Olsen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Stoklund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gith Noes-Holt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tommas T.E. Nielsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Anna M. Jansen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Herlo
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Massimo Pietropaolo
- Diabetes Research Center, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jens B. Simonsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Kjærulff
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L. Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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10
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Møller Nielsen AK, Nyboe C, Lund Ovesen AS, Udholm S, Larsen MM, Hjortdal VE, Larsen LA. Mutation burden in patients with small unrepaired atrial septal defects. INTERNATIONAL JOURNAL OF CARDIOLOGY CONGENITAL HEART DISEASE 2021. [DOI: 10.1016/j.ijcchd.2021.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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11
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Sveidahl Johansen O, Ma T, Hansen JB, Markussen LK, Schreiber R, Reverte-Salisa L, Dong H, Christensen DP, Sun W, Gnad T, Karavaeva I, Nielsen TS, Kooijman S, Cero C, Dmytriyeva O, Shen Y, Razzoli M, O'Brien SL, Kuipers EN, Nielsen CH, Orchard W, Willemsen N, Jespersen NZ, Lundh M, Sustarsic EG, Hallgren CM, Frost M, McGonigle S, Isidor MS, Broholm C, Pedersen O, Hansen JB, Grarup N, Hansen T, Kjær A, Granneman JG, Babu MM, Calebiro D, Nielsen S, Rydén M, Soccio R, Rensen PCN, Treebak JT, Schwartz TW, Emanuelli B, Bartolomucci A, Pfeifer A, Zechner R, Scheele C, Mandrup S, Gerhart-Hines Z. Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis. Cell 2021; 184:3502-3518.e33. [PMID: 34048700 PMCID: PMC8238500 DOI: 10.1016/j.cell.2021.04.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Thermogenic adipocytes possess a therapeutically appealing, energy-expending capacity, which is canonically cold-induced by ligand-dependent activation of β-adrenergic G protein-coupled receptors (GPCRs). Here, we uncover an alternate paradigm of GPCR-mediated adipose thermogenesis through the constitutively active receptor, GPR3. We show that the N terminus of GPR3 confers intrinsic signaling activity, resulting in continuous Gs-coupling and cAMP production without an exogenous ligand. Thus, transcriptional induction of Gpr3 represents the regulatory parallel to ligand-binding of conventional GPCRs. Consequently, increasing Gpr3 expression in thermogenic adipocytes is alone sufficient to drive energy expenditure and counteract metabolic disease in mice. Gpr3 transcription is cold-stimulated by a lipolytic signal, and dietary fat potentiates GPR3-dependent thermogenesis to amplify the response to caloric excess. Moreover, we find GPR3 to be an essential, adrenergic-independent regulator of human brown adipocytes. Taken together, our findings reveal a noncanonical mechanism of GPCR control and thermogenic activation through the lipolysis-induced expression of constitutively active GPR3.
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Affiliation(s)
- Olivia Sveidahl Johansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark; Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Jakob Bondo Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Lasse Kruse Markussen
- Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark; Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Renate Schreiber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Laia Reverte-Salisa
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Thorsten Gnad
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Iuliia Karavaeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Svava Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sander Kooijman
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Cheryl Cero
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Oksana Dmytriyeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Yachen Shen
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Maria Razzoli
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Birmingham, UK; Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, Würzburg, Germany
| | - Eline N Kuipers
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Carsten Haagen Nielsen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet, Copenhagen, Denmark
| | | | - Nienke Willemsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Naja Zenius Jespersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Morten Lundh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Elahu Gosney Sustarsic
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Mørch Hallgren
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Frost
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Seth McGonigle
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Marie Sophie Isidor
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Christa Broholm
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Bo Hansen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Kjær
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet, Copenhagen, Denmark
| | - James G Granneman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Birmingham, UK; Institute of Pharmacology and Toxicology and Bio-Imaging Center, University of Würzburg, Würzburg, Germany
| | - Søren Nielsen
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Raymond Soccio
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonas Thue Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thue Walter Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark
| | - Brice Emanuelli
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Camilla Scheele
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Mandrup
- Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark; Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Embark Biotech ApS, Copenhagen, Denmark; Center for Adipocyte Signaling, University of Southern Denmark, Odense, Denmark.
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12
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Kaplinski L, Möls M, Puurand T, Pajuste FD, Remm M. KATK: Fast genotyping of rare variants directly from unmapped sequencing reads. Hum Mutat 2021; 42:777-786. [PMID: 33715282 DOI: 10.1002/humu.24197] [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: 01/14/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/06/2022]
Abstract
KATK is a fast and accurate software tool for calling variants directly from raw next-generation sequencing reads. It uses predefined k-mers to retrieve only the reads of interest from the FASTQ file and calls genotypes by aligning retrieved reads locally. KATK does not use data about known polymorphisms and has NC (no call) as the default genotype. The reference or variant allele is called only if there is sufficient evidence for their presence in data. Thus it is not biased against rare variants or de-novo mutations. With simulated datasets, we achieved a false-negative rate of 0.23% (sensitivity 99.77%) and a false discovery rate of 0.19%. Calling all human exonic regions with KATK requires 1-2 h, depending on sequencing coverage.
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Affiliation(s)
- Lauris Kaplinski
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Märt Möls
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tarmo Puurand
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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13
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PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice. Sci Rep 2021; 11:6072. [PMID: 33727568 PMCID: PMC7966789 DOI: 10.1038/s41598-021-84919-x] [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: 04/10/2020] [Accepted: 02/04/2021] [Indexed: 11/29/2022] Open
Abstract
Recently, several genome-wide association studies identified PHACTR1 as key locus for five diverse vascular disorders: coronary artery disease, migraine, fibromuscular dysplasia, cervical artery dissection and hypertension. Although these represent significant risk factors or comorbidities for ischemic stroke, PHACTR1 role in brain small vessel ischemic disease and ischemic stroke most important survival mechanism, such as the recruitment of brain collateral arteries like posterior communicating arteries (PcomAs), remains unknown. Therefore, we applied exome and genome sequencing in a multi-ethnic cohort of 180 early-onset independent familial and apparently sporadic brain small vessel ischemic disease and CADASIL-like Caucasian patients from US, Portugal, Finland, Serbia and Turkey and in 2 C57BL/6J stroke mouse models (bilateral common carotid artery stenosis [BCCAS] and middle cerebral artery occlusion [MCAO]), characterized by different degrees of PcomAs patency. We report 3 very rare coding variants in the small vessel ischemic disease-CADASIL-like cohort (p.Glu198Gln, p.Arg204Gly, p.Val251Leu) and a stop-gain mutation (p.Gln273*) in one MCAO mouse. These coding variants do not cluster in PHACTR1 known pathogenic domains and are not likely to play a critical role in small vessel ischemic disease or brain collateral circulation. We also exclude the possibility that copy number variants (CNVs) or a variant enrichment in Phactr1 may be associated with PcomA recruitment in BCCAS mice or linked to diverse vascular traits (cerebral blood flow pre-surgery, PcomA size, leptomeningeal microcollateral length and junction density during brain hypoperfusion) in C57BL/6J mice, respectively. Genetic variability in PHACTR1 is not likely to be a common susceptibility factor influencing small vessel ischemic disease in patients and PcomA recruitment in C57BL/6J mice. Nonetheless, rare variants in PHACTR1 RPEL domains may influence the stroke outcome and are worth investigating in a larger cohort of small vessel ischemic disease patients, different ischemic stroke subtypes and with functional studies.
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14
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Clinical genetic diagnostics in Danish autosomal dominant polycystic kidney disease patients reveal possible founder variants. Eur J Med Genet 2021; 64:104183. [PMID: 33639313 DOI: 10.1016/j.ejmg.2021.104183] [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] [Received: 09/10/2020] [Revised: 01/04/2021] [Accepted: 02/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common heritable kidney disease. ADPKD leads to cysts, kidney enlargement and end-stage renal disease. ADPKD is mainly caused by variants in PKD1 and PKD2, with truncating PKD1 variants causing the most severe phenotype. This study aimed to characterize variants in Danish patients referred for screening of genes related to cystic kidney disease. METHODS 147 families were analysed for variants in PKD1, PKD2 and GANAB using next generation sequencing and multiplex ligation-dependent probe amplification. If a variant was identified, relatives were analysed for the specific variant using Sanger sequencing. RESULTS A pathogenic or possibly pathogenic variant was identified in 87% (103/118) of patients suspected to suffer from ADPKD, according to the requisition form. In total, 112 pathogenic or possibly pathogenic variants were observed, of which 94 were unique; 74 (79%) in PKD1 and 20 (21%) in PKD2, while 41 variants were novel. No variants in GANAB were observed. Ten recurrent variants were observed in 26 (26%) families. These were either PKD2 variants (N = 6) or non-truncating PKD1 variants (N = 4). Five of these were likely founder variants. CONCLUSIONS The distribution of pathogenic or possibly pathogenic variants in the Danish ADPKD population is similar to that in other populations, except that recurrent truncating PKD1 variants appear to be rare, i.e. founder variants tend to be variant types associated with a mild phenotype. Patients with a mild phenotype may remain undiagnosed, consequently the frequency of founder variants and prevalence of ADPKD may be underestimated.
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15
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Zarrizi R, Higgs MR, Voßgröne K, Rossing M, Bertelsen B, Bose M, Kousholt AN, Rösner H, Network TC, Ejlertsen B, Stewart GS, Nielsen FC, Sørensen CS. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability. J Clin Invest 2021; 130:4069-4080. [PMID: 32379725 DOI: 10.1172/jci127521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Haploinsufficiency of factors governing genome stability underlies hereditary breast and ovarian cancer. One significant pathway that is disabled as a result is homologous recombination repair (HRR). With the aim of identifying new candidate genes, we examined early-onset breast cancer patients negative for BRCA1 and BRCA2 pathogenic variants. Here, we focused on CtIP (RBBP8 gene), which mediates HRR through the end resection of DNA double-strand breaks (DSBs). Notably, these patients exhibited a number of rare germline RBBP8 variants. Functional analysis revealed that these variants did not affect DNA DSB end resection efficiency. However, expression of a subset of variants led to deleterious nucleolytic degradation of stalled DNA replication forks in a manner similar to that of cells lacking BRCA1 or BRCA2. In contrast to BRCA1 and BRCA2, CtIP deficiency promoted the helicase-driven destabilization of RAD51 nucleofilaments at damaged DNA replication forks. Taken together, our work identifies CtIP as a critical regulator of DNA replication fork integrity, which, when compromised, may predispose to the development of early-onset breast cancer.
