1
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Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024; 14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA.
| | - Yasmin Rajendran
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | | | - Maria Arvio
- Päijät-Häme Wellbeing Services, Neurology, Lahti, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Kristiina Avela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Johanna Granvik
- The Wellbeing Services County of Ostrobothnia, Kokkola, Finland
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Tuomo Määttä
- The Wellbeing Services County of Kainuu, Kajaani, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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2
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Tuiskula A, Rahikkala E, Kero A, Haanpää MK, Avela K. Jansen de Vries syndrome: Report of four new patients and review of the literature. Eur J Med Genet 2023:104807. [PMID: 37385405 DOI: 10.1016/j.ejmg.2023.104807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
Jansen de Vries syndrome (JDVS, OMIM: 617450) is a rare neurodevelopmental disorder associated with hypotonia, behavioral features, high threshold to pain, short stature, ophthalmological abnormalities, dysmorphism and occasionally a structural cardiac condition. It is caused by truncating variants of the last and penultimate exons of PPM1D. So far, 21 patients with JVDS have been reported in the literature. Here, we describe four novel cases of JVDS and review the current literature. Notably, our patients 1, 3 and 4 do not have intellectual disability albeit they have significant developmental difficulties. Thus, the phenotype may span from a classic intellectual disability syndrome to a milder neurodevelopmental disorder. Interestingly, two of our patients have received successful growth hormone treatment. Considering the phenotype of all the known JDVS patients, a cardiological consultation is recommended, as at least 7/25 patients showed a structural cardiac defect. Episodic fever and vomiting may associate with hypoglycemia and may even mimic a metabolic disorder. We also report the first JDVS patient with a mosaic gene defect and a mild neurodevelopmental phenotype.
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Affiliation(s)
- Anna Tuiskula
- Department of Pediatrics, Children's Hospital, University of Helsinki and Helsinki University Hospital (HUH), Helsinki, Finland.
| | - Elisa Rahikkala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Department of Clinical Genetics and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Andreina Kero
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Maria K Haanpää
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland; Genomics Department, Turku University Hospital, Turku, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital (HUH), Helsinki, Finland
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3
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Jacquemin V, Versbraegen N, Duerinckx S, Massart A, Soblet J, Perazzolo C, Deconinck N, Brischoux-Boucher E, De Leener A, Revencu N, Janssens S, Moorgat S, Blaumeiser B, Avela K, Touraine R, Abou Jaoude I, Keymolen K, Saugier-Veber P, Lenaerts T, Abramowicz M, Pirson I. Congenital hydrocephalus: new Mendelian mutations and evidence for oligogenic inheritance. Hum Genomics 2023; 17:16. [PMID: 36859317 PMCID: PMC9979489 DOI: 10.1186/s40246-023-00464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published series report a Mendelian cause in only a minority of cases. In this study, we analyzed exome data of PCH patients in search of novel causal genes and addressed the possibility of an underlying oligogenic mode of inheritance for PCH. MATERIALS AND METHODS We sequenced the exome in 28 unrelated probands with PCH, 12 of whom from families with at least two affected siblings and 9 of whom consanguineous, thereby increasing the contribution of genetic causes. Patient exome data were first analyzed for rare (MAF < 0.005) transmitted or de novo variants. Population stratification of unrelated PCH patients and controls was determined by principle component analysis, and outliers identified using Mahalanobis distance 5% as cutoff. Patient and control exome data for genes biologically related to cilia (SYScilia database) were analyzed by mutation burden test. RESULTS In 18% of probands, we identify a causal (pathogenic or likely pathogenic) variant of a known hydrocephalus gene, including genes for postnatal, syndromic hydrocephalus, not previously reported in isolated PCH. In a further 11%, we identify mutations in novel candidate genes. Through mutation burden tests, we demonstrate a significant burden of genetic variants in genes coding for proteins of the primary cilium in PCH patients compared to controls. CONCLUSION Our study confirms the low contribution of Mendelian mutations in PCH and reports PCH as a phenotypic presentation of some known genes known for syndromic, postnatal hydrocephalus. Furthermore, this study identifies novel Mendelian candidate genes, and provides evidence for oligogenic inheritance implicating primary cilia in PCH.
