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Kandolin M, Pöyhönen M, Jakkula E. Estimation of carrier frequencies utilizing the gnomAD database for ACMG recommended carrier screening and Finnish disease heritage conditions in non-Finnish European, Finnish, and Ashkenazi Jewish populations. Am J Med Genet A 2024; 194:e63588. [PMID: 38459613 DOI: 10.1002/ajmg.a.63588] [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: 08/17/2023] [Revised: 01/24/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
American College of Medical Genetics and Genomics (ACMG) recommends offering Tier 3 carrier screening to pregnant patients and those planning a pregnancy for conditions with a carrier frequency of ≥1/200 (96 genes for autosomal recessive [AR] conditions). Certain AR conditions referred to as Finnish disease heritage (FINDIS) have a higher prevalence in Finland than elsewhere. Data from gnomAD v2.1 were extracted to assess carrier frequencies for ACMG-recommended AR and FINDIS AR and X-linked genes in Finnish, non-Finnish European, and Ashkenazi Jewish populations. Following variants were considered: ClinVar pathogenic or likely pathogenic, loss-of-function, and Finnish founder variants. Gene carrier (GCR), cumulative carrier (CCR), and at-risk couple rates (ACR) were estimated. In Finnish population, 47 genes had a GCR of ≥0.5%. CCRs were 52.7% (Finnish), 48.9% (non-Finnish European), and 58.3% (Ashkenazi Jewish), whereas ACRs were 1.4%, 0.93%, and 2.3% respectively. Approximately 141 affected children with analyzed AR conditions are estimated to be born in Finland annually. Eighteen genes causing FINDIS conditions had a GCR of ≥0.5% in the Finnish population but were absent in the ACMG Tier 3 gene list. Two genes (RECQL4 and RMRP) had GCR of ≥0.5% either in non-Finnish Europeans or Ashkenazi Jewish populations. Results highlight the need for careful curation of carrier screening panels.
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Affiliation(s)
- Miska Kandolin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
| | - Minna Pöyhönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
| | - Eveliina Jakkula
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
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2
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Clancy J, Ritari J, Vaittinen E, Arvas M, Tammi S, Koskela S, Partanen J. Blood donor biobank as a resource in personalised biomedical genetic research. Eur J Hum Genet 2024:10.1038/s41431-023-01528-0. [PMID: 38212662 DOI: 10.1038/s41431-023-01528-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/14/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024] Open
Abstract
Health questionnaires and donation criteria result in accumulation of highly selected individuals in a blood donor population. To understand better the usefulness of a blood donor-based biobank in personalised disease-associated genetic studies, and for possible personalised blood donation policies, we evaluated the occurrence and distributions of common and rare disease-associated genetic variants in Finnish Blood Service Biobank. We analysed among 31,880 blood donors the occurrence and geographical distribution of (i) 53 rare Finnish-enriched disease-associated variants, (ii) mutations assumed to influence blood donation: four Bernard-Soulier syndrome and two hemochromatosis mutations, (iii) type I diabetes risk genotype HLA-DQ2/DQ8. In addition, we analysed the level of consanguinity in Blood Service Biobank. 80.3% of blood donors carried at least one (range 0-9 per donor) of the rare variants, many in homozygous form, as well. Donors carrying multiple rare variants were enriched in Eastern Finland. Haemochromatosis mutation HFE C282Y homozygosity was 43.8% higher than expected, whereas mutations leading to Bernard-Soulier thrombocytopenia were rare. The frequency of HLA-DQ2/DQ8 genotype was slightly lower than expected. First-degree consanguinity was higher in Blood Service Biobank than in the general population. We demonstrate that despite donor selection, the Blood Service Biobank is a valuable resource for personalised medical research and for genotype-selected samples from unaffected individuals. The geographical genetic substructure of Finland enables efficient recruitment of donors carrying rare variants. Furthermore, we show that blood donor biobank material can be utilised for personalised blood donation policies.
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Affiliation(s)
- Jonna Clancy
- Blood Service Biobank, Finnish Red Cross Blood Service, Vantaa, Finland.
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland.
| | - Jarmo Ritari
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | | | - Mikko Arvas
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Silja Tammi
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Satu Koskela
- Blood Service Biobank, Finnish Red Cross Blood Service, Vantaa, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Jukka Partanen
- Blood Service Biobank, Finnish Red Cross Blood Service, Vantaa, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
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3
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Lieb W, Strathmann EA, Röder C, Jacobs G, Gaede KI, Richter G, Illig T, Krawczak M. Population-Based Biobanking. Genes (Basel) 2024; 15:66. [PMID: 38254956 PMCID: PMC10815030 DOI: 10.3390/genes15010066] [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: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Population-based biobanking is an essential element of medical research that has grown substantially over the last two decades, and many countries are currently pursuing large national biobanking initiatives. The rise of individual biobanks is paralleled by various networking activities in the field at both the national and international level, such as BBMRI-ERIC in the EU. A significant contribution to population-based biobanking comes from large cohort studies and national repositories, including the United Kingdom Biobank (UKBB), the CONSTANCES project in France, the German National Cohort (NAKO), LifeLines in the Netherlands, FinnGen in Finland, and the All of Us project in the U.S. At the same time, hospital-based biobanking has also gained importance in medical research. We describe some of the scientific questions that can be addressed particularly well by the use of population-based biobanks, including the discovery and calibration of biomarkers and the identification of molecular correlates of health parameters and disease states. Despite the tremendous progress made so far, some major challenges to population-based biobanking still remain, including the need to develop strategies for the long-term sustainability of biobanks, the handling of incidental findings, and the linkage of sample-related and sample-derived data to other relevant resources.
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Affiliation(s)
- Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; (E.A.S.); (C.R.)
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany; (K.I.G.); (G.R.); (T.I.)
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
| | - Eike A. Strathmann
- Institute of Epidemiology and Biobank Popgen, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; (E.A.S.); (C.R.)
| | - Christian Röder
- Institute of Epidemiology and Biobank Popgen, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; (E.A.S.); (C.R.)
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
- Institute for Experimental Cancer Research (IET), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology and Biobank Popgen, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; (E.A.S.); (C.R.)
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
| | - Karoline I. Gaede
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany; (K.I.G.); (G.R.); (T.I.)
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
- BioMaterialBank (BMB) North, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Gesine Richter
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany; (K.I.G.); (G.R.); (T.I.)
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
- Institute of Experimental Medicine (IEM), Division of Biomedical Ethics, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Thomas Illig
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany; (K.I.G.); (G.R.); (T.I.)
- Hannover Unified Biobank (HUB), Hannover Medical School, 30625 Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), 30625 Hannover, Germany
| | - Michael Krawczak
- PopGen 2.0 Biobanking Network (P2N), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany;
- Institute of Medical Informatics and Statistics (IMIS), Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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4
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Aulanko I, Rahikkala E, Moilanen J. Psychiatric symptoms in Salla disease. Eur Child Adolesc Psychiatry 2023; 32:2043-2047. [PMID: 35796883 PMCID: PMC10533638 DOI: 10.1007/s00787-022-02031-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
Salla disease (SD) is a rare lysosomal storage disorder characterised by intellectual disability ataxia, athetosis, nystagmus, and central nervous system demyelination. Although the neurological spectrum of SD's clinical phenotype is well defined, psychotic symptoms in SD remain unreported. We reviewed the presence of psychiatric symptoms in patients diagnosed with SD. Medical records of all SD patients at Oulu University Hospital during the years 1982-2015 were systematically reviewed to evaluate the presence of psychiatric symptoms. Psychiatric symptoms were frequently associated with SD (10/24, 42%), and two patients were described as developing psychosis as adolescents. We reported their clinical characteristics in detail and assessed the prevalence of psychiatric symptoms in a cohort of 24 patients. Other psychiatric factors associated with SD were sleeping disorders (8/24, 32%), aggressive behaviour disorders or restlessness (6/24, 25%), and off-label antipsychotic medication (4/24, 17%). This report expands the knowledge of the phenotypic spectrum of SD and demonstrates the importance of recognising the possibility of psychiatric symptoms, including psychosis, in persons with SD.
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Affiliation(s)
- Ida Aulanko
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.
- Doctoral Programme in Clinical Research, University of Helsinki, Helsinki, Finland.
- Department of Clinical Genetics, Oulu University Hospital, OYS, P.O. Box 23, 90029, Oulu, Finland.
| | - Elisa Rahikkala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Genetics, Oulu University Hospital, OYS, P.O. Box 23, 90029, Oulu, Finland
| | - Jukka Moilanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, OYS, P.O. Box 23, 90029, Oulu, Finland
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5
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Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, Obeidat ME, Okafo G, Ollila HM, Palomäki A, Palotie T, Partanen J, Paul DS, Pelkonen M, Pendergrass RK, Petrovski S, Pitkäranta A, Platt A, Pulford D, Punkka E, Pussinen P, Raghavan N, Rahimov F, Rajpal D, Renaud NA, Riley-Gillis B, Rodosthenous R, Saarentaus E, Salminen A, Salminen E, Salomaa V, Schleutker J, Serpi R, Shen HY, Siegel R, Silander K, Siltanen S, Soini S, Soininen H, Sul JH, Tachmazidou I, Tasanen K, Tienari P, Toppila-Salmi S, Tukiainen T, Tuomi T, Turunen JA, Ulirsch JC, Vaura F, Virolainen P, Waring J, Waterworth D, Yang R, Nelis M, Reigo A, Metspalu A, Milani L, Esko T, Fox C, Havulinna AS, Perola M, Ripatti S, Jalanko A, Laitinen T, Mäkelä TP, Plenge R, McCarthy M, Runz H, Daly MJ, Palotie A. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 2023; 613:508-518. [PMID: 36653562 PMCID: PMC9849126 DOI: 10.1038/s41586-022-05473-8] [Citation(s) in RCA: 995] [Impact Index Per Article: 995.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
Abstract
Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.