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Affiliation(s)
- Reihaneh Zarrizi
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Karolin Voßgröne
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Muthiah Bose
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Heike Rösner
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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16
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Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease. Genome Med 2020; 12:76. [PMID: 32859249 PMCID: PMC7453558 DOI: 10.1186/s13073-020-00772-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD. METHODS We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model. RESULTS We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2, and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes. CONCLUSIONS The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.
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17
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A rare missense variant in APC interrupts splicing and causes AFAP in two Danish families. Hered Cancer Clin Pract 2020; 18:8. [PMID: 32292534 PMCID: PMC7140378 DOI: 10.1186/s13053-020-00140-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/11/2020] [Indexed: 11/30/2022] Open
Abstract
Background We report the first case of a missense variant in the APC gene that interrupts splicing by creating a new cryptic acceptor site. The variant, c.289G>A, p.(Gly97Arg), is located in exon 3, and qualitative and semi-quantitative RNA splicing analysis reveal that the variant results in skipping of the last 70 nucleotides of the exon, which leads to the introduction of a frameshift and a premature stop codon. Case presentation The variant was detected in two, apparently unrelated, Danish families with an accumulation of colorectal cancers, colonic adenomas and other cancers. The families both have an attenuated familial adenomatous polyposis phenotype, which is consistent with the association of pathogenic variants in the 5′ end of the gene. One variant-carrier also had Caroli Disease and a Caroli Disease associated hepatic mucinous cystadenocarcinoma. This is the first description of a person with both Caroli Disease and a pathogenic APC variant, and although the APC variant is not known to be connected to the development of the hepatic malformations in Caroli Disease, it remains unclear whether the variant could have contributed to the carcinogenesis of the liver tumour. Conclusions Based on functional and co-segregation data we classify the APC c.289G>A, p.(Gly97Arg) variant as pathogenic (class 5). Our findings emphasize the importance of a functional evaluation of missense variants although located far from the exon-intron boundaries.
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18
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Hansen L, Husein DM, Gericke B, Hansen T, Pedersen O, Tambe MA, Freeze HH, Naim HY, Henrissat B, Wandall HH, Clausen H, Bennett EP. A mutation map for human glycoside hydrolase genes. Glycobiology 2020; 30:500-515. [PMID: 32039448 DOI: 10.1093/glycob/cwaa010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolases (GHs) are found in all domains of life, and at least 87 distinct genes encoding proteins related to GHs are found in the human genome. GHs serve diverse functions from digestion of dietary polysaccharides to breakdown of intracellular oligosaccharides, glycoproteins, proteoglycans and glycolipids. Congenital disorders of GHs (CDGHs) represent more than 30 rare diseases caused by mutations in one of the GH genes. We previously used whole-exome sequencing of a homogenous Danish population of almost 2000 individuals to probe the incidence of deleterious mutations in the human glycosyltransferases (GTs) and developed a mutation map of human GT genes (GlyMAP-I). While deleterious disease-causing mutations in the GT genes were very rare, and in many cases lethal, we predicted deleterious mutations in GH genes to be less rare and less severe given the higher incidence of CDGHs reported worldwide. To probe the incidence of GH mutations, we constructed a mutation map of human GH-related genes (GlyMAP-II) using the Danish WES data, and correlating this with reported disease-causing mutations confirmed the higher prevalence of disease-causing mutations in several GH genes compared to GT genes. We identified 76 novel nonsynonymous single-nucleotide variations (nsSNVs) in 32 GH genes that have not been associated with a CDGH phenotype, and we experimentally validated two novel potentially damaging nsSNVs in the congenital sucrase-isomaltase deficiency gene, SI. Our study provides a global view of human GH genes and disease-causing mutations and serves as a discovery tool for novel damaging nsSNVs in CDGHs.
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Affiliation(s)
- Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Diab M Husein
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Bünteweg 2, 30559 Hannover, Germany
| | - Birthe Gericke
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Bünteweg 2, 30559 Hannover, Germany
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Mitali A Tambe
- Human Genetics Program, Sanford-Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford-Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hassan Y Naim
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Bünteweg 2, 30559 Hannover, Germany
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS) and Aix-Marseille University Marseille, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Mærsk Building, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.,School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Nørre Allé 20, DK-2200 Copenhagen N, Denmark
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19
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Hansen TH, Yan Y, Ahlberg G, Vad OB, Refsgaard L, Dos Santos JL, Mutsaers N, Svendsen JH, Olesen MS, Bentzen BH, Schmitt N. A Novel Loss-of-Function Variant in the Chloride Ion Channel Gene Clcn2 Associates with Atrial Fibrillation. Sci Rep 2020; 10:1453. [PMID: 31996765 PMCID: PMC6989500 DOI: 10.1038/s41598-020-58475-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/15/2020] [Indexed: 11/09/2022] Open
Abstract
Atrial Fibrillation (AF) is the most common cardiac arrhythmia. Its pathogenesis is complex and poorly understood. Whole exome sequencing of Danish families with AF revealed a novel four nucleotide deletion c.1041_1044del in CLCN2 shared by affected individuals. We aimed to investigate the role of genetic variation of CLCN2 encoding the inwardly rectifying chloride channel ClC-2 as a risk factor for the development of familiar AF. The effect of the CLCN2 variant was evaluated by electrophysiological recordings on transiently transfected cells. We used quantitative PCR to assess CLCN2 mRNA expression levels in human atrial and ventricular tissue samples. The nucleotide deletion CLCN2 c.1041_1044del results in a frame-shift and premature stop codon. The truncated ClC-2 p.V347fs channel does not conduct current. Co-expression with wild-type ClC-2, imitating the heterozygote state of the patients, resulted in a 50% reduction in macroscopic current, suggesting an inability of truncated ClC-2 protein to form channel complexes with wild type channel subunits. Quantitative PCR experiments using human heart tissue from healthy donors demonstrated that CLCN2 is expressed across all four heart chambers. Our genetic and functional data points to a possible link between loss of ClC-2 function and an increased risk of developing AF.
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Affiliation(s)
- Thea Hyttel Hansen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,ALK-Abelló A/S, 2970, Hørsholm, Denmark
| | - Yannan Yan
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Oliver Bundgaard Vad
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lena Refsgaard
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joana Larupa Dos Santos
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nancy Mutsaers
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Hastrup Svendsen
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Salling Olesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bo Hjorth Bentzen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Schmitt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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20
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Espregueira Themudo G, Leerschool AR, Rodriguez-Proano C, Christiansen SL, Andersen JD, Busch JR, Christensen MR, Banner J, Morling N. Targeted exon sequencing in deceased schizophrenia patients in Denmark. Int J Legal Med 2019; 134:135-147. [PMID: 31773318 DOI: 10.1007/s00414-019-02212-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022]
Abstract
Schizophrenia patients have higher mortality rates and lower life expectancy than the general population. However, forensic investigations of their deaths often fail to determine the cause of death, hindering prevention. As schizophrenia is a highly heritable condition and given recent advances in our understanding of the genetics of schizophrenia, it is now possible to investigate how genetic factors may contribute to mortality. We made use of findings from genome-wide association studies (GWAS) to design a targeted panel (PsychPlex) for sequencing of exons of 451 genes near index single nucleotide polymorphisms (SNPs) identified with GWAS. We sequenced the DNA of 95 deceased schizophrenia patients included in SURVIVE, a prospective, autopsy-based study of mentally ill persons in Denmark. We compared the allele frequencies of 1039 SNPs in these cases with the frequencies of 2000 Danes without psychiatric diseases and calculated their deleteriousness (CADD) scores. For 81 SNPs highly associated with schizophrenia and CADD scores above 15, expression profiles in the Genotype-Tissue Expression (GTEx) Project indicated that these variants were in exons, whose expressions are increased in several types of brain tissues, particularly in the cerebellum. Molecular pathway analysis indicated the involvement of 163 different pathways. As for rare SNP variants, most variants were scored as either benign or likely benign with an average of 17 variants of unknown significance per individual and no pathogenic variant. Our results highlight the potential of DNA sequencing of an exon panel to discover genetic factors that may be involved in the development of schizophrenia.
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Affiliation(s)
- Gonçalo Espregueira Themudo
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Anna-Roos Leerschool
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Complex Genetics, Maastricht University, PO Box 616 6200, MD, Maastricht, The Netherlands
| | - Carla Rodriguez-Proano
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Clinical Laboratory, Ambulatory Clinical Surgical Center and Day Hospital "El Batán", Quito, Ecuador
| | - Sofie Lindgren Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johannes Rødbro Busch
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Roest Christensen
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jytte Banner
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Paludan-Müller C, Ghouse J, Vad OB, Herfelt CB, Lundegaard P, Ahlberg G, Schmitt N, Svendsen JH, Haunsø S, Bundgaard H, Hansen T, Kanters JK, Olesen MS. Reappraisal of variants previously linked with sudden infant death syndrome: results from three population-based cohorts. Eur J Hum Genet 2019; 27:1427-1435. [PMID: 31043699 PMCID: PMC6777469 DOI: 10.1038/s41431-019-0416-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/21/2019] [Accepted: 04/06/2019] [Indexed: 12/23/2022] Open
Abstract
We aimed to investigate the pathogenicity of cardiac ion channel variants previously associated with SIDS. We reviewed SIDS-associated variants previously reported in databases and the literature in three large population-based cohorts; The ExAC database, the Inter99 study, and the UK Biobank (UKBB). Variants were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Of the 92 SIDS-associated variants, 59 (64%) were present in ExAC, 18 (20%) in Inter99, and 24 (26%) in UKBB. Using the Inter99 cohort, we found no difference in J-point amplitude and QTc-interval between carriers and non-carriers for 14/18 variants. There was no difference in the risk of syncope (P = 0.32), malignant ventricular arrhythmia (P = 0.96), and all-cause mortality (P = 0.59) between carriers and non-carriers. The ACMG guidelines reclassified 75% of all variants as variant-of-uncertain significance, likely benign, and benign. We identified ~2/3 of variants previously associated with SIDS and found no significant associations with electrocardiographic traits, syncope, malignant ventricular arrhythmia, or all-cause mortality. These data indicate that many of these variants are not highly penetrant, monogenic causes of SIDS and underline the importance of frequent reappraisal of genetic variants to avoid future misdiagnosis.