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Affiliation(s)
- Valerie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.
| | - Nassim Versbraegen
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Duerinckx
- grid.4989.c0000 0001 2348 0746Service de Neuropédiatrie, Hôpital Universitaire de Bruxelles and CUB Hôpital Erasme and Université Libre de Bruxelles, Brussels, Belgium
| | - Annick Massart
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium ,grid.411414.50000 0004 0626 3418Department of Nephrology, University Hospital of Antwerp, Edegem, Belgium
| | - Julie Soblet
- grid.412157.40000 0000 8571 829XHuman Genetics Department, CUB Hôpital Erasme, Brussels, Belgium
| | - Camille Perazzolo
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Deconinck
- grid.412209.c0000 0004 0578 1002Hopital Universitaire des Enfants Reine Fabiola and Hopital Universitaire de Bruxelles and Université Libre de Bruxelles, Brussels, Belgium
| | - Elise Brischoux-Boucher
- grid.493090.70000 0004 4910 6615Centre de génétique humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Anne De Leener
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Nicole Revencu
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Sandra Janssens
- grid.410566.00000 0004 0626 3303Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stèphanie Moorgat
- grid.452439.d0000 0004 0578 0894Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Bettina Blaumeiser
- grid.411414.50000 0004 0626 3418Center of Medical Genetics, Antwerp University and Antwerp University Hospital, Edegem, Belgium
| | - Kristiina Avela
- grid.15485.3d0000 0000 9950 5666Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Renaud Touraine
- grid.412954.f0000 0004 1765 1491Génétique Clinique Chromosomique et Moléculaire, CHU de Saint-Etienne, St-Priest-en-Jarez, France
| | - Imad Abou Jaoude
- Department of Gynecology and Obstetrics, Abou Jaoude Hospital, Jal El Dib, Lebanon
| | - Kathelijn Keymolen
- grid.411326.30000 0004 0626 3362Center for Medical Genetics, UZ Brussels, Jette, Belgium
| | - Pascale Saugier-Veber
- grid.10400.350000 0001 2108 3034Department of Genetics and Reference Center for Developmental Disorders, Université Rouen Normandie, Inserm U1245 and CHU Rouen, Rouen, France
| | - Tom Lenaerts
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium. .,Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
| | - Isabelle Pirson
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
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4
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Majander A, Sankila EM, Falck A, Vasara LK, Seitsonen S, Kulmala M, Haavisto AK, Avela K, Turunen JA. Natural history and biomarkers of retinal dystrophy caused by the biallelic TULP1 variant c.148delG. Acta Ophthalmol 2023; 101:215-221. [PMID: 36128853 DOI: 10.1111/aos.15252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/19/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE To report clinical features and potential disease markers of inherited retinal dystrophy (IRD) caused by the biallelic c.148delG variant in the tubby-like protein 1 (TULP1) gene. METHODS A retrospective observational study of 16 IRD patients carrying a homozygous pathogenic TULP1 c.148delG variant. Clinical data including fundus spectral-domain optical coherence tomography (SD-OCT) were assessed. A meta-analysis of visual acuity of previously reported other pathogenic TULP1 variants was performed for reference. RESULTS The biallelic TULP1 variant c.148delG was associated with infantile and early childhood onset IRD. Retinal ophthalmoscopy was primarily normal converting to peripheral pigmentary retinopathy and maculopathy characterized by progressive extra-foveal loss of the ellipsoid zone (EZ), the outer plexiform layer (OPL), and the outer nuclear layer (ONL) bands in the SD-OCT images. The horizontal width of the foveal EZ showed significant regression with the best-corrected visual acuity (BCVA) of the eye (p < 0.0001, R2 = 0.541, F = 26.0), the age of the patient (p < 0.0001, R2 = 0.433, F = 16.8), and mild correlation with the foveal OPL-ONL thickness (p = 0.014, R2 = 0.245, F = 7.2). Modelling of the BCVA data suggested a mean annual loss of logMAR 0.027. The level of visual loss was similar to that previously reported in patients carrying other truncating TULP1 variants. CONCLUSIONS This study describes the progression of TULP1 IRD suggesting a potential time window for therapeutic interventions. The width of the foveal EZ and the thickness of the foveal OPL-ONL layers could serve as biomarkers of the disease stage.