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Affiliation(s)
- Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Kati M Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mary P Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health, University of Tampere, Tampere, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Mattsson
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Päivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Pietro Della Briotta Parolo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Arto A Lehisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Masahiro Kanai
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumar Veerapen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sami Koskelainen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Paajanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vincent Llorens
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Kadri Reis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Benjamin Sun
- Translational Biology, Research and Development, Biogen, Cambridge, MA, USA
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher N Foley
- Optima Partners, Edinburgh, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | | | - Olli Carpen
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Oluwaseun A Dada
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Zhihao Ding
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | | | - Kari Eklund
- Division of Rheumatology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Orton Orthopedic Hospital, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | - Antti Hakanen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Åsa K Hedman
- Pfizer, New York, NY, USA
- Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Mikko Hiltunen
- Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Iiris Hovatta
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Laura Huilaja
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | | | | | | | - Heikki Joensuu
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Valtteri Julkunen
- Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Marc Jung
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Juhani Junttila
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Reetta Kälviäinen
- Epilepsy Center, Kuopio University Hospital, Kuopio, Finland
- Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Terhi Kilpi
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Veli-Matti Kosma
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Teijo Kuopio
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
| | - Venla Kurra
- Department of Clinical Genetics, Tampere University Hospital, Tampere, Finland
- Department of Clinical Genetics, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jari Laukkanen
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
- Department of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, Helsinki, Finland
| | - Anders Malarstig
- Pfizer, Cambridge, MA, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - Arto Mannermaa
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | | | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Tuomo Meretoja
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Marianna Niemi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- TAUCHI Research Center & Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Turku University Hospital and University of Turku, Turku, Finland
| | | | - Ma En Obeidat
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - George Okafo
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antti Palomäki
- Turku University Hospital and University of Turku, Turku, Finland
| | - Tuula Palotie
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Helsinki, Finland
- Finnish Hematological Biobank, Helsinki, Finland
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margit Pelkonen
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anne Pitkäranta
- Department of Otorhinolaryngology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Eero Punkka
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | | | | | - Deepak Rajpal
- Translational Sciences, Sanofi R&D, Framingham, MA, USA
| | - Nicole A Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rodosthenis Rodosthenous
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Eveliina Salminen
- Helsinki University Hospital, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Johanna Schleutker
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Raisa Serpi
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sanna Siltanen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Sirpa Soini
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Ioanna Tachmazidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kaisa Tasanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sanna Toppila-Salmi
- Department of Allergy, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, Helsinki University Hospital, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Felix Vaura
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- University of Turku, Turku, Finland
| | - Petri Virolainen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Mari Nelis
- Genomics Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tarja Laitinen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tomi P Mäkelä
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | | | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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6
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Rajala K, Kasanen E, Toiviainen‐Salo S, Valta H, Mäkitie O, Stefanovic V, Tanner L. Genetic spectrum of prenatally diagnosed skeletal dysplasias in a Finnish patient cohort. Prenat Diagn 2022; 42:1525-1537. [PMID: 35611473 PMCID: PMC9796183 DOI: 10.1002/pd.6186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/29/2022] [Accepted: 05/17/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE This retrospective cohort study aims to describe the genetic spectrum of fetal skeletal dysplasias detected in a Finnish patient cohort and the diagnostic yield of various analysis methods used. METHOD A total of 121 pregnancies with prenatally suspected or diagnosed skeletal dysplasia were analyzed between 2013 and 2020. Clinical details and findings from genetic testing were collected. RESULTS Abnormal ultrasound triggered further testing in most cases. However, there were several cases with increased nuchal translucency and/or abnormal risk ratio in the first trimester combined screening as the initial finding. Further genetic testing was performed in 84/121 (69.4%) cases. A genetic diagnosis was confirmed in 36/84 (42.9%) cases. Half of the identified cases could be attributed to a founder mutation specific to the Finnish Disease Heritage, whereas the other half consisted of a variety of other genetic defects. CONCLUSION In our patient cohort, the overall genetic spectrum of prenatally diagnosed skeletal dysplasias was wide. However, the impact of Finnish founder mutations was considerable, suggesting that the genetic spectrum of skeletal dysplasias may differ significantly between populations. This should be taken into consideration during the diagnostic process especially as initial ultrasound findings may be unspecific and the interpretation of ultrasound features is usually difficult.
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Affiliation(s)
- Katri Rajala
- Department of Clinical GeneticsKuopio University HospitalKuopioFinland,University of HelsinkiHelsinkiFinland
| | | | - Sanna Toiviainen‐Salo
- Department of Pediatric RadiologyHUS Medical Imaging CenterHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland,Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Helena Valta
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland,Children’s Hospital and Pediatric Research CenterHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Outi Mäkitie
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland,Children’s Hospital and Pediatric Research CenterHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Vedran Stefanovic
- Department of Obstetrics and GynecologyFetomaternal Medical CenterHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Laura Tanner
- Department of Obstetrics and GynecologyFetomaternal Medical CenterHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland,HUSLAB Department of Clinical GeneticsHelsinki University HospitalHelsinkiFinland,Department of Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland
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7
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Upasana K, Thakkar D, Gautam D, Sachdev MS, Yadav A, Kapoor R, Raghunathan V, Dhaliwal MS, Bhargava K, Nair S, Sharma J, Rastogi N, Yadav SP. Wilms tumor with Mulibrey Nanism: A case report and review of literature. Cancer Rep (Hoboken) 2022; 5:e1512. [PMID: 34309235 PMCID: PMC9124505 DOI: 10.1002/cnr2.1512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/21/2021] [Accepted: 07/02/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Mulibrey-Nanism (Muscle-liver-brain-eye Nanism = dwarfism; MUL) is a rare genetic syndrome. The underlying TRIM37 mutation predisposes these children to develop tumors frequently. In the largest published series of MUL, 8% patients were reported to develop Wilms tumor (WT). The published literature lacks data regarding the best treatment protocol and outcome of this cohort of children with WT and MUL. We report here a 2-year-old boy with WT and MUL and present a review of literature on WT in MUL. CASE Our patient had associated cardiac problems of atrial septal defect, atrial flutter and an episode of sudden cardiac arrest. We managed him successfully with chemotherapy, surgery and multi-speciality care. He is alive and in remission at follow-up of 6 months. CONCLUSION A total of 14 cases (including present case) of WT have been reported in MUL and treatment details were available for six cases. They were managed primarily with surgery, chemotherapy with/without radiotherapy, and all achieved remission. The outcome data is available only for two cases, one has been followed up till 15 years post treatment for WT and other is our patient.
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Affiliation(s)
- Karthik Upasana
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
| | - Dhwanee Thakkar
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
| | - Dheeraj Gautam
- Department of PathologyMedanta The MedicityGurgaonHaryanaIndia
| | | | - Anjali Yadav
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
| | - Rohit Kapoor
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
| | - Veena Raghunathan
- Pediatric Intensive Care Unit, Department of PediatricsMedanta The MedicityGurgaonHaryanaIndia
| | - Maninder Singh Dhaliwal
- Pediatric Intensive Care Unit, Department of PediatricsMedanta The MedicityGurgaonHaryanaIndia
| | - Kartikeya Bhargava
- Department of Electrophysiology and Pacing, Heart InstituteMedanta The MedicityGurgaonHaryanaIndia
| | | | | | - Neha Rastogi
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
| | - Satya Prakash Yadav
- Pediatric Hematology Oncology and Bone Marrow Transplant Unit, Cancer InstituteMedanta The Medicity HospitalGurgaonHaryanaIndia
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8
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Siami H, Parsamanesh N, Besharati Kivi S. Young woman with hypophosphatasia: A case report. Clin Case Rep 2022; 10:e05633. [PMID: 35356190 PMCID: PMC8958189 DOI: 10.1002/ccr3.5633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/23/2022] [Accepted: 03/09/2022] [Indexed: 11/11/2022] Open
Abstract
Hypophosphatasia is a rare inherited disease defined by teeth and bone mineralization impairment leading to depletion of tissue non-specific alkaline phosphatase. We define a young woman diagnosed with hypophosphatasia (after several times alkaline phosphatase levels were low) was discovered following femoral fracture. A 30-year-old woman who presented for a history of early permanent teeth loss during the last 5 years and HPP-like symptoms in family history and bone radiograph verified bowing, deficient mineralization, and symmetrical subtrochanteric stress fractures of femurs was referred to our clinic for further management. Blood test findings defined raised phosphorus levels on two occasions at 6.2 and 5.7 mg/dl and insufficient 25-hydroxy vitamin D level. HPP early diagnosis and adequate treatment, depending on the clinical symptoms along with laboratory tests, could be effective in decreasing the suffering of the disease and side effects.
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Affiliation(s)
- Haleh Siami
- School of MedicineIslamic Azad University of Medical ScienceTehranIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical ScienceZanjanIran
| | - Shahin Besharati Kivi
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical ScienceZanjanIran
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9
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Bharadwaj T, Schrauwen I, Acharya A, Nouel‐Saied LM, Väisänen M, Kraatari M, Rahikkala E, Jarvela I, Kotimäki J, Leal SM. Autosomal recessive nonsyndromic hearing impairment in two Finnish families due to the population enriched CABP2 c.637+1G>T variant. Mol Genet Genomic Med 2022; 10:e1866. [PMID: 35150090 PMCID: PMC8922966 DOI: 10.1002/mgg3.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genetic architecture of hearing impairment in Finland is largely unknown. Here, we investigated two Finnish families with autosomal recessive nonsyndromic symmetrical moderate-to-severe hearing impairment. METHODS Exome and custom capture next-generation sequencing were used to detect the underlying cause of hearing impairment. RESULTS In both Finnish families, we identified a homozygous pathogenic splice site variant c.637+1G>T in CAPB2 that is known to cause autosomal recessive nonsyndromic hearing impairment. Four CABP2 variants have been reported to underlie autosomal recessive nonsyndromic hearing impairment in eight families from Iran, Turkey, Pakistan, Italy, and Denmark. Of these variants, the pathogenic splice site variant c.637+1G>T is the most prevalent. The c.637+1G>T variant is enriched in the Finnish population, which has undergone multiple bottlenecks that can lead to the higher frequency of certain variants including those involved in disease. CONCLUSION We report two Finnish families with hearing impairment due to the CABP2 splice site variant c.637+1G>T.