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Affiliation(s)
- Christian Paludan-Müller
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Ghouse
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oliver B Vad
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie B Herfelt
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pia Lundegaard
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Schmitt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper H Svendsen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Unit for Inherited Cardiac Diseases, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Herlev and Gentofte University Hospitals, Copenhagen, Denmark
| | - Morten S Olesen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Abstract
Genome-wide association studies have identified hundreds of genomic variants associated with human T2D risk, but translating such findings to clinically useful information has proved challenging. A new study in Nature (Flannick et al., 2019) breaks this gridlock, using direct exome sequencing to identify functional coding variants, providing critical complementary gene-level information.
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Affiliation(s)
- Laura C Alonso
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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23
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Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, Teslovich TM, Caulkins L, Koesterer R, Barajas-Olmos F, Blackwell TW, Boerwinkle E, Brody JA, Centeno-Cruz F, Chen L, Chen S, Contreras-Cubas C, Córdova E, Correa A, Cortes M, DeFronzo RA, Dolan L, Drews KL, Elliott A, Floyd JS, Gabriel S, Garay-Sevilla ME, García-Ortiz H, Gross M, Han S, Heard-Costa NL, Jackson AU, Jørgensen ME, Kang HM, Kelsey M, Kim BJ, Koistinen HA, Kuusisto J, Leader JB, Linneberg A, Liu CT, Liu J, Lyssenko V, Manning AK, Marcketta A, Malacara-Hernandez JM, Martínez-Hernández A, Matsuo K, Mayer-Davis E, Mendoza-Caamal E, Mohlke KL, Morrison AC, Ndungu A, Ng MCY, O'Dushlaine C, Payne AJ, Pihoker C, Post WS, Preuss M, Psaty BM, Vasan RS, Rayner NW, Reiner AP, Revilla-Monsalve C, Robertson NR, Santoro N, Schurmann C, So WY, Soberón X, Stringham HM, Strom TM, Tam CHT, Thameem F, Tomlinson B, Torres JM, Tracy RP, van Dam RM, Vujkovic M, Wang S, Welch RP, Witte DR, Wong TY, Atzmon G, Barzilai N, Blangero J, Bonnycastle LL, Bowden DW, Chambers JC, Chan E, Cheng CY, Cho YS, Collins FS, de Vries PS, Duggirala R, Glaser B, Gonzalez C, Gonzalez ME, Groop L, Kooner JS, Kwak SH, Laakso M, Lehman DM, Nilsson P, Spector TD, Tai ES, Tuomi T, Tuomilehto J, Wilson JG, Aguilar-Salinas CA, Bottinger E, Burke B, Carey DJ, Chan JCN, Dupuis J, Frossard P, Heckbert SR, Hwang MY, Kim YJ, Kirchner HL, Lee JY, Lee J, Loos RJF, Ma RCW, Morris AD, O'Donnell CJ, Palmer CNA, Pankow J, Park KS, Rasheed A, Saleheen D, Sim X, Small KS, Teo YY, Haiman C, Hanis CL, Henderson BE, Orozco L, Tusié-Luna T, Dewey FE, Baras A, Gieger C, Meitinger T, Strauch K, Lange L, Grarup N, Hansen T, Pedersen O, Zeitler P, Dabelea D, Abecasis G, Bell GI, Cox NJ, Seielstad M, Sladek R, Meigs JB, Rich SS, Rotter JI, Altshuler D, Burtt NP, Scott LJ, Morris AP, Florez JC, McCarthy MI, Boehnke M. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature 2019; 570:71-76. [PMID: 31118516 PMCID: PMC6699738 DOI: 10.1038/s41586-019-1231-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 04/23/2019] [Indexed: 02/08/2023]
Abstract
Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.
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Affiliation(s)
- Jason Flannick
- Program in Metabolism, Broad Institute, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Josep M Mercader
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Miriam S Udler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA
- Diabetes Translational Research Center, Indiana University, Indianapolis, IN, USA
| | - Tanya M Teslovich
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Lizz Caulkins
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Ryan Koesterer
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ling Chen
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Siying Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Emilio Córdova
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Maria Cortes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph A DeFronzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lawrence Dolan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly L Drews
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Amanda Elliott
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James S Floyd
- Department of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Maria Eugenia Garay-Sevilla
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sohee Han
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Anne U Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Megan Kelsey
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Heikki A Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | | | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Juan Manuel Malacara-Hernandez
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Karen Matsuo
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Karen L Mohlke
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anne Ndungu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maggie C Y Ng
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Anthony J Payne
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Preuss
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Preventive Medicine & Epidemiology, Medicine, Boston University School of Medicine, Boston, MA, USA
| | - N William Rayner
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Neil R Robertson
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Santoro
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Claudia Schurmann
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Heather M Stringham
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Farook Thameem
- Health Science Center, Department of Biochemistry, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason M Torres
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Rob M van Dam
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Marijana Vujkovic
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan P Welch
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Faculty of Natural Science, University of Haifa, Haifa, Israel
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donald W Bowden
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clicerio Gonzalez
- Unidad de Diabetes y Riesgo Cardiovascular, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
| | - Jaspal Singh Kooner
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | - Donna M Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Peter Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Tiinamaija Tuomi
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Center for Vascular Prevention, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Instituto de Investigacion Sanitaria del Hospital Universario LaPaz (IdiPAZ), University Hospital LaPaz, Autonomous University of Madrid, Madrid, Spain
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Erwin Bottinger
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Brian Burke
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | | | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Josée Dupuis
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | | | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Jong-Young Lee
- Department of Business Data Convergence, Chungbuk National University, Gyeonggi-do, South Korea
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Ruth J F Loos
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
- The Mindich Child Health and Development Insititute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrew D Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Christopher J O'Donnell
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Section of Cardiology, Department of Medicine, VA Boston Healthcare, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Intramural Administration Management Branch, National Heart Lung and Blood Institute, NIH, Framingham, MA, USA
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - James Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Kyong Soo Park
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, Departamento de Medicina Genómica y Toxicología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Frederick E Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Deutsches Forschungszentrum für Herz-Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Neuherberg, Germany
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philip Zeitler
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Graeme I Bell
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Mark Seielstad
- Department of Laboratory Medicine & Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Quebec, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - James B Meigs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David Altshuler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Noël P Burtt
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Laura J Scott
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jose C Florez
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
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24
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Abstract
PURPOSE OF REVIEW Soon after the first genome-wide association study (GWAS) for type 2 diabetes (T2D) was published, it was hypothesized that rare and low-frequency variants might explain a substantial proportion of disease risk. Rare coding variants in particular were emphasized given their large expected role in disease. This review summarizes the extent to which recent T2D genetic studies provide evidence for or against this hypothesis. RECENT FINDINGS Following a comprehensive study of T2D genetic architecture using three sequencing and genotyping technologies, four even larger studies have provided a yet higher resolution view of the role of rare and low-frequency coding variation in T2D susceptibility. Empirical evidence strongly suggests that common regulatory variants are the dominant contributor to T2D heritability. However, rare coding variants may nonetheless be pervasive across T2D-relevant genes. A strategy using common variants to map disease genes, and rare coding variants to link molecular gene perturbations to cellular and phenotypic effects, may be an effective means to investigate T2D pathogenesis and potential new therapies.
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Affiliation(s)
- Jason Flannick
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- Programs in Medical and Population Genetics and Metabolism, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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25
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Vidal EA, Moyano TC, Bustos BI, Pérez-Palma E, Moraga C, Riveras E, Montecinos A, Azócar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nürnberg P, Buch S, Hampe J, Allende ML, Cambiazo V, González M, Hodar C, Montecino M, Muñoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 2019; 9:2132. [PMID: 30765821 PMCID: PMC6376018 DOI: 10.1038/s41598-019-39391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bernabé I Bustos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Pérez-Palma
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Carol Moraga
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eleodoro Riveras
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Montecinos
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azócar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela C Soto
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mabel Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Klaus Puschel
- Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stephan Buch
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Angélica Reyes-Jara
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Paula Vizoso
- FONDAP Center for Genome Regulation, Santiago, Chile.,Centro de Propagación y Conservación Vegetal (CEPROVEG), Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Mauricio Moraga
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Susana Eyheramendy
- Departmento de Estadística, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile.,Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile.
| | - Juan Francisco Miquel
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile. .,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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26
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Vaeth S, Christensen R, Dunø M, Lildballe DL, Thorsen K, Vissing J, Svenstrup K, Hertz JM, Andersen H, Jensen UB. Genetic analysis of Charcot-Marie-Tooth disease in Denmark and the implementation of a next generation sequencing platform. Eur J Med Genet 2019; 62:1-8. [DOI: 10.1016/j.ejmg.2018.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/27/2018] [Accepted: 04/10/2018] [Indexed: 12/17/2022]
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27
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A study of familial Char syndrome involving the TFAP2B gene with a focus on facial shape characteristics. Clin Dysmorphol 2018; 27:71-77. [PMID: 29683802 DOI: 10.1097/mcd.0000000000000222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this case study, we investigate a child presenting with patent ductus arteriosus, short philtrum, duck-bill lips, strabismus, a flat nasal bridge, a broad forehead, low-set ears, hypertelorism, up-slanting palpebral fissures, almond-shaped eyes, and hypodontia, all leading to the clinical diagnosis of Char syndrome. Genetic analysis showed heterozygosity for the novel variant c.851T>C, p. Leu284Ser in the TFAP2B gene. Family analysis suggested that at least 20 members, extending six generations back, were affected. All 10 members available for genetic testing were heterozygous for the novel pathogenic variant. Qualitative analysis of the facial dysmorphology in the proband and three of the affected family members using three-dimensional surface scanning showed that the major deviations were observed in the forehead/eyebrow, nose, upper lip, and chin regions with, for example, a flattened nose and reduced height of the upper lip and the face. Furthermore, it is suggested that Char syndrome is associated with disturbances of tooth formation and eruption.