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Affiliation(s)
- Anna Majander
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eeva-Marja Sankila
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aura Falck
- Department of Ophthalmology, PEDEGO Research Unit and Medical Research Center, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Laura Kristiina Vasara
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sanna Seitsonen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maarit Kulmala
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna-Kaisa Haavisto
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Joni A Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
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5
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Krootila J, Kaukonen M, Sankila E, Paavo M, Seitsonen S, Repo P, Backlund MP, Majander A, Lindahl P, Vasara K, Avela K, Salminen E, MacLaren RE, Kivelä TT, Turunen JA. Genetic findings in over 600 individuals with inherited retinal disorders in Finland. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.0364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Julia Krootila
- Folkhälsan Research Center, Biomedicum Helsinki Eye Genetics Group
| | - Maria Kaukonen
- Nuffield Department of Clinical Neuroscience University of Oxford UK
- Oxford University Hospitals NHS Foundation Trust, Oxford Eye Hospital UK
| | - Eeva‐Marja Sankila
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Maarjaliis Paavo
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Sanna Seitsonen
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Pauliina Repo
- Folkhälsan Research Center, Biomedicum Helsinki Eye Genetics Group
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | | | - Anna Majander
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Päivi Lindahl
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Kristiina Vasara
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Kristiina Avela
- Department of Clinical Genetics University of Helsinki and Helsinki University Hospital Finland
| | - Eveliina Salminen
- Department of Clinical Genetics University of Helsinki and Helsinki University Hospital Finland
| | - Robert E. MacLaren
- Nuffield Department of Clinical Neuroscience University of Oxford UK
- Oxford University Hospitals NHS Foundation Trust, Oxford Eye Hospital UK
| | - Tero T. Kivelä
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
| | - Joni A. Turunen
- Folkhälsan Research Center, Biomedicum Helsinki Eye Genetics Group
- Department of Ophthalmology University of Helsinki and Helsinki University Hospital Finland
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6
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Ignatius E, Puosi R, Palomäki M, Forsbom N, Pohjanpelto M, Alitalo T, Anttonen AK, Avela K, Haataja L, Carroll CJ, Lönnqvist T, Isohanni P. Duplication/triplication mosaicism of EBF3 and expansion of the EBF3 neurodevelopmental disorder phenotype. Eur J Paediatr Neurol 2022; 37:1-7. [PMID: 34999443 DOI: 10.1016/j.ejpn.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/06/2021] [Accepted: 12/18/2021] [Indexed: 11/15/2022]
Abstract
Deleterious variants in the transcription factor early B-cell factor 3 (EBF3) are known to cause a neurodevelopmental disorder (EBF3-NDD). We report eleven individuals with EBF3 variants, including an individual with a duplication/triplication mosaicism of a region encompassing EBF3 and a phenotype consistent with EBF3-NDD, which may reflect the importance of EBF3 gene-dosage for neurodevelopment. The phenotype of individuals in this cohort was quite mild compared to the core phenotype of previously described individuals. Although ataxia tended to wane with age, we show that cognitive difficulties may increase, and we recommend that individuals with EBF3-NDD have systematic neuropsychological follow-up.
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Affiliation(s)
- Erika Ignatius
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riina Puosi
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maarit Palomäki
- Department of Radiology, HUS Medical Imaging Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Noora Forsbom
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Max Pohjanpelto
- Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Alitalo
- Laboratory of Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna-Kaisa Anttonen
- Laboratory of Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Leena Haataja
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Christopher J Carroll
- Genetics Research Centre, Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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7
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Närhi A, Fernandes A, Toiviainen-Salo S, Harris J, McInerney-Leo A, Lazarus S, Avela K, Duncan EL. A family with partially penetrant multicentric carpotarsal osteolysis due to gonadal mosaicism: First reported case. Am J Med Genet A 2021; 185:2477-2481. [PMID: 33988298 DOI: 10.1002/ajmg.a.62257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/17/2021] [Accepted: 04/10/2021] [Indexed: 01/30/2023]
Abstract
Multicentric carpotarsal osteolysis (MCTO) is an autosomal dominant condition characterized by carpal-tarsal abnormalities; over half of affected individuals also develop renal disease. MCTO is caused by mutations of MAFB; however, there is no clear phenotype-genotype correlation. We describe the first reported family of variable MCTO phenotype due to mosaicism: the proband had classical skeletal features and renal involvement due to focal segmental glomerulosclerosis (FSGS), and the father had profound renal impairment due to FSGS, necessitating kidney transplantation. Mosaicism was first suspected in this family due to unequal allele ratios in the sequencing chromatograph of the initial blood sample of proband's father and confirmed by sequencing DNA extracted from the father's hair, collected from different bodily parts. This case highlights the need for a high index of clinical suspicion to detect low-level parental mosaicism, as well as a potential role for MAFB mutation screening in individuals with isolated FSGS.