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Affiliation(s)
- Thashi Bharadwaj
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Isabelle Schrauwen
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Anushree Acharya
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Liz M. Nouel‐Saied
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
| | - Marja‐Leena Väisänen
- Northern Finland Laboratory Centre NordLab and Medical Research CentreOulu University Hospital and University of OuluOuluFinland
| | - Minna Kraatari
- Department of Clinical GeneticsPEDEGO Research Unit and Medical Research Center OuluOulu University Hospital and University of OuluOuluFinland
| | - Elisa Rahikkala
- Department of Clinical GeneticsPEDEGO Research Unit and Medical Research Center OuluOulu University Hospital and University of OuluOuluFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Irma Jarvela
- Department of Medical GeneticsUniversity of HelsinkiHelsinkiFinland
| | - Jouko Kotimäki
- Department of OtorhinolaryngologyKainuu Central HospitalKajaaniFinland
| | - Suzanne M. Leal
- Center for Statistical GeneticsGertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNYUSA
- Taub Institute for Alzheimer’s Disease and the Aging BrainColumbia University Medical CenterNew YorkNYUSA
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10
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Zárybnický T, Heikkinen A, Kangas SM, Karikoski M, Martínez-Nieto GA, Salo MH, Uusimaa J, Vuolteenaho R, Hinttala R, Sipilä P, Kuure S. Modeling Rare Human Disorders in Mice: The Finnish Disease Heritage. Cells 2021; 10:cells10113158. [PMID: 34831381 PMCID: PMC8621025 DOI: 10.3390/cells10113158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/31/2022] Open
Abstract
The modification of genes in animal models has evidently and comprehensively improved our knowledge on proteins and signaling pathways in human physiology and pathology. In this review, we discuss almost 40 monogenic rare diseases that are enriched in the Finnish population and defined as the Finnish disease heritage (FDH). We will highlight how gene-modified mouse models have greatly facilitated the understanding of the pathological manifestations of these diseases and how some of the diseases still lack proper models. We urge the establishment of subsequent international consortiums to cooperatively plan and carry out future human disease modeling strategies. Detailed information on disease mechanisms brings along broader understanding of the molecular pathways they act along both parallel and transverse to the proteins affected in rare diseases, therefore also aiding understanding of common disease pathologies.
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Affiliation(s)
- Tomáš Zárybnický
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland;
| | - Anne Heikkinen
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- Oulu Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland
| | - Salla M. Kangas
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
| | - Marika Karikoski
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
| | - Guillermo Antonio Martínez-Nieto
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
- Turku Center for Disease Modelling (TCDM), Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Miia H. Salo
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
| | - Johanna Uusimaa
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
- Clinic for Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 20, 90029 Oulu, Finland
| | - Reetta Vuolteenaho
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
| | - Reetta Hinttala
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
| | - Petra Sipilä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
- Turku Center for Disease Modelling (TCDM), Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
| | - Satu Kuure
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland;
- GM-Unit, Laboratory Animal Center, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
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11
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Ghesh L, Musquer MD, Devisme L, Stichelbout M, Boutaud L, Elkhartoufi N, Vaast P, Boute O, Riteau AS, Le Vaillant C, Winer N, Joubert M, Bezieau S, Thomas S, Attie-Bitach T, Beneteau C. The first two non-Finnish HYLS1 variants: Expanding the phenotypic spectrum of hydrolethalus syndrome. Clin Genet 2021; 100:462-467. [PMID: 34212369 DOI: 10.1111/cge.14021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/30/2022]
Abstract
Hydrolethalus syndrome (HLS) is a rare lethal fetal malformation disorder related to ciliogenesis disruption. This condition is more frequent in Finland where a founder missense variant in the HYLS1 gene was identified. No other HYLS1 variant has hitherto been implicated in HLS. We report two unrelated French fetuses presenting with a phenotype of HLS with brain abnormalities, limbs malformations with pre and postaxial hexadactyly and abnormal genitalia. These two fetuses have compound heterozygous variants in HYLS1. The first allele carries the same Finnish missense variant (NM_145014.2: c.632A > G, p.[Asp211Gly]) in both fetuses and the second allele carries a new missense variant (c.662G > C, p.[Arg221Pro]) in the first fetus, and a new nonsense variant (c.613C > T, p.[Arg205*]) in the second fetus. This is the first report of HYLS1 mutated cases outside Finland. Both cases presented here are consistent with HLS with additional malformations, allowing expansion of the phenotypic presentation previously described.
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Affiliation(s)
- Leïla Ghesh
- Service de Génétique Médicale, CHU Nantes, Nantes, France.,UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France
| | - Marie Denis Musquer
- UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France.,Service d'Anatomie et Cytologie Pathologiques, CHU Nantes, Nantes, France
| | - Louise Devisme
- Service d'Anatomie et Cytologie Pathologiques, CHRU de Lille, Lille, France
| | | | - Lucile Boutaud
- Service d'Histo-Embryologie et de Cytogénétique, Unité d'Embryofoetopathologie, Hôpital Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris, Paris, France.,Institut Imagine, INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - Nadia Elkhartoufi
- Service d'Histo-Embryologie et de Cytogénétique, Unité d'Embryofoetopathologie, Hôpital Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Pascal Vaast
- Service d'Echographie Fœtale et de Médecine Fœtale, CHRU de Lille, Lille, France
| | - Odile Boute
- Service de Génétique Médicale, CHRU de Lille, Lille, France
| | - Anne-Sophie Riteau
- Service de Gynécologie-Obstétrique, CHU Nantes, Nantes, France.,Service de Gynécologie-Obstétrique, Clinique Jules Vernes, Nantes, France
| | | | - Norbert Winer
- Service de Gynécologie-Obstétrique, CHU Nantes, Nantes, France.,UMR PhAN 1280 NUN INRAE F-44000, Université de Nantes, Nantes, France
| | - Madeleine Joubert
- UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France.,Service d'Anatomie et Cytologie Pathologiques, CHU Nantes, Nantes, France
| | - Stéphane Bezieau
- Service de Génétique Médicale, CHU Nantes, Nantes, France.,L'institut du Thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Sophie Thomas
- Institut Imagine, INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - Tania Attie-Bitach
- Service d'Histo-Embryologie et de Cytogénétique, Unité d'Embryofoetopathologie, Hôpital Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris, Paris, France.,Institut Imagine, INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - Claire Beneteau
- Service de Génétique Médicale, CHU Nantes, Nantes, France.,UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France
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12
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SLC26A2-Associated Diastrophic Dysplasia and rMED-Clinical Features in Affected Finnish Children and Review of the Literature. Genes (Basel) 2021; 12:genes12050714. [PMID: 34064542 PMCID: PMC8151170 DOI: 10.3390/genes12050714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Diastrophic dysplasia (DTD) is a rare osteochondrodysplasia characterized by short-limbed short stature and joint dysplasia. DTD is caused by mutations in SLC26A2 and is particularly common in the Finnish population. However, the disease incidence in Finland and clinical features in affected individuals have not been recently explored. This registry-based study aimed to investigate the current incidence of DTD in Finland, characterize the national cohort of pediatric subjects with DTD and review the disease-related literature. Subjects with SLC26A2-related skeletal dysplasia, born between 2000 and 2020, were identified from the Skeletal dysplasia registry and from hospital patient registry and their clinical and molecular data were reviewed. Fourteen subjects were identified. Twelve of them were phenotypically classified as DTD and two, as recessive multiple epiphyseal dysplasia (rMED). From the subjects with available genetic data, 75% (9/12) were homozygous for the Finnish founder mutation c.-26+2T>C. Two subjects with rMED phenotype were compound heterozygous for p.Arg279Trp and p.Thr512Lys variants. The variable phenotypes in our cohort highlight the wide spectrum of clinical features, ranging from a very severe form of DTD to milder forms of DTD and rMED. The incidence of DTD in Finland has significantly decreased over the past decades, most likely due to increased prenatal diagnostics.
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13
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Jain A, Sharma D, Bajaj A, Gupta V, Scaria V. Founder variants and population genomes-Toward precision medicine. ADVANCES IN GENETICS 2021; 107:121-152. [PMID: 33641745 DOI: 10.1016/bs.adgen.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Human migration and community specific cultural practices have contributed to founder events and enrichment of the variants associated with genetic diseases. While many founder events in isolated populations have remained uncharacterized, the application of genomics in clinical settings as well as for population scale studies in the recent years have provided an unprecedented push towards identification of founder variants associated with human health and disease. The discovery and characterization of founder variants could have far reaching implications not only in understanding the history or genealogy of the disease, but also in implementing evidence based policies and genetic testing frameworks. This further enables precise diagnosis and prevention in an attempt towards precision medicine. This review provides an overview of founder variants along with methods and resources cataloging them. We have also discussed the public health implications and examples of prevalent disease associated founder variants in specific populations.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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14
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Pirttisalo A, Soilu‐Hänninen M, Sumelahti M, Krökki O, Murtonen A, Hänninen K, Sipilä JOT. Changes in multiple sclerosis epidemiology in Finland over five decades. Acta Neurol Scand 2020; 142:200-209. [PMID: 32500607 DOI: 10.1111/ane.13295] [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: 04/06/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 02/03/2023]
Abstract
Finland is a high-risk region for multiple sclerosis (MS) with several epidemiological studies on the subject published since 1964, but these have not been comprehensively scrutinized. The objective of this study was to review previous studies of Finnish MS epidemiology, introduce new data on MS prevalence in western parts of Finland and do further analyses on data from previous studies. We performed a systematic search on articles regarding MS epidemiology in Finland in PubMed database, and all relevant articles were included in this review. MS prevalences in the western hospital districts of Vaasa, South Ostrobothnia and Pirkanmaa were calculated in 1980-2007 by using previously unpublished data obtained from a retrospective search from hospital administrative registries. To enhance comparability of the epidemiological figures, we calculated age-standardized prevalence of MS from the new data from western hospital districts and previous data from North Ostrobothnia, Southwest Finland and North Karelia. Marked regional differences in MS epidemiology were confirmed with concentration of the disease in the western and south-western parts of the country. The highest regional age-standardized MS prevalence of 288/100 000 was reported in South Ostrobothnia in 2007. A clear and stable increase in MS prevalence was observed through the decades, but the only marked increase in incidence happened in 1990s. Methodological differences hampered direct comparisons of different studies, highlighting the importance of common principles of reporting and standardizing the epidemiological figures. More comprehensive studies on MS epidemiology are still warranted to yield important information concerning the aetiology of the disease.