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28
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Ahlberg G, Refsgaard L, Lundegaard PR, Andreasen L, Ranthe MF, Linscheid N, Nielsen JB, Melbye M, Haunsø S, Sajadieh A, Camp L, Olesen SP, Rasmussen S, Lundby A, Ellinor PT, Holst AG, Svendsen JH, Olesen MS. Rare truncating variants in the sarcomeric protein titin associate with familial and early-onset atrial fibrillation. Nat Commun 2018; 9:4316. [PMID: 30333491 PMCID: PMC6193003 DOI: 10.1038/s41467-018-06618-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
A family history of atrial fibrillation constitutes a substantial risk of developing the disease, however, the pathogenesis of this complex disease is poorly understood. We perform whole-exome sequencing on 24 families with at least three family members diagnosed with atrial fibrillation (AF) and find that titin-truncating variants (TTNtv) are significantly enriched in these patients (P = 1.76 × 10−6). This finding is replicated in an independent cohort of early-onset lone AF patients (n = 399; odds ratio = 36.8; P = 4.13 × 10−6). A CRISPR/Cas9 modified zebrafish carrying a truncating variant of titin is used to investigate TTNtv effect in atrial development. We observe compromised assembly of the sarcomere in both atria and ventricle, longer PR interval, and heterozygous adult zebrafish have a higher degree of fibrosis in the atria, indicating that TTNtv are important risk factors for AF. This aligns with the early onset of the disease and adds an important dimension to the understanding of the molecular predisposition for AF. Common genetic variants in structural proteins contribute to risk of atrial fibrillation (AF). Here, using whole-exome sequencing, the authors identify rare truncating variants in TTN that associate with familial and early-onset AF and show defects in cardiac sarcomere assembly in ttn.2-mutant zebrafish.
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Affiliation(s)
- Gustav Ahlberg
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Lena Refsgaard
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Pia R Lundegaard
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Laura Andreasen
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Mattis F Ranthe
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, 2300 S, Denmark
| | - Nora Linscheid
- Cardiac Proteomics Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Jonas B Nielsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, 2300 S, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark
| | - Ahmad Sajadieh
- Department of Cardiology, Copenhagen University Hospital, Bispebjerg, Copenhagen, 2400, Denmark
| | - Lu Camp
- The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, 2200 N, Denmark
| | - Søren-Peter Olesen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs, Lyngby, 2800, Denmark
| | - Alicia Lundby
- Cardiac Proteomics Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Patrick T Ellinor
- Cardiovascular Research Centre, Massachusetts General Hospital, Boston, 02114, MA, USA.,Program in Population and Medical Genetics, The Broad Institute of Harvard and MIT, Cambridge, 02114, MA, USA
| | - Anders G Holst
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark
| | - Jesper H Svendsen
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark
| | - Morten S Olesen
- Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, 2100 Ø, Denmark. .,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, 2200 N, Denmark.
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29
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Wojcik GL, Fuchsberger C, Taliun D, Welch R, Martin AR, Shringarpure S, Carlson CS, Abecasis G, Kang HM, Boehnke M, Bustamante CD, Gignoux CR, Kenny EE. Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies. G3 (BETHESDA, MD.) 2018; 8:3255-3267. [PMID: 30131328 PMCID: PMC6169386 DOI: 10.1534/g3.118.200502] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/03/2018] [Indexed: 01/26/2023]
Abstract
The emergence of very large cohorts in genomic research has facilitated a focus on genotype-imputation strategies to power rare variant association. These strategies have benefited from improvements in imputation methods and association tests, however little attention has been paid to ways in which array design can increase rare variant association power. Therefore, we developed a novel framework to select tag SNPs using the reference panel of 26 populations from Phase 3 of the 1000 Genomes Project. We evaluate tag SNP performance via mean imputed r2 at untyped sites using leave-one-out internal validation and standard imputation methods, rather than pairwise linkage disequilibrium. Moving beyond pairwise metrics allows us to account for haplotype diversity across the genome for improve imputation accuracy and demonstrates population-specific biases from pairwise estimates. We also examine array design strategies that contrast multi-ethnic cohorts vs. single populations, and show a boost in performance for the former can be obtained by prioritizing tag SNPs that contribute information across multiple populations simultaneously. Using our framework, we demonstrate increased imputation accuracy for rare variants (frequency < 1%) by 0.5-3.1% for an array of one million sites and 0.7-7.1% for an array of 500,000 sites, depending on the population. Finally, we show how recent explosive growth in non-African populations means tag SNPs capture on average 30% fewer other variants than in African populations. The unified framework presented here will enable investigators to make informed decisions for the design of new arrays, and help empower the next phase of rare variant association for global health.
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Affiliation(s)
- Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), affiliated with the University of Lübeck, Bolzano, Bozen, 39100, Italy
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Suyash Shringarpure
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christopher S Carlson
- Fred Hutchinson Cancer Center, University of Washington, 1100 Fairview Ave. N., Seattle, WA 98109
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christopher R Gignoux
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Icahn Institute of Multiscale Biology and Genomics, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
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Gibbs C, Thalamus J, Tveten K, Busk ØL, Hysing J, Haugaa KH, Holla ØL. Genetic and Phenotypic Characterization of Community Hospital Patients With QT Prolongation. J Am Heart Assoc 2018; 7:e009706. [PMID: 30369311 PMCID: PMC6201409 DOI: 10.1161/jaha.118.009706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
Abstract
Background Congenital long- QT syndrome ( LQTS ) is a genetic disorder characterized by prolongation of the corrected QT interval ( QT c) on an ECG . The aim of the present study was to estimate the prevalence of pathogenic and likely pathogenic sequence variants in patients who had at least 1 ECG with a QT c ≥500 ms. Methods and Results Telemark Hospital Trust is a community hospital within the Norwegian national health system, serving ≈173 000 inhabitants. We searched the ECG database at Telemark Hospital Trust, Norway, from January 2004 to December 2014, and identified 1531 patients with at least 1 ECG with a QT c ≥500 ms. At the time of inclusion in this study (2015), 766 patients were alive. A total of 733 patients were invited to participate, and 475 accepted. The 17 genes that have been reported to cause monogenic LQTS were sequenced among the patients. Pro- QT c score was calculated for each patient. A molecular genetic cause of LQTS was detected in 31 (6.5%) of 475 patients. These patients had a lower pro- QT c score than those without pathogenic or likely pathogenic variants (1.7±1.0 versus 2.8±1.6; P<0.001). Conclusions Compared with the general population, hospitalized patients with a QT c ≥500 ms in at least 1 ECG recording had an increased likelihood for pathogenic and likely pathogenic variants in LQTS genes. We recommend increased awareness of the possibility of LQTS in patients with at least 1 ECG with a QT c ≥500 ms.
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Affiliation(s)
- Charlotte Gibbs
- Department of Internal MedicineTelemark Hospital TrustSkienNorway
- Institute of Clinical MedicineFaculty of MedicineUniversity of OsloNorway
| | - Jacob Thalamus
- Department of Internal MedicineTelemark Hospital TrustSkienNorway
| | - Kristian Tveten
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
| | - Øyvind L. Busk
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
| | - Jan Hysing
- Department of Internal MedicineTelemark Hospital TrustSkienNorway
| | - Kristina H. Haugaa
- Institute of Clinical MedicineFaculty of MedicineUniversity of OsloNorway
- Center for Cardiological InnovationDepartment of CardiologyOslo University HospitalRikshospitalet and University of OsloNorway
| | - Øystein L. Holla
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
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31
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Barbitoff YA, Serebryakova EA, Nasykhova YA, Predeus AV, Polev DE, Shuvalova AR, Vasiliev EV, Urazov SP, Sarana AM, Scherbak SG, Gladyshev DV, Pokrovskaya MS, Sivakova OV, Meshkov AN, Drapkina OM, Glotov OS, Glotov AS. Identification of Novel Candidate Markers of Type 2 Diabetes and Obesity in Russia by Exome Sequencing with a Limited Sample Size. Genes (Basel) 2018; 9:genes9080415. [PMID: 30126146 PMCID: PMC6115942 DOI: 10.3390/genes9080415] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) and obesity are common chronic disorders with multifactorial etiology. In our study, we performed an exome sequencing analysis of 110 patients of Russian ethnicity together with a multi-perspective approach based on biologically meaningful filtering criteria to detect novel candidate variants and loci for T2D and obesity. We have identified several known single nucleotide polymorphisms (SNPs) as markers for obesity (rs11960429), T2D (rs9379084, rs1126930), and body mass index (BMI) (rs11553746, rs1956549 and rs7195386) (p < 0.05). We show that a method based on scoring of case-specific variants together with selection of protein-altering variants can allow for the interrogation of novel and known candidate markers of T2D and obesity in small samples. Using this method, we identified rs328 in LPL (p = 0.023), rs11863726 in HBQ1 (p = 8 × 10−5), rs112984085 in VAV3 (p = 4.8 × 10−4) for T2D and obesity, rs6271 in DBH (p = 0.043), rs62618693 in QSER1 (p = 0.021), rs61758785 in RAD51B (p = 1.7 × 10−4), rs34042554 in PCDHA1 (p = 1 × 10−4), and rs144183813 in PLEKHA5 (p = 1.7 × 10−4) for obesity; and rs9379084 in RREB1 (p = 0.042), rs2233984 in C6orf15 (p = 0.030), rs61737764 in ITGB6 (p = 0.035), rs17801742 in COL2A1 (p = 8.5 × 10−5), and rs685523 in ADAMTS13 (p = 1 × 10−6) for T2D as important susceptibility loci in Russian population. Our results demonstrate the effectiveness of whole exome sequencing (WES) technologies for searching for novel markers of multifactorial diseases in cohorts of limited size in poorly studied populations.