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Affiliation(s)
- Anu Närhi
- Department of Clinical Genetics, Helsinki University Hospital, Helenski, Finland
| | - Andrea Fernandes
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Herston, Australia.,Faculty of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Faculty of Medicine, Herston, University of Queensland, Herston, Australia
| | - Sanna Toiviainen-Salo
- Department of Radiology, New Children's Hospital, Helsinki University Hospital, Helenski, Finland
| | - Jessica Harris
- University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Australia
| | - Aideen McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Australia
| | - Syndia Lazarus
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Herston, Australia.,Faculty of Medicine, Herston, University of Queensland, Herston, Australia.,Department of Internal Medicine (Endocrinology), The Prince Charles Hospital, Chermside, Australia
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital, Helenski, Finland
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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8
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Strang-Karlsson S, von Willebrand M, Avela K, Wallgren-Pettersson C. A novel MPLKIP-variant in three Finnish patients with non-photosensitive trichothiodystrophy type 4. Am J Med Genet A 2021; 185:1875-1882. [PMID: 33729667 DOI: 10.1002/ajmg.a.62168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/27/2021] [Accepted: 02/26/2021] [Indexed: 11/09/2022]
Abstract
Trichothiodystrophy is a group of multisystem neuroectodermal disorders with dysplastic hair as the cardinal symptom. We describe three patients from two Finnish families in whom whole-exome sequencing revealed a novel homozygous variant, c.26del, p.(Pro9Glnfs*144) in the MPLKIP-gene, confirming the diagnosis of non-photosensitive trichothiodystrophy type 4 (TTD4). The variant was confirmed by Sanger sequencing and inherited from unaffected carrier parents. This report adds to the literature by expanding the genetic and phenotypic spectra of MPLKIP-related trichothiodystrophy. We describe dysmorphic features in the patients and provide a comparison of clinical characteristics in patients with TTD4 reported to date.
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Affiliation(s)
- Sonja Strang-Karlsson
- The Folkhaelsan Department of Medical Genetics, Helsinki, Finland.,Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maria von Willebrand
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- The Folkhaelsan Department of Medical Genetics, The Folkhaelsan Institute of Genetics and the Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
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9
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Hakonen AH, Lehtonen J, Kivirikko S, Keski-Filppula R, Moilanen J, Kivisaari R, Almusa H, Jakkula E, Saarela J, Avela K, Aittomäki K. Recessive MYH3 variants cause "Contractures, pterygia, and variable skeletal fusions syndrome 1B" mimicking Escobar variant multiple pterygium syndrome. Am J Med Genet A 2020; 182:2605-2610. [PMID: 32902138 DOI: 10.1002/ajmg.a.61836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/06/2020] [Accepted: 08/01/2020] [Indexed: 11/09/2022]
Abstract
The multiple pterygium syndromes (MPS) are rare disorders with disease severity ranging from lethal to milder forms. The nonlethal Escobar variant MPS (EVMPS) is characterized by multiple pterygia and arthrogryposis, as well as various additional features including congenital anomalies. The genetic etiology of EVMPS is heterogeneous and the diagnosis has been based either on the detection of pathogenic CHRNG variants (~23% of patients), or suggestive clinical features. We describe four patients with a clinical suspicion of EVMPS who manifested with multiple pterygia, mild flexion contractures of several joints, and vertebral anomalies. We revealed recessively inherited MYH3 variants as the underlying cause in all patients: two novel variants, c.1053C>G, p.(Tyr351Ter) and c.3102+5G>C, as compound heterozygous with the hypomorphic MYH3 variant c.-9+1G>A. Recessive MYH3 variants have been previously associated with spondylocarpotarsal synostosis syndrome. Our findings now highlight multiple pterygia as an important feature in patients with recessive MYH3 variants. Based on all patients with recessive MYH3 variants reported up to date, we consider that this disease entity should be designated as "Contractures, pterygia, and variable skeletal fusions syndrome 1B," as recently suggested by OMIM. Our findings underline the importance of analyzing MYH3 in the differential diagnosis of EVMPS, particularly as the hypomorphic MYH3 variant might remain undetected by routine exome sequencing.