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Affiliation(s)
- Anna‐Leena Pirttisalo
- Division of Clinical Neurosciences Turku University Hospital University of Turku Turku Finland
| | - Merja Soilu‐Hänninen
- Division of Clinical Neurosciences Turku University Hospital University of Turku Turku Finland
| | | | - Olga Krökki
- Department of Medical Rehabilitation Oulu University Hospital Oulu Finland
| | - Annukka Murtonen
- Faculty of Medicine and Health Technology University of Tampere Tampere Finland
| | - Katariina Hänninen
- Division of Clinical Neurosciences Turku University Hospital University of Turku Turku Finland
| | - Jussi O. T. Sipilä
- Division of Clinical Neurosciences Turku University Hospital University of Turku Turku Finland
- Department of Neurology Siun sote, North Karelia Central Hospital Joensuu Finland
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15
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Ignatius E, Isohanni P, Pohjanpelto M, Lahermo P, Ojanen S, Brilhante V, Palin E, Suomalainen A, Lönnqvist T, Carroll CJ. Genetic background of ataxia in children younger than 5 years in Finland. NEUROLOGY-GENETICS 2020; 6:e444. [PMID: 32637629 PMCID: PMC7323479 DOI: 10.1212/nxg.0000000000000444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/27/2020] [Indexed: 11/15/2022]
Abstract
Objective To characterize the genetic background of molecularly undefined childhood-onset ataxias in Finland. Methods This study examined a cohort of patients from 50 families with onset of an ataxia syndrome before the age of 5 years collected from a single tertiary center, drawing on the advantages offered by next generation sequencing. A genome-wide genotyping array (Illumina Infinium Global Screening Array MD-24 v.2.0) was used to search for copy number variation undetectable by exome sequencing. Results Exome sequencing led to a molecular diagnosis for 20 probands (40%). In the 23 patients examined with a genome-wide genotyping array, 2 additional diagnoses were made. A considerable proportion of probands with a molecular diagnosis had de novo pathogenic variants (45%). In addition, the study identified a de novo variant in a gene not previously linked to ataxia: MED23. Patients in the cohort had medically actionable findings. Conclusions There is a high heterogeneity of causative mutations in this cohort despite the defined age at onset, phenotypical overlap between patients, the founder effect, and genetic isolation in the Finnish population. The findings reflect the heterogeneous genetic background of ataxia seen worldwide and the substantial contribution of de novo variants underlying childhood ataxia.
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Affiliation(s)
- Erika Ignatius
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Pirjo Isohanni
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Max Pohjanpelto
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Päivi Lahermo
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Simo Ojanen
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Virginia Brilhante
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Eino Palin
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Anu Suomalainen
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Tuula Lönnqvist
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
| | - Christopher J Carroll
- Department of Child Neurology (E.I., P.I., T.L.), Children's Hospital, University of Helsinki and Helsinki University Hospital; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine (E.I., P.I., M.P., S.O., V.B., E.P., A.S.), Institute for Molecular Medicine Finland (FIMM) (P.L.), Neuroscience Center (A.S.), HiLife, University of Helsinki, Finland; and Genetics Research Centre (C.J.C.), Molecular and Clinical Sciences Research Institute, St. George's, University of London, United Kingdom
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16
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Avela K, Salonen‐Kajander R, Laitinen A, Ramsden S, Barton S, Rudanko S. The genetic aetiology of retinal degeneration in children in Finland - new founder mutations identified. Acta Ophthalmol 2019; 97:805-814. [PMID: 31087526 DOI: 10.1111/aos.14128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/10/2019] [Indexed: 01/22/2023]
Abstract
PURPOSE To study the genetic aetiology and phenotypes of retinal degeneration (RD) in Finnish children born during 1993-2009. METHODS Children with retinal degeneration (N = 68) were investigated during 2012-2014 with a targeted gene analysis or a next-generation sequencing (NGS) based gene panel. Also, a full clinical ophthalmological examination was performed. RESULTS The cohort covered 44% (68/153) of the Finnish children with inherited RD born 1993-2009. X-linked retinoschisis, retinitis pigmentosa, Leber congenital amaurosis and cone-rod dystrophy were the most common clinical diagnoses in the study group. Pathogenic mutations were found in 17 retinal genes. The molecular genetic aetiology was identified in 77% of the patients (in 77% of the families) analysed by NGS method. Several founder mutations were detected including three novel founder mutations c.148delG in TULP1, c.2314C>R (p.Gln772Ter) in RPGRIP1 and c.533G>A (Trp178Ter) in TYR. We also confirmed the previous tentative finding of c.2944 + 1delG in GYCU2D being the most frequent cause of Leber congenital amaurosis (LCA) in Finland. CONCLUSIONS Globally, RD is genetically heterogeneous with over 260 disease genes reported so far. This was shown not to be the case in Finland, where the genetic aetiology of RD is caused by a small group of genes, due to several founder mutations that are enriched in the population. We found that X-chromosomal retinoschisis constitutes the major group in Finnish paediatric RD population and is almost exclusively caused by two founder mutations. Several other founder mutations were detected including three novel founder mutations. All in all, the genetic aetiology of 77% of families was identified which is higher than previously reported from other populations, likely due to the specific genomic constitution of the Finns.
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Affiliation(s)
- Kristiina Avela
- The Department of Clinical Genetics Helsinki University Hospital, HUSLAB Helsinki Finland
| | | | - Arja Laitinen
- The Department of Ophthalmology Helsinki University Hospital Helsinki Finland
| | - Simon Ramsden
- St Mary′s Hospital Central Manchester University Hospitals and Manchester Centre for Genomic Medicine Manchester UK
| | - Stephanie Barton
- St Mary′s Hospital Central Manchester University Hospitals and Manchester Centre for Genomic Medicine Manchester UK
| | - Sirkka‐Liisa Rudanko
- Visio Low Vision Research Centre Finnish Federation of the Visually Impaired Helsinki Finland
- Finnish Register of Visual Impairment by National Institute for Health and Welfare Helsinki Finland
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17
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Schwartz PJ, Crotti L, George AL. Modifier genes for sudden cardiac death. Eur Heart J 2018; 39:3925-3931. [PMID: 30215713 PMCID: PMC6247660 DOI: 10.1093/eurheartj/ehy502] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/28/2018] [Indexed: 01/07/2023] Open
Abstract
Genetic conditions, even those associated with identical gene mutations, can present with variable clinical manifestations. One widely accepted explanation for this phenomenon is the existence of genetic factors capable of modifying the consequences of disease-causing mutations (modifier genes). Here, we address the concepts and principles by which genetic factors may be involved in modifying risk for cardiac arrhythmia, then discuss the current knowledge and interpretation of their contribution to clinical heterogeneity. We illustrate these concepts in the context of two important clinical conditions associated with risk for sudden cardiac death including a monogenic disorder (congenital long QT syndrome) in which the impact of modifier genes has been established, and a complex trait (life-threatening arrhythmias in acute myocardial infarction) for which the search for genetic modifiers of arrhythmic risk is more challenging. Advances in understanding the contribution of modifier genes to a higher or lower propensity towards sudden death should improve patient-specific risk stratification and be a major step towards precision medicine.
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Affiliation(s)
- Peter J Schwartz
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Via Pier Lombardo, 22, Milan, Italy
- Corresponding author. Tel: +39 02 55000408, Fax: +39 02 55000411, ;
| | - Lia Crotti
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Via Pier Lombardo, 22, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Via Cadore, 48, Monza, Italy
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Piazzale Brescia 20, Milan, Italy
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Searle 8-510, East Superior Street, Chicago, IL, USA
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18
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Huhtaniemi I. MECHANISMS IN ENDOCRINOLOGY: Hormonal regulation of spermatogenesis: mutant mice challenging old paradigms. Eur J Endocrinol 2018; 179:R143-R150. [PMID: 29959220 DOI: 10.1530/eje-18-0396] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/28/2018] [Indexed: 11/08/2022]
Abstract
The two pituitary gonadotrophins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH), and in particular LH-stimulated high intratesticular testosterone (ITT) concentration, are considered crucial for spermatogenesis. We have revisited these concepts in genetically modified mice, one being the LH receptor (R)-knockout mouse (LuRKO), the other a transgenic mouse expressing in Sertoli cells a highly constitutively active mutated Fshr (Fshr-CAM). It was found that full spermatogenesis was induced by exogenous testosterone treatment in LuRKO mice at doses that restored ITT concentration to a level corresponding to the normal circulating testosterone level in WT mice, ≈5 nmol/L, which is 1.4% of the normal high ITT concentration. When hypogonadal LuRKO and Fshr-CAM mice were crossed, the double-mutant mice with strong FSH signaling, but minimal testosterone production, showed near-normal spermatogenesis, even when their residual androgen action was blocked with the strong antiandrogen flutamide. In conclusion, our findings challenge two dogmas of the hormonal regulation of male fertility: (1) high ITT concentration is not necessary for spermatogenesis and (2) strong FSH stimulation can maintain spermatogenesis without testosterone. These findings have clinical relevance for the development of hormonal male contraception and for the treatment of idiopathic oligozoospermia.
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Affiliation(s)
- Ilpo Huhtaniemi
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Hammersmith Campus, London, UK
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
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19
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Abstract
Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP) and FineSTRUCTURE (FS) we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Nöteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.
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20
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Genetics in an isolated population like Finland: a different basis for genomic medicine? J Community Genet 2017; 8:319-326. [PMID: 28730583 PMCID: PMC5614886 DOI: 10.1007/s12687-017-0318-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/29/2017] [Indexed: 11/24/2022] Open
Abstract
A unique genetic background in an isolated population like that of Finland offers special opportunities for genetic research as well as for applying the genetic developments to the health care. On the other hand, the different genetic background may require local attempts to develop diagnostics and treatment as the selection of diseases and mutations differs from that in the other populations. In this review, we describe the experiences of research and health care in this genetic isolate starting from the identification of specific monogenic diseases enriched in the Finnish population all the way to implementing the knowledge of the unique genetic background to genomic medicine at population level.
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21
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Leinonen H, Keksa-Goldsteine V, Ragauskas S, Kohlmann P, Singh Y, Savchenko E, Puranen J, Malm T, Kalesnykas G, Koistinaho J, Tanila H, Kanninen KM. Retinal Degeneration In A Mouse Model Of CLN5 Disease Is Associated With Compromised Autophagy. Sci Rep 2017; 7:1597. [PMID: 28487519 PMCID: PMC5431647 DOI: 10.1038/s41598-017-01716-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/04/2017] [Indexed: 11/25/2022] Open
Abstract
The Finnish variant of late infantile neuronal ceroid lipofuscinosis (CLN5 disease) belongs to a family of neuronal ceroid lipofuscinosis (NCLs) diseases. Vision loss is among the first clinical signs in childhood forms of NCLs. Mutations in CLN5 underlie CLN5 disease. The aim of this study was to characterize how the lack of normal functionality of the CLN5 protein affects the mouse retina. Scotopic electroretinography (ERG) showed a diminished c-wave amplitude in the CLN5 deficient mice already at 1 month of age, indicative of pathological events in the retinal pigmented epithelium. A- and b-waves showed progressive impairment later from 2 and 3 months of age onwards, respectively. Structural and immunohistochemical (IHC) analyses showed preferential damage of photoreceptors, accumulation of autofluorescent storage material, apoptosis of photoreceptors, and strong inflammation in the CLN5 deficient mice retinas. Increased levels of autophagy-associated proteins Beclin-1 and P62, and increased LC3b-II/LC3b-I ratio, were detected by Western blotting from whole retinal extracts. Photopic ERG, visual evoked potentials, IHC and cell counting indicated relatively long surviving cone photoreceptors compared to rods. In conclusion, CLN5 deficient mice develop early vision loss that reflects the condition reported in clinical childhood forms of NCLs. The vision loss in CLN5 deficient mice is primarily caused by photoreceptor degeneration.