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Affiliation(s)
- Yury A Barbitoff
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Bioinformatics Institute, 194100 Saint Petersburg, Russia.
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Elena A Serebryakova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Yulia A Nasykhova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
| | | | - Dmitrii E Polev
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Anna R Shuvalova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | | | | | - Andrey M Sarana
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Sergey G Scherbak
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | | | - Maria S Pokrovskaya
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oksana V Sivakova
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Aleksey N Meshkov
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oxana M Drapkina
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oleg S Glotov
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Andrey S Glotov
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
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32
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Kulanuwat S, Tangjittipokin W, Jungtrakoon P, Chanprasert C, Sujjitjoon J, Binnima N, Yenchitsomanus PT, Plengvidhya N. DNAJC3 mutation in Thai familial type 2 diabetes mellitus. Int J Mol Med 2018; 42:1064-1073. [PMID: 29767246 DOI: 10.3892/ijmm.2018.3678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/08/2018] [Indexed: 11/05/2022] Open
Abstract
Type 2 diabetes mellitus (T2D) is a heterogeneous disease, with certain cases presenting an autosomal dominant type. The rare coding variants of disease‑causing genes in T2D remain mostly unclear. The present study aimed to identify the disease‑causing gene conducting whole exome sequencing in a Thai T2D family with an autosomal dominant transmission of T2D with no evidence of mutations in known maturity‑onset diabetes of the young (MODY) genes. Candidate variants were selected according to certain criteria of mutation prediction programs, followed by segregation analysis with diabetes in the family. The results demonstrated that, of the 68,817 variants obtained, 122 were considered as candidate variants subsequent to the filtering processes. Genotyping of these variants revealed that DnaJ homolog subfamily C member 3 (DNAJC3) p.H238N segregated with diabetes in the family. This mutation was also identified in another proband from the autosomal dominant T2D family without mutation in known MODY genes and was segregated with diabetes. This variant was also identified in 14/1,000 older‑onset T2D patients [minor allele frequency (MAF)=0.007], 2/500 non‑diabetic controls (MAF=0.002) and 3 prediabetic individuals who were previously classified as non‑diabetic controls. In silico mutagenesis and protein modeling of p.H238N revealed changes of the polar contacts across the tetratricopeptide repeat (TPR) motif and TPR subdomains, which may affect the protein tertiary structure. Furthermore, the expression of DNAJC3 H238N protein was 0.68±0.08 fold (P<0.05) lower when compared with that of the wild‑type, possibly due to protein instability. Thus, DNAJC3 p.H238N is likely to be a variant causing diabetes.
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Affiliation(s)
- Sirikul Kulanuwat
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Watip Tangjittipokin
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Prapaporn Jungtrakoon
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chutima Chanprasert
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jatuporn Sujjitjoon
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Ninareeman Binnima
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nattachet Plengvidhya
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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33
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Corominas J, Colijn JM, Geerlings MJ, Pauper M, Bakker B, Amin N, Lores Motta L, Kersten E, Garanto A, Verlouw JAM, van Rooij JGJ, Kraaij R, de Jong PTVM, Hofman A, Vingerling JR, Schick T, Fauser S, de Jong EK, van Duijn CM, Hoyng CB, Klaver CCW, den Hollander AI. Whole-Exome Sequencing in Age-Related Macular Degeneration Identifies Rare Variants in COL8A1, a Component of Bruch's Membrane. Ophthalmology 2018; 125:1433-1443. [PMID: 29706360 PMCID: PMC6104593 DOI: 10.1016/j.ophtha.2018.03.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/19/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Genome-wide association studies and targeted sequencing studies of candidate genes have identified common and rare variants that are associated with age-related macular degeneration (AMD). Whole-exome sequencing (WES) studies allow a more comprehensive analysis of rare coding variants across all genes of the genome and will contribute to a better understanding of the underlying disease mechanisms. To date, the number of WES studies in AMD case-control cohorts remains scarce and sample sizes are limited. To scrutinize the role of rare protein-altering variants in AMD cause, we performed the largest WES study in AMD to date in a large European cohort consisting of 1125 AMD patients and 1361 control participants. DESIGN Genome-wide case-control association study of WES data. PARTICIPANTS One thousand one hundred twenty-five AMD patients and 1361 control participants. METHODS A single variant association test of WES data was performed to detect variants that are associated individually with AMD. The cumulative effect of multiple rare variants with 1 gene was analyzed using a gene-based CMC burden test. Immunohistochemistry was performed to determine the localization of the Col8a1 protein in mouse eyes. MAIN OUTCOME MEASURES Genetic variants associated with AMD. RESULTS We detected significantly more rare protein-altering variants in the COL8A1 gene in patients (22/2250 alleles [1.0%]) than in control participants (11/2722 alleles [0.4%]; P = 7.07×10-5). The association of rare variants in the COL8A1 gene is independent of the common intergenic variant (rs140647181) near the COL8A1 gene previously associated with AMD. We demonstrated that the Col8a1 protein localizes at Bruch's membrane. CONCLUSIONS This study supported a role for protein-altering variants in the COL8A1 gene in AMD pathogenesis. We demonstrated the presence of Col8a1 in Bruch's membrane, further supporting the role of COL8A1 variants in AMD pathogenesis. Protein-altering variants in COL8A1 may alter the integrity of Bruch's membrane, contributing to the accumulation of drusen and the development of AMD.
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Affiliation(s)
- Jordi Corominas
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johanna M Colijn
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maartje J Geerlings
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marc Pauper
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bjorn Bakker
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Najaf Amin
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Laura Lores Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline Kersten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost A M Verlouw
- Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, The Netherlands
| | - Paulus T V M de Jong
- Netherlands Institute of Neurosciences (NIN), Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Departments of Ophthalmology, Amsterdam Medical Center, Amsterdam, and Leiden University Medical Center, Leiden, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany; Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelia M van Duijn
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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Grarup N, Moltke I, Andersen MK, Dalby M, Vitting-Seerup K, Kern T, Mahendran Y, Jørsboe E, Larsen CVL, Dahl-Petersen IK, Gilly A, Suveges D, Dedoussis G, Zeggini E, Pedersen O, Andersson R, Bjerregaard P, Jørgensen ME, Albrechtsen A, Hansen T. Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nat Genet 2018; 50:172-174. [PMID: 29311636 PMCID: PMC5828106 DOI: 10.1038/s41588-017-0022-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/29/2017] [Indexed: 01/08/2023]
Abstract
We have identified a variant in ADCY3 (encoding adenylate cyclase 3) associated with markedly increased risk of obesity and type 2 diabetes in the Greenlandic population. The variant disrupts a splice acceptor site, and carriers have decreased ADCY3 RNA expression. Additionally, we observe an enrichment of rare ADCY3 loss-of-function variants among individuals with type 2 diabetes in trans-ancestry cohorts. These findings provide new information on disease etiology relevant for future treatment strategies.
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Affiliation(s)
- Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Dalby
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yuvaraj Mahendran
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emil Jørsboe
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina V L Larsen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Inger K Dahl-Petersen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Arthur Gilly
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Suveges
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robin Andersson
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Bjerregaard
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Marit E Jørgensen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark.
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland.
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.
| | - Anders Albrechtsen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
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35
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Broendberg AK, Christiansen MK, Nielsen JC, Pedersen LN, Jensen HK. Targeted next generation sequencing in a young population with suspected inherited malignant cardiac arrhythmias. Eur J Hum Genet 2018; 26:303-313. [PMID: 29343803 PMCID: PMC5838968 DOI: 10.1038/s41431-017-0060-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/19/2017] [Accepted: 11/18/2017] [Indexed: 12/19/2022] Open
Abstract
Aborted sudden cardiac death in the young often is due to inherited heart disease. However, the clinical phenotype in these patients is not always evident. The aim of this study was to identify pathogenic molecular genetic variants in a population with suspected inherited cardiac arrhythmias. Eligible patients were admitted to Aarhus University Hospital, Denmark during the period 1999–2013 with arrhythmias assumed caused by a hereditary heart disease, and in whom no genotype had been established. We used the Danish national pacemaker and ICD registry to identify this cohort. One third (24/80) of the study population had first-line genetic testing with a targeted next-generation sequencing (NGS) panel, and two-third (56/80) of the study population had second-line genetic testing with NGS where prior Sanger sequencing did not reveal a causative variant. Variants were assessed according to the American College of Medical Genetics and Genomics (ACMG) guidelines. We included 80 patients. Median age (IQR) was 38 (28–43) years, 54 (68%) were males. First-line genetic testing identified a genetic variant in 33% (8/24) of the cases and second-line genetic testing revealed a variant in 20% (11/56) of the cases. Eleven variants were considered pathogenic, three likely pathogenic and 10 were variants of unknown significance (VUS). Seventeen variants were very rare with a minor allele frequency (MAF) ≤0.02% in all population databases used in the study. Molecular genetic testing of patients with suspected inherited cardiac arrhythmias with NGS identifies a molecular-genetic cause in a significant proportion of patients.
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Affiliation(s)
- Anders Krogh Broendberg
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark.
| | - Morten Krogh Christiansen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Jens Cosedis Nielsen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | | | - Henrik Kjaerulf Jensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
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36
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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet 2018; 50:20-25. [PMID: 29255259 PMCID: PMC5742068 DOI: 10.1038/s41588-017-0010-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Nicholas W VanKuren
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Roy Zhao
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Shannon Kalsow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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37
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Laursen AH, Bjerrum OW, Friis-Hansen L, Hansen TO, Marott JL, Magnussen K. Causes of iron overload in blood donors - a clinical study. Vox Sang 2017; 113:110-119. [PMID: 29230833 DOI: 10.1111/vox.12619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Despite the obligate iron loss from blood donation, some donors present with hyperferritinaemia that can result from a wide range of acute and chronic conditions including hereditary haemochromatosis (HH). The objective of our study was to investigate the causes of hyperferritinaemia in the blood donor population and explore the value of extensive HH mutational analyses. MATERIALS AND METHODS Forty-nine consecutive donors (f = 6, m = 43) were included prospectively from the Capital Regional Blood Center. Inclusion criteria were a single ferritin value >1000 μg/l or repeated hyperferritinaemia with at least one value >500 μg/l. All donors were questioned about their medical history and underwent a physical examination, biochemical investigations and next-generation sequencing of HH-related genes, including the HFE gene, the haemojuvelin gene (HFE2/HJV), the hepcidin gene (HAMP), the ferroportin 1 gene (SLC40A1) and the transferrin receptor 2 gene (TFR2). RESULTS Forty of 49 donors were mutation positive with a combined 69 mutations, 54 of which were located in the HFE gene. There were 11 mutations in the TFR2 gene, two mutations in the HFE2 gene and two mutations in the HAMP gene. Only four donors had apparent alternative causes of hyperferritinaemia. CONCLUSION HH-related mutations were the most frequent cause of hyperferritinaemia in a Danish blood donor population, and it appears that several different HH-genotypes can contribute to hyperferritinaemia. HH screening in blood donors with high ferritin levels could be warranted. HH-related iron overload should not in itself result in donor ineligibility.
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Affiliation(s)
- A H Laursen
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - O W Bjerrum
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - L Friis-Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Biochemistry, Nordsjaellands Hospital, Hillerod, Denmark
| | - T O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - J L Marott
- The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark
| | - K Magnussen
- Blood Centre Lab, Hvidovre Hospital, Hvidovre, Denmark.,Department of Immunology and Transfusion Medicine, Sorlandet hospital Kristiansand, Kristiansand, Norway
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38
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Zhang R, Wang Y, Ye K, Picard M, Gu Z. Independent impacts of aging on mitochondrial DNA quantity and quality in humans. BMC Genomics 2017; 18:890. [PMID: 29157198 PMCID: PMC5697406 DOI: 10.1186/s12864-017-4287-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/08/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes. However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes. In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts. RESULTS We report a high prevalence of pathogenic mtDNA heteroplasmies in this population. We also find an increase in mtDNA heteroplasmies with age (β = 0.011, P = 5.77e-6), and showed that, on average, individuals aged 70-years or older had 58.5% more mtDNA heteroplasmies than those under 40-years old. Conversely, mtDNA copy number decreased by an average of 0.4 copies per year (β = -0.395, P = 0.0097). Multiple regression analyses also showed that age had independent effects on mtDNA copy number decrease and heteroplasmy accumulation. Finally, mtDNA copy number was positively associated with serum bicarbonate level (P = 4.46e-5), and inversely correlated with white blood cell count (P = 0.0006). Moreover, the aggregated heteroplasmy load was associated with blood apolipoprotein B level (P = 1.33e-5), linking the accumulation of mtDNA mutations to age-related physiological markers. CONCLUSIONS Our population-based study indicates that both mtDNA quality and quantity are influenced by age. An open question for the future is whether interventions that would contribute to maintain optimal mtDNA copy number and prevent the expansion of heteroplasmy could promote healthy aging.
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Affiliation(s)
- Ruoyu Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Yiqin Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Kaixiong Ye
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Department of Neurology and Columbia Translational Neuroscience Initiative, Columbia Aging Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA.
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SCA28: Novel Mutation in the AFG3L2 Proteolytic Domain Causes a Mild Cerebellar Syndrome with Selective Type-1 Muscle Fiber Atrophy. THE CEREBELLUM 2017; 16:62-67. [PMID: 26868664 DOI: 10.1007/s12311-016-0765-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The spinocerebellar ataxias (SCA) are a group of rare inherited neurodegenerative diseases characterized by slowly progressive cerebellar ataxia, resulting in unsteady gait, clumsiness, and dysarthria. The disorders are predominantly inherited in an autosomal dominant manner. Mutations in the gene AFG3L2 that encodes a subunit of the mitochondrial m-AAA protease have previously been shown to cause spinocerebellar ataxia type 28 (SCA28). Here, we present the clinical phenotypes of three patients from a family with autosomal dominant cerebellar ataxia and show by molecular genetics and in silico modelling that this is caused by a novel missense mutation in the AFG3L2 gene. Furthermore, we show, for the first time, fluorodeoxyglucose-positron emission tomography (FDG-PET) scans of the brain and selective type I fiber atrophy of skeletal muscle of SCA28 patients indicating non-nervous-system involvement in SCA28 as well.
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Abstract
PURPOSE OF REVIEW Genome-wide association studies (GWAS) for type 2 diabetes (T2D) risk have identified a large number of genetic loci associated with disease susceptibility. However, progress moving from association signals through causal genes to functional understanding has so far been slow, hindering clinical translation. This review discusses the benefits and limitations of emerging, unbiased approaches for prioritising causal genes at T2D risk loci. RECENT FINDINGS Candidate causal genes can be identified by a number of different strategies that rely on genetic data, genomic annotations, and functional screening of selected genes. To overcome the limitations of each particular method, integration of multiple data sets is proving essential for establishing confidence in the prioritised genes. Previous studies have also highlighted the need to support these efforts through identification of causal variants and disease-relevant tissues. Prioritisation of causal genes at T2D risk loci by integrating complementary lines of evidence promises to accelerate our understanding of disease pathology and promote translation into new therapeutics.
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Affiliation(s)
- Antje K Grotz
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Soren K Thomsen
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK.
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41
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Xu R, Li Q, Liu R, Shen J, Li M, Zhao M, Wang M, Liao Q, Mao H, Li Z, Zhou N, Yin P, Li Y, Tang X, Wu T, Zhong Z, Wang Y, Ai Z, Wang O, Chen N, Yang X, Fang J, Fu P, Gu J, Ye K, Chen J, Dai L, Liu H, Liu Z, Liao Y, Wan J, Ding G, Zhao J, Zhang H, Fu S, Sun L, Zhang X, Yang H, Wang J, Wang J, Liu J, Li Y, Yu X. Association Analysis of the MHC in Lupus Nephritis. J Am Soc Nephrol 2017; 28:3383-3394. [PMID: 28754791 DOI: 10.1681/asn.2016121331] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/29/2017] [Indexed: 02/05/2023] Open
Abstract
Lupus nephritis (LN) is one of the most prevalent and serious complications of SLE, with significant effects on patient and renal survival. Although a large number of genetic variants associated with SLE have been identified, biomarkers that correlate with LN are extremely limited. In this study, we performed a comprehensive sequencing analysis of the whole MHC region in 1331 patients with LN and 1296 healthy controls and validated the independent associations in another 950 patients with LN and 1000 controls. We discovered five independent risk variants for LN within the MHC region, including HLA-DRβ1 amino acid 11 (Pomnibus<0.001), HLA-DQβ1 amino acid 45 (P<0.001; odds ratio, 0.58; 95% confidence interval, 0.52 to 0.65), HLA-A amino acid 156 (Pomnibus<0.001), HLA-DPβ1 amino acid 76 (Pomnibus<0.001), and a missense variant in PRRC2A (rs114580964; P<0.001; odds ratio, 0.38; 95% confidence interval, 0.30 to 0.49) at genome-wide significance. These data implicate aberrant peptide presentation by MHC classes 1 and 2 molecules and sex hormone modulation in the development of LN.
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Affiliation(s)
- Ricong Xu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China.,Department of Nephrology, Shenzhen Second People's Hospital and the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qibin Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Rongjun Liu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China.,Nephrology and Rheumatology Department, Guangzhou Panyu Central Hospital, Guangzhou, Guangdong, China
| | - Juan Shen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ming Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Minghui Zhao
- Renal Division, Peking University First Hospital, Peking University, Institute of Nephrology, Beijing, China
| | - Meng Wang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Qijun Liao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Haiping Mao
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Zhijian Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Na Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Peiran Yin
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Yue Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xueqing Tang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Tian Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhong Zhong
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Yan Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhen Ai
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China
| | - Ou Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Nan Chen
- Department of Nephrology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Ping Fu
- Department of Nephrology, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jieruo Gu
- Department of Rheumatology, The Third Affiliated Hospital and
| | - Kun Ye
- Department of Nephrology, The People's Hospital of Guangxi Autonomous Region, Nanning, Guangxi, China
| | - Jian Chen
- Department of Nephrology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian, China
| | - Lie Dai
- Department of Rheumatology and Clinical Immunology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huafeng Liu
- Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Zhangsuo Liu
- Department of Nephrology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Yunhua Liao
- Department of Nephrology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Jianxin Wan
- Department of Nephrology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Guohua Ding
- Department of Nephrology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Jinghong Zhao
- Department of Nephrology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuxia Fu
- Department of Nephrology, The Second Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital and.,Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui, China
| | - Xuejun Zhang
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Huanming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jun Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Dermatology and Department of Dermatology, No. 1 Hospital and
| | - Jianjun Liu
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital and.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia; and.,School of Biological Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yingrui Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China;
| | - Xueqing Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, Guangdong, China; .,Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong, China
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Abstract
STUDY DESIGN Mutation analysis of a candidate disease gene in a cohort of patients with moderate to severe Adolescent idiopathic scoliosis (AIS). OBJECTIVE To investigate if damaging mutations in the planar cell polarity gene VANGL1 could be identified in AIS patients. SUMMARY OF BACKGROUND DATA AIS is a spinal deformity which occurs in 1% to 3% of the population. The cause of AIS is often unknown, but genetic factors are important in the etiology. Rare variants in genes encoding regulators of WNT/planar cell polarity (PCP) signaling were recently identified in AIS patients. METHODS We analyzed the coding region of the VANGL1 gene for mutations using Sanger sequencing in 157 unrelated patients with moderate to severe AIS. The frequency of mutations in the patient cohort was compared with their frequency in a large cohort of controls. Functional effect of mutations were predicted in silico and analyzed in vitro by transfection of normal and mutant recombinant VANGL1 protein in Madin-Darby Canine Kidney (MDCK) cells. Cellular localization of recombinant proteins was analyzed by immunofluorescence microscopy analysis. RESULTS In the patient cohort, we identified two rare missense mutations in VANGL1, encoding a receptor involved in WNT/PCP signaling. The mutations, p.I136N and p.F440 V, are very rare in the normal population. Both mutations are predicted to be damaging, and to affect evolutionary conserved amino acid residues of VANGL1. Functional analysis in MDCK cells showed that the mutations abolished the normal translocation of VANGL1 to the cell membrane. CONCLUSION Our data support that mutations in genes involved in WNT/PCP signaling may be associated with AIS, but replication in other patient cohorts and further analysis of the role of WNT/PCP signaling in AIS is needed. LEVEL OF EVIDENCE 4.