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Affiliation(s)
- Henri Leinonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
| | - Velta Keksa-Goldsteine
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Philip Kohlmann
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Yajuvinder Singh
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ekaterina Savchenko
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Giedrius Kalesnykas
- Experimentica Ltd., Kuopio, Finland
- Research and Development Centre for Ophthalmic Innovations (SILK), Department of Ophthalmology, University of Tampere, Tampere, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Heikki Tanila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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Lescai F, Als TD, Li Q, Nyegaard M, Andorsdottir G, Biskopstø M, Hedemand A, Fiorentino A, O'Brien N, Jarram A, Liang J, Grove J, Pallesen J, Eickhardt E, Mattheisen M, Bolund L, Demontis D, Wang AG, McQuillin A, Mors O, Wang J, Børglum AD. Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder. Transl Psychiatry 2017; 7:e1034. [PMID: 28195573 PMCID: PMC5438033 DOI: 10.1038/tp.2017.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022] Open
Abstract
Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations might help finding variants with a recent origin, more likely to have drifted to higher frequency by chance. Following this approach, we investigated 28 bipolar cases and 214 controls from the Faroe Islands by whole exome sequencing, and the results were followed-up in a British sample of 2025 cases and 1358 controls. Seventeen variants in 16 genes in the single-variant analysis, and 3 genes in the gene-based statistics surpassed exome-wide significance in the discovery phase. The discovery findings were supported by enrichment analysis of common variants from genome-wide association studies (GWAS) data and interrogation of protein-protein interaction networks. The replication in the British sample confirmed the association with NOS1 (missense variant rs79487279) and NCL (gene-based test). A number of variants from the discovery set were not present in the replication sample, including a novel PITPNM2 missense variant, which is located in a highly significant schizophrenia GWAS locus. Likewise, PIK3C2A identified in the gene-based analysis is located in a combined bipolar and schizophrenia GWAS locus. Our results show support both for existing findings in the literature, as well as for new risk genes, and identify rare variants that might provide additional information on the underlying biology of bipolar disorder.
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Affiliation(s)
- F Lescai
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - T D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Q Li
- BGI-Shenzhen, Shenzhen, China
| | - M Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - G Andorsdottir
- Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - M Biskopstø
- Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - A Hedemand
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - A Fiorentino
- Division of Psychiatry, University College London, London, UK
| | - N O'Brien
- Division of Psychiatry, University College London, London, UK
| | - A Jarram
- Division of Psychiatry, University College London, London, UK
| | - J Liang
- BGI-Shenzhen, Shenzhen, China
| | - J Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BiRC—Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - J Pallesen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - E Eickhardt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - M Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - L Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - D Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - A G Wang
- Mental Health Centre Amager, Copenhagen, Denmark
| | | | - O Mors
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - J Wang
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - A D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
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Simons YB, Sella G. The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev 2016; 41:150-158. [PMID: 27744216 DOI: 10.1016/j.gde.2016.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 01/22/2023]
Abstract
Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.
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Affiliation(s)
- Yuval B Simons
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Enrichment of rare variants in population isolates: single AICDA mutation responsible for hyper-IgM syndrome type 2 in Finland. Eur J Hum Genet 2016; 24:1473-8. [PMID: 27142677 PMCID: PMC5027683 DOI: 10.1038/ejhg.2016.37] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/12/2016] [Accepted: 03/15/2016] [Indexed: 01/21/2023] Open
Abstract
Antibody class-switch recombination and somatic hypermutation critically depend on the function of activation-induced cytidine deaminase (AID). Rare variants in its gene AICDA have been reported to cause autosomal recessive AID deficiency (autosomal recessive hyper-IgM syndrome type 2 (HIGM2)). Exome sequencing of a multicase Finnish family with an HIGM2 phenotype identified a rare, homozygous, variant (c.416T>C, p.(Met139Thr)) in the AICDA gene, found to be significantly enriched in the Finnish population compared with other populations of European origin (38.56-fold, P<0.001). The population history of Finland, characterized by a restricted number of founders, isolation and several population bottlenecks, has caused enrichment of certain rare disease-causing variants and losses of others, as part of a phenomenon called the Finnish Disease Heritage. Accordingly, rare founder mutations cause the majority of observed Finnish cases in these mostly autosomal recessive disorders that consequently are more frequent in Finland than elsewhere. Screening of all currently known Finnish patients with an HIGM2 phenotype showed them to be homozygous for p.(Met139Thr). All the Finnish p.(Met139Thr) carriers with available data on their geographic descent originated from the eastern and northeastern parts of Finland. They were observed to share more of their genome identity by descent (IBD) than Finns in general (P<0.001), and they all carried a 207.5-kb ancestral haplotype containing the variant. In conclusion, the identified p.(Met139Thr) variant is significantly enriched in Finns and explains all thus far found AID deficiencies in Finland.
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Erzurumluoglu AM, Shihab HA, Rodriguez S, Gaunt TR, Day INM. Importance of Genetic Studies in Consanguineous Populations for the Characterization of Novel Human Gene Functions. Ann Hum Genet 2016; 80:187-96. [PMID: 27000383 PMCID: PMC4949565 DOI: 10.1111/ahg.12150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/04/2023]
Abstract
Consanguineous offspring have elevated levels of homozygosity. Autozygous stretches within their genome are likely to harbour loss of function (LoF) mutations which will lead to complete inactivation or dysfunction of genes. Studying consanguineous offspring with clinical phenotypes has been very useful for identifying disease causal mutations. However, at present, most of the genes in the human genome have no disorder associated with them or have unknown function. This is presumably mostly due to the fact that homozygous LoF variants are not observed in outbred populations which are the main focus of large sequencing projects. However, another reason may be that many genes in the genome—even when completely “knocked out,” do not cause a distinct or defined phenotype. Here, we discuss the benefits and implications of studying consanguineous populations, as opposed to the traditional approach of analysing a subset of consanguineous families or individuals with disease. We suggest that studying consanguineous populations “as a whole” can speed up the characterisation of novel gene functions as well as indicating nonessential genes and/or regions in the human genome. We also suggest designing a single nucleotide variant (SNV) array to make the process more efficient.
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Affiliation(s)
- A Mesut Erzurumluoglu
- Bristol Genetic Epidemiology Laboratories (BGEL), School of Social and Community Medicine, University of Bristol, Bristol, UK.,Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Santiago Rodriguez
- Bristol Genetic Epidemiology Laboratories (BGEL), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- Bristol Genetic Epidemiology Laboratories (BGEL), School of Social and Community Medicine, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ian N M Day
- Bristol Genetic Epidemiology Laboratories (BGEL), School of Social and Community Medicine, University of Bristol, Bristol, UK
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Al Saadi T, Alkhatib M, Turk T, Turkmani K, Abbas F, Khouri L. Report of two Syrian siblings with Mulibrey nanism. Oxf Med Case Reports 2015; 2015:367-70. [PMID: 26664725 PMCID: PMC4672230 DOI: 10.1093/omcr/omv065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/08/2015] [Accepted: 11/03/2015] [Indexed: 11/14/2022] Open
Abstract
Mulibrey (MUscle–LIver–BRain–EYe) nanism is a rare autosomal recessive disease characterized by growth failure, dysmorphic features and a wide range of abnormalities affecting multiple organ systems. This report is the first to present two cases of Mulibrey nanism affecting two siblings from Syria. Mulibrey nanism can be suspected clinically due to the distinctive features of the patients. The aim of this report is to document the presence of Mulibrey nanism in Syria and to familiarize physicians in and out of Syria with this rare disease and encourage them to develop high clinical suspicion if faced with patients with similar presentations.
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Affiliation(s)
- Tareq Al Saadi
- Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
| | - Mahmoud Alkhatib
- Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
| | - Tarek Turk
- Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
| | - Khaled Turkmani
- Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
| | - Fatima Abbas
- Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
| | - Lina Khouri
- Department of Pediatrics, Faculty of Medicine , University of Damascus , Damascus , Syrian Arab Republic
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Pedersen NC, Brucker L, Tessier NG, Liu H, Penedo MCT, Hughes S, Oberbauer A, Sacks B. The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease. Canine Genet Epidemiol 2015; 2:14. [PMID: 26401342 PMCID: PMC4579369 DOI: 10.1186/s40575-015-0026-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/06/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century. Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA) region have been non-productive. However, such studies led us to hypothesize that positive selection for desired phenotypic traits that arose in the mid-twentieth century led to intense inbreeding and the inadvertent amplification of AD and SA associated traits. RESULTS This hypothesis was tested with genetic studies of 761 Standard, Miniature, and Miniature/Standard Poodle crosses from the USA, Canada and Europe, coupled with extensive pedigree analysis of thousands more dogs. Genome-wide diversity across the world-wide population was measured using a panel of 33 short tandem repeat (STR) loci. Allele frequency data were also used to determine the internal relatedness of individual dogs within the population as a whole. Assays based on linkage between STR genomic loci and DLA genes were used to identify class I and II haplotypes and disease associations. Genetic diversity statistics based on genomic STR markers indicated that Standard Poodles from North America and Europe were closely related and reasonably diverse across the breed. However, genetic diversity statistics, internal relatedness, principal coordinate analysis, and DLA haplotype frequencies showed a marked imbalance with 30 % of the diversity in 70 % of the dogs. Standard Poodles with SA and AD were strongly linked to this inbred population, with dogs suffering with SA being the most inbred. No single strong association was found between STR defined DLA class I or II haplotypes and SA or AD in the breed as a whole, although certain haplotypes present in a minority of the population appeared to confer moderate degrees of risk or protection against either or both diseases. Dogs possessing minor DLA class I haplotypes were half as likely to develop SA or AD as dogs with common haplotypes. Miniature/Standard Poodle crosses being used for outcrossing were more genetically diverse than Standard Poodles and genetically distinguishable across the genome and in the DLA class I and II region. CONCLUSIONS Ancestral genetic polymorphisms responsible for SA and AD entered Standard Poodles through separate lineages, AD earlier and SA later, and were increasingly fixed by a period of close linebreeding that was related to popular bloodlines from the mid-twentieth century. This event has become known as the midcentury bottleneck or MCB. Sustained positive selection resulted in a marked imbalance in genetic diversity across the genome and in the DLA class I and II region. Both SA and AD were concentrated among the most inbred dogs, with genetic outliers being relatively disease free. No specific genetic markers other than those reflecting the degree of inbreeding were consistently associated with either disease. Standard Poodles as a whole remain genetically diverse, but steps should be taken to rebalance diversity using genetic outliers and if necessary, outcrosses to phenotypically similar but genetically distinct breeds.