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Hove MN, Kilic-Biyik KZ, Trotter A, Grønskov K, Sander B, Larsen M, Carroll J, Bech-Hansen T, Rosenberg T. Clinical Characteristics, Mutation Spectrum, and Prevalence of Åland Eye Disease/Incomplete Congenital Stationary Night Blindness in Denmark. Invest Ophthalmol Vis Sci 2017; 57:6861-6869. [PMID: 28002560 PMCID: PMC5215230 DOI: 10.1167/iovs.16-19445] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To assess clinical characteristics, foveal structure, mutation spectrum, and prevalence rate of Åland eye disease (AED)/incomplete congenital stationary night blindness (iCSNB). Methods A retrospective survey included individuals diagnosed with AED at a national low-vision center from 1980 to 2014. A subset of affected males underwent ophthalmologic examinations including psychophysical tests, full-field electroretinography, and spectral-domain optical coherence tomography. Results Over the 34-year period, 74 individuals from 35 families were diagnosed with AED. Sixty individuals from 29 families participated in a follow-up study of whom 59 harbored a CACNA1F mutation and 1 harbored a CABP4 mutation. Among the subjects with a CACNA1F mutation, subnormal visual acuity was present in all, nystagmus was present in 63%, and foveal hypoplasia was observed in 25/43 subjects. Foveal pit volume was significantly reduced as compared to normal (P < 0.0001). Additionally, outer segment length at the fovea was measured in 46 subjects and found to be significantly reduced as compared to normal (P < 0.001). Twenty-nine CACNA1F variations were detected among 34 families in the total cohort, and a novel CABP4 variation was identified in one family. The estimated mean birth prevalence rate was 1 per 22,000 live-born males. Conclusions Our data support the viewpoint that AED, iCSNB, and X-linked cone–rod dystrophy 3 are designations that refer to a broad, continuous spectrum of clinical appearances caused in the majority by a variety of mutations in CACNA1F. We argue that the original designation AED should be used for this entity.
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Affiliation(s)
- Marianne N Hove
- Department of Ophthalmology, National Eye Clinic for the Visually Impaired and Kennedy Center, Rigshospitalet, Glostrup, Denmark 2Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark
| | - Kevser Z Kilic-Biyik
- Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark 3Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alana Trotter
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Karen Grønskov
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen, Denmark
| | - Birgit Sander
- Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark 3Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Larsen
- Department of Ophthalmology, National Eye Clinic for the Visually Impaired and Kennedy Center, Rigshospitalet, Glostrup, Denmark 2Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark 3Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Carroll
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Torben Bech-Hansen
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Thomas Rosenberg
- Department of Ophthalmology, National Eye Clinic for the Visually Impaired and Kennedy Center, Rigshospitalet, Glostrup, Denmark 3Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Konigorski S, Yilmaz YE, Pischon T. Comparison of single-marker and multi-marker tests in rare variant association studies of quantitative traits. PLoS One 2017; 12:e0178504. [PMID: 28562689 PMCID: PMC5451057 DOI: 10.1371/journal.pone.0178504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/15/2017] [Indexed: 11/19/2022] Open
Abstract
In genetic association studies of rare variants, low statistical power and potential violations of established estimator properties are among the main challenges of association tests. Multi-marker tests (MMTs) have been proposed to target these challenges, but any comparison with single-marker tests (SMTs) has to consider that their aim is to identify causal genomic regions instead of variants. Valid power comparisons have been performed for the analysis of binary traits indicating that MMTs have higher power, but there is a lack of conclusive studies for quantitative traits. The aim of our study was therefore to fairly compare SMTs and MMTs in their empirical power to identify the same causal loci associated with a quantitative trait. The results of extensive simulation studies indicate that previous results for binary traits cannot be generalized. First, we show that for the analysis of quantitative traits, conventional estimation methods and test statistics of single-marker approaches have valid properties yielding association tests with valid type I error, even when investigating singletons or doubletons. Furthermore, SMTs lead to more powerful association tests for identifying causal genes than MMTs when the effect sizes of causal variants are large, and less powerful tests when causal variants have small effect sizes. For moderate effect sizes, whether SMTs or MMTs have higher power depends on the sample size and percentage of causal SNVs. For a more complete picture, we also compare the power in studies of quantitative and binary traits, and the power to identify causal genes with the power to identify causal rare variants. In a genetic association analysis of systolic blood pressure in the Genetic Analysis Workshop 19 data, SMTs yielded smaller p-values compared to MMTs for most of the investigated blood pressure genes, and were least influenced by the definition of gene regions.
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Affiliation(s)
- Stefan Konigorski
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Yildiz E. Yilmaz
- Department of Mathematics and Statistics, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany
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45
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Gregers E, Ahlberg G, Christensen T, Jabbari J, Larsen KO, Herfelt CB, Henningsen KM, Andreasen L, Thiis JJ, Lund J, Holme S, Haunsø S, Bentzen BH, Schmitt N, Svendsen JH, Olesen MS. Deep sequencing of atrial fibrillation patients with mitral valve regurgitation shows no evidence of mosaicism but reveals novel rare germline variants. Heart Rhythm 2017; 14:1531-1538. [PMID: 28549997 DOI: 10.1016/j.hrthm.2017.05.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Atrial fibrillation (AF) is the most common cardiac arrhythmia. Valvular heart disease is a strong predictor, yet the underlying molecular mechanisms are unknown. OBJECTIVE The purpose of this study was to investigate the prevalence of somatic variants in AF candidate genes in an AF patient population undergoing surgery for mitral valve regurgitation (MVR) to determine whether these patients are genetically predisposed to AF. METHODS DNA was extracted from blood and left atrial tissue from 44 AF patients with MVR. Using next-generation sequencing, we investigated 110 genes using the HaloPlex Target Enrichment System. MuTect software was used for identification of somatic point variants. We functionally characterized selected variants using electrophysiologic techniques. RESULTS No somatic variants were identified in the cardiac tissue. Thirty-three patients (75%) had a rare germline variation in ≥1 candidate genes. Fourteen variants were novel. Fifteen variants were predicted damaging or likely damaging in ≥6 in silico predictions. We identified rare variants in genes never directly associated with AF: KCNE4, SCN4B, NEURL1, and CAND2. Interestingly, 7 patients (16%) had variants in genes involved in cellular potassium handling. The variants KCNQ1 (p.G272S) and KCNH2 (p.A913V) resulted in gain of function due to faster activation (KCNQ1) and slowed deactivation kinetics (KCNQ1, KCNH2). CONCLUSION We did not find any somatic variants in patients with AF and MVR. Surprisingly, we found that our cohort of non-lone AF patients might, like lone AF patients, be predisposed to AF by rare germline variants. Our findings emphasize the extent of still unknown factors in the pathogenesis of AF.
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Affiliation(s)
- Emilie Gregers
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thea Christensen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Javad Jabbari
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kirstine O Larsen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie B Herfelt
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer M Henningsen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Andreasen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Thiis
- Department of Cardiothoracic Surgery, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jens Lund
- Department of Cardiothoracic Surgery, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Holme
- Department of Cardiothoracic Surgery, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo H Bentzen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Schmitt
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Jesper H Svendsen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Morten S Olesen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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46
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Gjesing AP, Rui G, Lauenborg J, Have CT, Hollensted M, Andersson E, Grarup N, Sun J, Quan S, Brandslund I, Damm P, Pedersen O, Wang J, Hansen T. High Prevalence of Diabetes-Predisposing Variants in MODY Genes Among Danish Women With Gestational Diabetes Mellitus. J Endocr Soc 2017; 1:681-690. [PMID: 29264522 PMCID: PMC5686663 DOI: 10.1210/js.2017-00040] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 01/09/2023] Open
Abstract
Context: Gestational diabetes mellitus (GDM), defined as any degree of glucose intolerance with first recognition during pregnancy, is a heterogeneous form of diabetes characterized by various degrees of β-cell dysfunction. Objectives: We aimed to estimate the prevalence of possibly pathogenic variants in the maturity-onset diabetes of the young genes GCK, HNF1A, HNF4A, HNF1B, and INS among women with GDM. Furthermore, we examined the glucose tolerance status in variant carriers vs noncarriers at follow-up. Design, Setting, and Patients: We sequenced the coding regions and intron/exon boundaries of GCK, HNF1A, HNF4A, HNF1B, and INS using targeted region capture and next-generation sequencing in 354 Danish women with diet-treated GDM. Glucose tolerance was examined at follow-up 10 years after the index pregnancy. Main Outcome Measures: The prevalence of possibly pathogenic variants in GCK, HNF1A, HNF4A, HNF1B, and INS was estimated, and differences in anthropometric traits, high-sensitivity C-Reactive Protein (CRP), and glucose metabolism were measured. Results: At baseline, 17 possibly disease-causing variants were found in 21 women, revealing a combined GCK, HNF1A, HNF4A, HNF1B, and INS variant prevalence of 5.9% (95% confidence interval: 3.5% to 8.4%). At follow-up, 15 out of 135 women with diabetes (11%) were carriers of variants in GCK, HNF1A, HNF4A, HNF1B, or INS. Conclusions: Almost 6% of Danish women with diet-treated GDM have possibly pathogenic variants in GCK, HNF1A, HNF4A, HNF1B, or INS. These women are at high risk of developing diabetes after pregnancy. Thus screening for variants in GCK, HNF1A, HNF4A, HNF1B, and INS should be considered among women with GDM.