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Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, 95616 Davis, CA USA
| | - Lynn Brucker
- 1635 Grange Hall Road, 45432 Beavercreek, OH USA
| | | | - Hongwei Liu
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, 95616 Davis, CA USA
| | - Maria Cecilia T Penedo
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, One Shields Avenue, 95616 Davis, CA USA
| | - Shayne Hughes
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, One Shields Avenue, 95616 Davis, CA USA
| | - Anita Oberbauer
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, One Shields Avenue, 95616 Davis, CA USA
| | - Ben Sacks
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, One Shields Avenue, 95616 Davis, CA USA
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Paavola LE, Remes AM, Harila MJ, Varho TT, Korhonen TT, Majamaa K. A 13-year follow-up of Finnish patients with Salla disease. J Neurodev Disord 2015; 7:20. [PMID: 26171070 PMCID: PMC4499899 DOI: 10.1186/s11689-015-9116-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/10/2015] [Indexed: 12/03/2022] Open
Abstract
Background Salla disease (SD) is a rare lysosomal storage disorder leading to severe intellectual disability. SD belongs to the Finnish disease heritage, and it is caused by mutations in the SLC17A5 gene. The aim of the study was to investigate the course of neurocognitive features of SD patients in a long-term follow-up. Methods Neuropsychological and neurological investigations were carried out on 24 SD patients, aged 16–65 years, 13 years after a similar examination. Results The survival analysis showed excess mortality among patients with SD after the age of 30 years. The course of the disease was progressive, but follow-up of SD patients revealed that motor skills improved till the age of 20 years, while mental abilities improved in most patients till 40 years of age. Verbal comprehension skills did not diminish during the follow-up, but productive speech deteriorated because of dyspraxia and dysarthria. Motor deficits were marked. Ataxia was prominent in childhood, but it was replaced by athetotic movements during the teens. Spasticity became more obvious with age especially in severely disabled SD patients. Conclusions Younger SD patients performed better in almost every task measuring mental abilities that then seem to remain fairly constant till early sixties. Thus, the results indicate better prognosis in cognitive skills than earlier assumed. There is an apparent decline in motor skills after the age of 20 years. The early neurocognitive development predicts the later course of motor and cognitive development.
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Affiliation(s)
- Liisa E Paavola
- Department of Neurology, Oulu University Hospital, P.O. Box 20, 90029 Oulu, Finland ; Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland ; Department of Clinical Neurology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland ; Neural Ltd, Center of Neuropsychology, Isokatu 16 B 18, 90100 Oulu, Finland
| | - Anne M Remes
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland ; Department of Neurology, Kuopio University Hospital, P.O. Box 1777, 70211 Kuopio, Finland
| | - Marika J Harila
- Neural Ltd, Center of Neuropsychology, Isokatu 16 B 18, 90100 Oulu, Finland
| | - Tarja T Varho
- The Neuropediatric Unit of Turku City Welfare Division, P. O. Box 670, 20101 Turku, Finland
| | - Tapio T Korhonen
- Department of Psychology, University of Turku, Turku, 20014 Finland
| | - Kari Majamaa
- Department of Neurology, Oulu University Hospital, P.O. Box 20, 90029 Oulu, Finland ; Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
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Anwar WA, Khyatti M, Hemminki K. Consanguinity and genetic diseases in North Africa and immigrants to Europe. Eur J Public Health 2015; 24 Suppl 1:57-63. [PMID: 25107999 DOI: 10.1093/eurpub/cku104] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Endemic diseases are caused by environmental and genetic factors. While in this special issue several chapters deal with environmental factors, including infections, the present focus is on genetic causes of disease clustering due to inbreeding and recessive disease mechanisms. Consanguinity is implying sharing of genetic heritage because of marriage between close relatives originating from a common ancestor. With limited natural selection, recessive genes may become more frequent in an inbred compared with an outbred population. Consanguinity is common in North Africa (NA), and the estimates range from 40 to 49% of all marriages in Tunisia and 29-33% in Morocco. As a consequence, recessive disorders are common in the NA region, and we give some examples. Thalassaemia and sickle cell disease/anaemia constitute the most common inherited recessive disorders globally and they are common in NA, but with immigration they have spread to Europe and to other parts of the world. Another example is familial Mediterranean fever, which is common in the Eastern Mediterranean area. With immigrantion from that area to Sweden, it has become the most common hereditary autoinflammatory disease in that country, and there is no evidence that any native Swede would have been diagnosed with this disease. The examples discussed in this chapter show that the historic movement of populations and current immigration are influencing the concept of 'endemic' disease.
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Affiliation(s)
- Wagida A Anwar
- 1 Community Medicine Department, Ain Shams University, Cairo, Egypt
| | | | - Kari Hemminki
- 3 Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany4 Center for Primary Health Care Research, Lund University, 205 02, Malmö, Sweden
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Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process. BIOMED RESEARCH INTERNATIONAL 2015; 2015:923491. [PMID: 26106619 PMCID: PMC4461748 DOI: 10.1155/2015/923491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/17/2015] [Indexed: 01/10/2023]
Abstract
Recent technological advances have created challenges for geneticists and a need to adapt to a wide range of new bioinformatics tools and an expanding wealth of publicly available data (e.g., mutation databases, and software). This wide range of methods and a diversity of file formats used in sequence analysis is a significant issue, with a considerable amount of time spent before anyone can even attempt to analyse the genetic basis of human disorders. Another point to consider that is although many possess “just enough” knowledge to analyse their data, they do not make full use of the tools and databases that are available and also do not fully understand how their data was created. The primary aim of this review is to document some of the key approaches and provide an analysis schema to make the analysis process more efficient and reliable in the context of discovering highly penetrant causal mutations/genes. This review will also compare the methods used to identify highly penetrant variants when data is obtained from consanguineous individuals as opposed to nonconsanguineous; and when Mendelian disorders are analysed as opposed to common-complex disorders.
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Pastores GM, Hughes DA. Non-neuronopathic lysosomal storage disorders: Disease spectrum and treatments. Best Pract Res Clin Endocrinol Metab 2015; 29:173-82. [PMID: 25987171 DOI: 10.1016/j.beem.2014.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Distinctive facial features, hepatosplenomegaly or cardiomyopathy with or without associated skeletal dysplasia are clinical manifestations that may be suggestive of an underlying lysosomal storage disorder (LSD), However, these features may not be evident in certain subtypes associated primarily with central nervous system involvement. Age at onset can be broad, ranging from infancy to adulthood. Diagnosis may be delayed, as manifestations may be slow to evolve (taking months to years), particularly in those with later (adult-)onset, and in isolated cases (i.e., those without a prior family history). Diagnosis of individual subtypes can be confirmed using a combination of biochemical and molecular assays. In a few LSDs, treatment with hematopoietic stem cell transplantation, enzyme replacement or substrate reduction therapy is available. Symptomatic and palliative measure may enhance quality of life for both treatable and currently untreatable cases. Genetic counseling is important, so patients and their families can be informed of reproductive risks, disease prognosis and therapeutic options. Investigations of underlying disease mechanisms are enhancing knowledge about rare diseases, but also other more common medical conditions, on account of potential convergent disease pathways.
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Affiliation(s)
- Gregory M Pastores
- National Center for Inherited Metabolic Diseases - Adult Services, Department of Medicine, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland.
| | - Derralynn A Hughes
- Department of Haematology, Royal Free London NHS Foundation Trust and University College London, United Kingdom
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Syvänen J, Nietosvaara Y, Ritvanen A, Koskimies E, Kauko T, Helenius I. High risk for major nonlimb anomalies associated with lower-limb deficiency: a population-based study. J Bone Joint Surg Am 2014; 96:1898-904. [PMID: 25410508 DOI: 10.2106/jbjs.n.00155] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND The aims of this study were to determine the prevalence of congenital lower-limb reduction defects and associated mortality, to evaluate lower-limb deficiencies by type of reduction, and to identify patterns of associated anomalies. METHODS We conducted a population-based study with use of data from the Finnish Register of Congenital Malformations and Care Register for Health Care. All cases of lower-limb deficiency among live births, stillbirths, spontaneous abortions, and terminations of pregnancy due to fetal anomalies from 1993 to 2008 were included. We analyzed medical records and classified lower-limb reduction defects. Associated major anomalies were recorded, and perinatal mortality and infant mortality were calculated. RESULTS Two hundred and sixty-six cases with lower-limb deficiency were identified, with a total prevalence of 2.8 per 10,000 births, a birth prevalence of 2.2 per 10,000 births, and a live-birth prevalence of 2.1 per 10,000 live births. Terminal transverse limb reductions accounted for 44.7% of the cases; longitudinal reductions, 22.9%; intercalary reductions, 7.9%; multiple reductions, 8.3%; and split-foot malformations, 4.5%. In addition to lower-limb deficiency, 47.7% of the cases had other major anomalies; anomalies of internal organs were noted in 26.3% of the cases, anomalies of the axial skeleton in 13.5% of cases, and central nervous system anomalies in 12.8%. Upper-limb reductions were observed in 32.0% of the cases. The relative risk (RR) for associated major anomalies was 12.54 (95% confidence interval [CI], 11.06 to 14.23) compared with the general figures for major congenital anomalies in Finland. The RR for associated anomalies was higher (1.75; 95% CI, 1.20 to 2.53) for longitudinal preaxial lower-limb deficiencies than for the other types of lower-limb reductions. Perinatal mortality was seventy-eight per 1000 births. All infant deaths were associated with chromosomal abnormalities, other known syndromes, or additional congenital malformations. CONCLUSIONS Nearly half of the cases with lower-limb deficiencies were found to have other major anomalies. In cases of preaxial lower-limb deficiencies, the risk for associated major anomalies was highest.
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Affiliation(s)
- Johanna Syvänen
- Departments of Paediatric Orthopaedic Surgery (J.S., E.K., and I.H.) and Orthopaedic Surgery (J.S.), Turku University Central Hospital, Kiinamyllynkatu 4-8, 20520 Turku, Finland. E-mail address for J. Syvänen:
| | - Yrjänä Nietosvaara
- Department of Paediatric Orthopaedic Surgery, Helsinki University Central Hospital, Stenbäckinkatu 11, 00290 Helsinki, Finland
| | - Annukka Ritvanen
- Finnish Register of Congenital Malformations, National Institute for Health and Welfare, PL 30, 00271Helsinki, Finland
| | - Eeva Koskimies
- Departments of Paediatric Orthopaedic Surgery (J.S., E.K., and I.H.) and Orthopaedic Surgery (J.S.), Turku University Central Hospital, Kiinamyllynkatu 4-8, 20520 Turku, Finland. E-mail address for J. Syvänen:
| | - Tommi Kauko
- Biostatistics, University of Turku, Turku, Finland
| | - Ilkka Helenius
- Departments of Paediatric Orthopaedic Surgery (J.S., E.K., and I.H.) and Orthopaedic Surgery (J.S.), Turku University Central Hospital, Kiinamyllynkatu 4-8, 20520 Turku, Finland. E-mail address for J. Syvänen:
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Peischl S, Dupanloup I, Kirkpatrick M, Excoffier L. On the accumulation of deleterious mutations during range expansions. Mol Ecol 2013; 22:5972-82. [PMID: 24102784 DOI: 10.1111/mec.12524] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/15/2022]
Abstract
We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations cosegregate. We perform individual-based simulations of 1D and 2D range expansions and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front, but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load for thousands of generations after the expansion. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyse functional genetic diversity in humans and find patterns that are consistent with our model.
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Affiliation(s)
- S Peischl
- Institute of Ecology and Evolution, University of Berne, 3012, Berne, Switzerland; Section of Integrative Biology, University of Texas, Austin, TX, 78712, USA; Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
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Polvi A, Linturi H, Varilo T, Anttonen AK, Byrne M, Fokkema IFAC, Almusa H, Metzidis A, Avela K, Aula P, Kestilä M, Muilu J. The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era. Hum Mutat 2013; 34:1458-66. [PMID: 23904198 DOI: 10.1002/humu.22389] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 07/22/2013] [Indexed: 11/11/2022]
Abstract
The Finnish Disease Heritage Database (FinDis) (http://findis.org) was originally published in 2004 as a centralized information resource for rare monogenic diseases enriched in the Finnish population. The FinDis database originally contained 405 causative variants for 30 diseases. At the time, the FinDis database was a comprehensive collection of data, but since 1994, a large amount of new information has emerged, making the necessity to update the database evident. We collected information and updated the database to contain genes and causative variants for 35 diseases, including six more genes and more than 1,400 additional disease-causing variants. Information for causative variants for each gene is collected under the LOVD 3.0 platform, enabling easy updating. The FinDis portal provides a centralized resource and user interface to link information on each disease and gene with variant data in the LOVD 3.0 platform. The software written to achieve this has been open-sourced and made available on GitHub (http://github.com/findis-db), allowing biomedical institutions in other countries to present their national data in a similar way, and to both contribute to, and benefit from, standardized variation data. The updated FinDis portal provides a unique resource to assist patient diagnosis, research, and the development of new cures.
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Affiliation(s)
- Anne Polvi
- The Institute for Molecular Medicine Finland FIMM Technology Centre, University of Helsinki, Helsinki, Finland
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Västinsalo H, Jalkanen R, Bergmann C, Neuhaus C, Kleemola L, Jauhola L, Bolz HJ, Sankila EM. Extended mutation spectrum of Usher syndrome in Finland. Acta Ophthalmol 2013; 91:325-34. [PMID: 22681893 DOI: 10.1111/j.1755-3768.2012.02397.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE The Finnish distribution of clinical Usher syndrome (USH) types is 40% USH3, 34% USH1 and 12% USH2. All patients with USH3 carry the founder mutation in clarin 1 (CLRN1), whereas we recently reported three novel myosin VIIA (MYO7A) mutations in two unrelated patients with USH1. This study was carried out to further investigate the USH mutation spectrum in Finnish patients. METHODS We analysed samples from nine unrelated USH patients/families without known mutations and two USH3 families with atypically severe phenotype. The Asper Ophthalmics USH mutation chip was used to screen for known mutations and to evaluate the chip in molecular diagnostics of Finnish patients. RESULTS The chip revealed a heterozygous usherin (USH2A) mutation, p.N346H, in one patient. Sequencing of MYO7A and/or USH2A in three index patients revealed two novel heterozygous mutations, p.R873W in MYO7A and c.14343+2T>C in USH2A. We did not identify definite pathogenic second mutations in the patients, but identified several probably nonpathogenic variations that may modify the disease phenotype. Possible digenism could not be excluded in two families segregating genomic variations in both MYO7A and USH2A, and two families with CLRN1 and USH2A. CONCLUSION We conclude that there is considerable genetic heterogeneity of USH1 and USH2 in Finland, making molecular diagnostics and genetic counselling of patients and families challenging.
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Affiliation(s)
- Hanna Västinsalo
- The Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland.
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Güzel-Ozantürk A, Özgül RK, Ünal Ö, Hişmi B, Aydın Hİ, Sivri S, Tokatlı A, Coşkun T, Aksöz E, Dursun A. Molecular and clinical evaluation of Turkish patients with lysinuric protein intolerance. Gene 2013; 521:293-5. [DOI: 10.1016/j.gene.2013.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/08/2013] [Indexed: 11/29/2022]
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Polvi A, Linnankivi T, Kivelä T, Herva R, Keating J, Mäkitie O, Pareyson D, Vainionpää L, Lahtinen J, Hovatta I, Pihko H, Lehesjoki AE. Mutations in CTC1, encoding the CTS telomere maintenance complex component 1, cause cerebroretinal microangiopathy with calcifications and cysts. Am J Hum Genet 2012; 90:540-9. [PMID: 22387016 PMCID: PMC3309194 DOI: 10.1016/j.ajhg.2012.02.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/27/2012] [Accepted: 02/02/2012] [Indexed: 01/26/2023] Open
Abstract
Cerebroretinal microangiopathy with calcifications and cysts (CRMCC) is a rare multisystem disorder characterized by extensive intracranial calcifications and cysts, leukoencephalopathy, and retinal vascular abnormalities. Additional features include poor growth, skeletal and hematological abnormalities, and recurrent gastrointestinal bleedings. Autosomal-recessive inheritance has been postulated. The pathogenesis of CRMCC is unknown, but its phenotype has key similarities with Revesz syndrome, which is caused by mutations in TINF2, a gene encoding a member of the telomere protecting shelterin complex. After a whole-exome sequencing approach in four unrelated individuals with CRMCC, we observed four recessively inherited compound heterozygous mutations in CTC1, which encodes the CTS telomere maintenance complex component 1. Sanger sequencing revealed seven more compound heterozygous mutations in eight more unrelated affected individuals. Two individuals who displayed late-onset cerebral findings, a normal fundus appearance, and no systemic findings did not have CTC1 mutations, implying that systemic findings are an important indication for CTC1 sequencing. Of the 11 mutations identified, four were missense, one was nonsense, two resulted in in-frame amino acid deletions, and four were short frameshift-creating deletions. All but two affected individuals were compound heterozygous for a missense mutation and a frameshift or nonsense mutation. No individuals with two frameshift or nonsense mutations were identified, which implies that severe disturbance of CTC1 function from both alleles might not be compatible with survival. Our preliminary functional experiments did not show evidence of severely affected telomere integrity in the affected individuals. Therefore, determining the underlying pathomechanisms associated with deficient CTC1 function will require further studies.
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Affiliation(s)
- Anne Polvi
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland
- Molecular Medicine Research Program, Research Programs Unit and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki 00290, Finland
- Neuroscience Center, University of Helsinki, Helsinki 00290, Finland
| | - Tarja Linnankivi
- Department of Pediatric Neurology, Children's Castle, Helsinki University Central Hospital, Helsinki 00290, Finland
| | - Tero Kivelä
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki 00290, Finland
| | - Riitta Herva
- Department of Pathology, Oulu University Hospital, Oulu 90029, Finland
| | - James P. Keating
- Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, Missouri 63110, USA
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki 00290, Finland
| | - Davide Pareyson
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, Department of Clinical Neurosciences, Fondazione Instituto di Ricovero e Cura a Carattere Scientifico, C. Besta Neurological Institute, Milan 20133, Italy
| | - Leena Vainionpää
- Department of Pediatrics, Oulu University Hospital, Oulu 90029, Finland
| | - Jenni Lahtinen
- Molecular Neurology Research Program, Research Programs Unit and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki 00290, Finland
| | - Iiris Hovatta
- Molecular Neurology Research Program, Research Programs Unit and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki 00290, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Helena Pihko
- Department of Pediatric Neurology, Children's Castle, Helsinki University Central Hospital, Helsinki 00290, Finland
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland
- Molecular Medicine Research Program, Research Programs Unit and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki 00290, Finland
- Neuroscience Center, University of Helsinki, Helsinki 00290, Finland
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Abstract
Cohen syndrome (CS) (OMIM#216550) is an uncommon autosomal recessive developmental disorder that has been attributed to mutations in the COH1 gene in at least 200 patients of diverse ethnic background so far. The clinical heterogeneity of CS is evident when comparing patients of different ethnic backgrounds, especially when evaluating specific system phenotypes separately, such as the ophthalmic and central nervous systems. We reviewed the available clinical data on CS cohorts of patients who share a founder effect and demonstrated that most features associated so far with CS are less than those always present in the patients who share a founder mutation thus representing clinical heterogeneity. Furthermore, there is a wide clinical variability of CS in the distinct founder mutation cohorts, the Finnish, Greek/Mediterranean, Amish and Irish travelers. The Greek/Mediterranean founder mutation is correlated to a CS phenotype characterized by specific and persistent skeletal features, corneal changes, periodontal disease, a distinct neurocognitive phenotype for the high recurrence of autism and non-verbal communication and inconstant microcephaly.