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Affiliation(s)
- Anette P Gjesing
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Gao Rui
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Jeannet Lauenborg
- Department of Gynecology and Obstetrics, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Christian Theil Have
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mette Hollensted
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ehm Andersson
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jihua Sun
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Shi Quan
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Vejle Hospital, DK-7100 Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Peter Damm
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, 2100 Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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47
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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48
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Minică CC, Genovese G, Hultman CM, Pool R, Vink JM, Neale MC, Dolan CV, Neale BM. The Weighting is the Hardest Part: On the Behavior of the Likelihood Ratio Test and the Score Test Under a Data-Driven Weighting Scheme in Sequenced Samples. Twin Res Hum Genet 2017; 20:108-118. [PMID: 28238293 PMCID: PMC5357183 DOI: 10.1017/thg.2017.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Sequence-based association studies are at a critical inflexion point with the increasing availability of exome-sequencing data. A popular test of association is the sequence kernel association test (SKAT). Weights are embedded within SKAT to reflect the hypothesized contribution of the variants to the trait variance. Because the true weights are generally unknown, and so are subject to misspecification, we examined the efficiency of a data-driven weighting scheme. We propose the use of a set of theoretically defensible weighting schemes, of which, we assume, the one that gives the largest test statistic is likely to capture best the allele frequency-functional effect relationship. We show that the use of alternative weights obviates the need to impose arbitrary frequency thresholds. As both the score test and the likelihood ratio test (LRT) may be used in this context, and may differ in power, we characterize the behavior of both tests. The two tests have equal power, if the weights in the set included weights resembling the correct ones. However, if the weights are badly specified, the LRT shows superior power (due to its robustness to misspecification). With this data-driven weighting procedure the LRT detected significant signal in genes located in regions already confirmed as associated with schizophrenia - the PRRC2A (p = 1.020e-06) and the VARS2 (p = 2.383e-06) - in the Swedish schizophrenia case-control cohort of 11,040 individuals with exome-sequencing data. The score test is currently preferred for its computational efficiency and power. Indeed, assuming correct specification, in some circumstances, the score test is the most powerful test. However, LRT has the advantageous properties of being generally more robust and more powerful under weight misspecification. This is an important result given that, arguably, misspecified models are likely to be the rule rather than the exception in weighting-based approaches.
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Affiliation(s)
- Camelia C. Minică
- Department of Biological Psychology, Vrije Universiteit, Amsterdam
1081 BT, The Netherlands
- The EMGO Institute for Health and Care Research,
Amsterdam 1081 BT, The Netherlands
| | - Giulio Genovese
- The Stanley Center for Psychiatric Research, Broad Institute of the
Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- The Program in Medical and Population Genetics, Broad Institute of
the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142,
USA
- Department of Genetics, Harvard Medical School, Cambridge, MA 02115,
USA
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska
Institute, Stockholm SE-171 77, Sweden
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit, Amsterdam
1081 BT, The Netherlands
- The EMGO Institute for Health and Care Research,
Amsterdam 1081 BT, The Netherlands
| | - Jacqueline M. Vink
- Behavioural Science Institute, Radboud University, Nijmegen, The
Netherlands
| | - Michael C. Neale
- Department of Biological Psychology, Vrije Universiteit, Amsterdam
1081 BT, The Netherlands
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia
Commonwealth University, Richmond, USA
| | - Conor V. Dolan
- Department of Biological Psychology, Vrije Universiteit, Amsterdam
1081 BT, The Netherlands
- The EMGO Institute for Health and Care Research,
Amsterdam 1081 BT, The Netherlands
| | - Benjamin M. Neale
- The Stanley Center for Psychiatric Research, Broad Institute of the
Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- The Program in Medical and Population Genetics, Broad Institute of
the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142,
USA
- The Analytical and Translational Genetics Unit, Department of
Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
02114, USA
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49
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Witting N, Werlauff U, Duno M, Vissing J. Phenotypes, genotypes, and prevalence of congenital myopathies older than 5 years in Denmark. NEUROLOGY-GENETICS 2017; 3:e140. [PMID: 28357410 PMCID: PMC5362145 DOI: 10.1212/nxg.0000000000000140] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022]
Abstract
Objective: Congenital myopathy as a nosologic entity has long been recognized, but knowledge of overall and subtype prevalence and phenotype-genotype relationship is scarce, especially in the adult population. Methods: A national cohort of 107 patients ≥5 years diagnosed with congenital myopathy were prospectively assessed clinically, histologically, and genetically. Results: Twenty-five patients were excluded because of atypical features or alternative etiologies. The remaining 82 were on average 28 years old. Histologic examination revealed 14 (17%) with core disease, 15 (18%) centronuclear myopathy, 12 (15%) nemaline rods, 27 (33%) congenital fiber-type disproportion or type I predominance, and 14 (17%) nonspecific myopathic changes. Genetic etiology was identified in 46 patients (56.1%); 22.0% were heterozygous or compound heterozygous for mutations in RYR1, 7.3% had DNM2 mutations, and 7.3% NEB mutations. Less than 5% had mutations in ACTA1, TPM2/3, MTM1, TTN, SEPN1, or SC4NA. A genetic cause was established in 83% with specific histology (cores/rods/centronuclear myopathy) vs 29% with unspecific histology. The detailed clinical examination found gene-dependent discrepancies in the pattern of muscle affection and walking ability. Although walking ability was delayed in patients with ACTA1, TPM2/3, and RYR1 mutations, it was within normal limits in patients with NEB and DNM2 mutations. Conclusions: We found that overall, genetic and histologic prevalence of congenital myopathy in Denmark differs from previous retrospective reports. Less RYR1 and more DNM2 and NEB mutations and less core histology were present in our cohort. These differences may be explained by our prospective design, the older cohort of patients, and by differences in genetic background.
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Affiliation(s)
- Nanna Witting
- Copenhagen Neuromuscular Center (N.W., J.V.), Department of Neurology, and Department of Clinical Genetics (U.W.), Rigshospitalet, University of Copenhagen; and The Danish National Rehabilitation Centre for Neuromuscular Diseases (M.D.), Aarhus, Denmark
| | - Ulla Werlauff
- Copenhagen Neuromuscular Center (N.W., J.V.), Department of Neurology, and Department of Clinical Genetics (U.W.), Rigshospitalet, University of Copenhagen; and The Danish National Rehabilitation Centre for Neuromuscular Diseases (M.D.), Aarhus, Denmark
| | - Morten Duno
- Copenhagen Neuromuscular Center (N.W., J.V.), Department of Neurology, and Department of Clinical Genetics (U.W.), Rigshospitalet, University of Copenhagen; and The Danish National Rehabilitation Centre for Neuromuscular Diseases (M.D.), Aarhus, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center (N.W., J.V.), Department of Neurology, and Department of Clinical Genetics (U.W.), Rigshospitalet, University of Copenhagen; and The Danish National Rehabilitation Centre for Neuromuscular Diseases (M.D.), Aarhus, Denmark
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50
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Loehlein Fier H, Prokopenko D, Hecker J, Cho MH, Silverman EK, Weiss ST, Tanzi RE, Lange C. On the association analysis of genome-sequencing data: A spatial clustering approach for partitioning the entire genome into nonoverlapping windows. Genet Epidemiol 2017; 41:332-340. [PMID: 28318110 DOI: 10.1002/gepi.22040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/20/2016] [Accepted: 02/04/2017] [Indexed: 12/16/2022]
Abstract
For the association analysis of whole-genome sequencing (WGS) studies, we propose an efficient and fast spatial-clustering algorithm. Compared to existing analysis approaches for WGS data, that define the tested regions either by sliding or consecutive windows of fixed sizes along variants, a meaningful grouping of nearby variants into consecutive regions has the advantage that, compared to sliding window approaches, the number of tested regions is likely to be smaller. In comparison to consecutive, fixed-window approaches, our approach is likely to group nearby variants together. Given existing biological evidence that disease-associated mutations tend to physically cluster in specific regions along the chromosome, the identification of meaningful groups of nearby located variants could thus lead to a potential power gain for association analysis. Our algorithm defines consecutive genomic regions based on the physical positions of the variants, assuming an inhomogeneous Poisson process and groups together nearby variants. As parameters are estimated locally, the algorithm takes the differing variant density along the chromosome into account and provides locally optimal partitioning of variants into consecutive regions. An R-implementation of the algorithm is provided. We discuss the theoretical advances of our algorithm compared to existing, window-based approaches and show the performance and advantage of our introduced algorithm in a simulation study and by an application to Alzheimer's disease WGS data. Our analysis identifies a region in the ITGB3 gene that potentially harbors disease susceptibility loci for Alzheimer's disease. The region-based association signal of ITGB3 replicates in an independent data set and achieves formally genome-wide significance. Software Implementation: An implementation of the algorithm in R is available at: https://github.com/heidefier/cluster_wgs_data.
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Affiliation(s)
- Heide Loehlein Fier
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.,Working Group of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julian Hecker
- Working Group of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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