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Affiliation(s)
- S Douzgou
- Department of Genetics, Institute of Child Health, Aghia Sophia Children's Hospital, Athens, Greece.
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Jaakkola E, Mustonen A, Olsen P, Miettinen S, Savuoja T, Raams A, Jaspers NGJ, Shao H, Wu BL, Ignatius J. ERCC6 founder mutation identified in Finnish patients with COFS syndrome. Clin Genet 2011; 78:541-7. [PMID: 20456449 DOI: 10.1111/j.1399-0004.2010.01424.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cerebro-oculo-facio-skeletal (COFS) syndrome is an autosomal recessive disorder characterized by microcephaly, congenital cataracts, facial dysmorphism, neurogenic arthrogryposis, growth failure and severe psychomotor retardation. We report a large consanguineous pedigree from northern Finland with six individuals belonging into four different sibships and affected with typical COFS syndrome phenotype. Two deceased patients have been published previously in 1982 as the first cases exhibiting cerebral calcifications typical for this disorder. Two living and one of the deceased patients were all shown to possess a novel homozygous mutation in the ERCC6 [Cockayne syndrome B (CSB)] gene, thereby confirming the diagnosis on molecular genetic level even for the earlier published cases. Genealogical investigation showed a common ancestor living in a northeastern village in Finland in the 18th century for all six patients implying a founder effect.
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Affiliation(s)
- E Jaakkola
- Department of Clinical Genetics, Oulu University Hospital, University of Oulu, Oulu, Finland.
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Johansson A, Marroni F, Hayward C, Franklin CS, Kirichenko AV, Jonasson I, Hicks AA, Vitart V, Isaacs A, Axenovich T, Campbell S, Floyd J, Hastie N, Knott S, Lauc G, Pichler I, Rotim K, Wild SH, Zorkoltseva IV, Wilson JF, Rudan I, Campbell H, Pattaro C, Pramstaller P, Oostra BA, Wright AF, van Duijn CM, Aulchenko YS, Gyllensten U. Linkage and genome-wide association analysis of obesity-related phenotypes: association of weight with the MGAT1 gene. Obesity (Silver Spring) 2010; 18:803-8. [PMID: 19851299 DOI: 10.1038/oby.2009.359] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As major risk-factors for diabetes and cardiovascular diseases, the genetic contribution to obesity-related traits has been of interest for decades. Recently, a limited number of common genetic variants, which have replicated in different populations, have been identified. One approach to increase the statistical power in genetic mapping studies is to focus on populations with increased levels of linkage disequilibrium (LD) and reduced genetic diversity. We have performed joint linkage and genome-wide association analyses for weight and BMI in 3,448 (linkage) and 3,925 (association) partly overlapping healthy individuals from five European populations. A total of four chromosomal regions (two for weight and two for BMI) showed suggestive linkage (lod >2.69) either in one of the populations or in the joint data. At the genome-wide level (nominal P < 1.6 x 10(-7), Bonferroni-adjusted P < 0.05) one single-nucleotide polymorphism (SNP) (rs12517906) (nominal P = 7.3 x 10(-8)) was associated with weight, whereas none with BMI. The SNP associated with weight is located close to MGAT1. The monoacylglycerol acyltransferase (MGAT) enzyme family is known to be involved in dietary fat absorption. There was no overlap between the linkage regions and the associated SNPs. Our results show that genetic effects influencing weight and BMI are shared across diverse European populations, even though some of these populations have experienced recent population bottlenecks and/or been affected by genetic drift. The analysis enabled us to identify a new candidate gene, MGAT1, associated with weight in women.
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Affiliation(s)
- Asa Johansson
- Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
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Abstract
Founder populations, characterized by a single ancestor affected by long QT syndrome (LQTS) and by a large number of individuals and families who all are related to the ancestor and thereby carry the same disease-causing mutation, represent the ideal human model for studying the role of "modifier genes" in LQTS. This article reviews some of the fundamental concepts related to founder populations and provides the necessary historical background to understand why so many can be found in South Africa. The focus then moves to a specific LQT1 founder population, carrier of the A341V mutation, that has been studied extensively during the last 10 years and has provided a significant amount of previously unforeseen information. These novel findings range from an unusually high clinical severity not explained by the electrophysiologic characteristics of the mutation, to the importance of tonic and reflex control of heart rate for risk stratification, to the identification of the first modifier genes for clinical severity of LQTS.
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Affiliation(s)
- Paul A Brink
- Department of Internal Medicine, University of Stellenbosch, South Africa
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Abstract
The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of 'Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects.
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Johansson Å, Jonasson I, Gyllensten U. Extended haplotypes in the growth hormone releasing hormone receptor gene (GHRHR) are associated with normal variation in height. PLoS One 2009; 4:e4464. [PMID: 19209235 PMCID: PMC2637425 DOI: 10.1371/journal.pone.0004464] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 12/16/2008] [Indexed: 11/18/2022] Open
Abstract
Mutations in the gene for growth hormone releasing hormone receptor (GHRHR) cause isolated growth hormone deficiency (IGHD) but this gene has not been found to affect normal variation in height. We performed a whole genome linkage analysis for height in a population from northern Sweden and identified a region on chromosome 7 with a lod-score of 4.7. The GHRHR gene is located in this region and typing of tagSNPs identified a haplotype that is associated with height (p = 0.00077) in the original study population. Analysis of a sample from an independent population from the most northern part of Sweden also showed an association with height (p = 0.0039) but with another haplotype in the GHRHR gene. Both haplotypes span the 3′ part of the GHRHR gene, including the region in which most of the mutations in IGHD have been located. The effect size of these haplotypes are larger than that of any gene previously associated with height, which indicates that GHRHR might be one of the most important genes so far identified affecting normal variation in human height.
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Affiliation(s)
- Åsa Johansson
- Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
| | - Inger Jonasson
- Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Pharmacogenetic variation at CYP2C9, CYP2C19, and CYP2D6 at global and microgeographic scales. Pharmacogenet Genomics 2009; 19:170-9. [DOI: 10.1097/fpc.0b013e32831ebb30] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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48
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Jakkula E, Rehnström K, Varilo T, Pietiläinen OP, Paunio T, Pedersen NL, deFaire U, Järvelin MR, Saharinen J, Freimer N, Ripatti S, Purcell S, Collins A, Daly MJ, Palotie A, Peltonen L. The genome-wide patterns of variation expose significant substructure in a founder population. Am J Hum Genet 2008; 83:787-94. [PMID: 19061986 DOI: 10.1016/j.ajhg.2008.11.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 02/06/2023] Open
Abstract
Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.
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Götz A, Isohanni P, Pihko H, Paetau A, Herva R, Saarenpää-Heikkilä O, Valanne L, Marjavaara S, Suomalainen A. Thymidine kinase 2 defects can cause multi-tissue mtDNA depletion syndrome. Brain 2008; 131:2841-50. [PMID: 18819985 DOI: 10.1093/brain/awn236] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA depletion syndrome (MDS) is a severe recessively inherited disease of childhood. It manifests most often in infancy, is rapidly progressive and leads to early death. MDS is caused by an increasing number of nuclear genes leading to multisystemic or tissue-specific decrease in mitochondrial DNA (mtDNA) copy number. Thymidine kinase 2 (TK2) has been reported to cause a myopathic form of MDS. We report here the clinical, autopsy and molecular genetic findings of rapidly progressive fatal infantile mitochondrial syndrome. All of our seven patients had rapidly progressive myopathy/encephalomyopathy, leading to respiratory failure within the first 3 years of life, with high creatine kinase values and dystrophic changes in the muscle with cytochrome c oxidase-negative fibres. In addition, two patients also had terminal-phase seizures, one had epilepsia partialis continua and one had cortical laminar necrosis. We identified two different homozygous or compound heterozygous mutations in the TK2 gene in all the patients: c.739 C s -> T and c.898 C -> T, leading to p.R172W and p.R225W changes at conserved protein sites. R172W mutation led to myopathy or encephalomyopathy with the onset during the first months of life, and was associated with severe mtDNA depletion in the muscle, brain and liver. Homozygosity for R225W mutation manifested during the second year of life as a myopathy, and showed muscle-specific mtDNA depletion. Both mutations originated from single ancient founders, with Finnish origin and enrichment for the new R172W mutation, and possibly Scandinavian ancestral origin for the R225W. We conclude that TK2 mutations may manifest as infantile-onset fatal myopathy with dystrophic features, but should be considered also in infantile progressive encephalomyopathy with wide-spread mtDNA depletion.
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Affiliation(s)
- Alexandra Götz
- Research Programme of Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
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50
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Hannelius U, Salmela E, Lappalainen T, Guillot G, Lindgren CM, von Döbeln U, Lahermo P, Kere J. Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs. BMC Genet 2008; 9:54. [PMID: 18713460 PMCID: PMC2527025 DOI: 10.1186/1471-2156-9-54] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 08/19/2008] [Indexed: 08/30/2023] Open
Abstract
Background Despite several thousands of years of close contacts, there are genetic differences between the neighbouring countries of Finland and Sweden. Within Finland, signs of an east-west duality have been observed, whereas the population structure within Sweden has been suggested to be more subtle. With a fine-scale substructure like this, inferring the cluster membership of individuals requires a large number of markers. However, some studies have suggested that this number could be reduced if the individual spatial coordinates are taken into account in the analysis. Results We genotyped 34 unlinked autosomal single nucleotide polymorphisms (SNPs), originally designed for zygosity testing, from 2044 samples from Sweden and 657 samples from Finland, and 30 short tandem repeats (STRs) from 465 Finnish samples. We saw significant population structure within Finland but not between the countries or within Sweden, and isolation by distance within Finland and between the countries. In Sweden, we found a deficit of heterozygotes that we could explain by simulation studies to be due to both a small non-random genotyping error and hidden substructure caused by immigration. Geneland, a model-based Bayesian clustering algorithm, clustered the individuals into groups that corresponded to Sweden and Eastern and Western Finland when spatial coordinates were used, whereas in the absence of spatial information, only one cluster was inferred. Conclusion We show that the power to cluster individuals based on their genetic similarity is increased when including information about the spatial coordinates. We also demonstrate the importance of estimating the size and effect of genotyping error in population genetics in order to strengthen the validity of the results.
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Affiliation(s)
- Ulf Hannelius
- Department of Biosciences and Nutrition, Karolinska Institutet, 14157 Huddinge, Sweden.
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