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Affiliation(s)
- Anna H Hakonen
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Lehtonen
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Sirpa Kivirikko
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Riikka Keski-Filppula
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Jukka Moilanen
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Reetta Kivisaari
- HUS Medical Imaging Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Eveliina Jakkula
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.,Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway.,HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Avela
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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10
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Kahila H, Marjonen H, Auvinen P, Avela K, Riikonen R, Kaminen‐Ahola N. 18q12.3-q21.1 microdeletion detected in the prenatally alcohol-exposed dizygotic twin with discordant fetal alcohol syndrome phenotype. Mol Genet Genomic Med 2020; 8:e1192. [PMID: 32096599 PMCID: PMC7196488 DOI: 10.1002/mgg3.1192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A pair of dizygotic twins discordantly affected by heavy prenatal alcohol exposure (PAE) was reported previously by Riikonen, suggesting the role of genetic risk or protective factors in the etiology of alcohol-induced developmental disorders. Now, we have re-examined these 25-year-old twins and explored genetic origin of the phenotypic discordancy reminiscent with fetal alcohol syndrome (FAS). Furthermore, we explored alterations in DNA methylation profile of imprinting control region at growth-related insulin-like growth factor 2 (IGF2)/H19 locus in twins' white blood cells (WBC), which have been associated earlier with alcohol-induced genotype-specific changes in placental tissue. METHODS Microarray-based comparative genomic hybridization (aCGH) was used to detect potential submicroscopic chromosomal abnormalities, and developmental as well as phenotypic information about twins were collected. Traditional bisulfite sequencing was used for DNA methylation analysis. RESULTS Microarray-based comparative genomic hybridization revealed a microdeletion 18q12.3-q21.1. in affected twin, residing in a known 18q deletion syndrome region. This syndrome has been associated with growth restriction, developmental delay or intellectual deficiency, and abnormal facial features in previous studies, and thus likely explains the phenotypic discordancy between the twins. We did not observe association between WBCs' DNA methylation profile and PAE, but interestingly, a trend of decreased DNA methylation at the imprinting control region was seen in the twin with prenatal growth retardation at birth. CONCLUSIONS The microdeletion emphasizes the importance of adequate chromosomal testing in examining the etiology of complex alcohol-induced developmental disorders. Furthermore, the genotype-specific decreased DNA methylation at the IGF2/H19 locus cannot be considered as a biological mark for PAE in adult WBCs.
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Affiliation(s)
- Hanna Kahila
- Department of Obstetrics and GynecologyHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Heidi Marjonen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Pauliina Auvinen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Kristiina Avela
- Department of Clinical GeneticsHelsinki University HospitalHUSLABHelsinkiFinland
| | - Raili Riikonen
- Children's HospitalKuopio University HospitalUniversity of Eastern FinlandKuopioFinland
| | - Nina Kaminen‐Ahola
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Cyrus SS, Cohen ASA, Agbahovbe R, Avela K, Yeung KS, Chung BHY, Luk HM, Tkachenko N, Choufani S, Weksberg R, Lopez-Rangel E, Brown K, Saenz MS, Svihovec S, McCandless SE, Bird LM, Garcia AG, Gambello MJ, McWalter K, Schnur RE, An J, Jones SJM, Bhalla SK, Pinz H, Braddock SR, Gibson WT. Rare SUZ12 variants commonly cause an overgrowth phenotype. Am J Med Genet C Semin Med Genet 2019; 181:532-547. [PMID: 31736240 DOI: 10.1002/ajmg.c.31748] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/31/2022]
Abstract
The Polycomb repressive complex 2 is an epigenetic writer and recruiter with a role in transcriptional silencing. Constitutional pathogenic variants in its component proteins have been found to cause two established overgrowth syndromes: Weaver syndrome (EZH2-related overgrowth) and Cohen-Gibson syndrome (EED-related overgrowth). Imagawa et al. (2017) initially reported a singleton female with a Weaver-like phenotype with a rare coding SUZ12 variant-the same group subsequently reported two additional affected patients. Here we describe a further 10 patients (from nine families) with rare heterozygous SUZ12 variants who present with a Weaver-like phenotype. We report four frameshift, two missense, one nonsense, and two splice site variants. The affected patients demonstrate variable pre- and postnatal overgrowth, dysmorphic features, musculoskeletal abnormalities and developmental delay/intellectual disability. Some patients have genitourinary and structural brain abnormalities, and there may be an association with respiratory issues. The addition of these 10 patients makes a compelling argument that rare pathogenic SUZ12 variants frequently cause overgrowth, physical abnormalities, and abnormal neurodevelopmental outcomes in the heterozygous state. Pathogenic SUZ12 variants may be de novo or inherited, and are sometimes inherited from a mildly-affected parent. Larger samples sizes will be needed to elucidate whether one or more clinically-recognizable syndromes emerge from different variant subtypes.
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Affiliation(s)
- Sharri S Cyrus
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Ana S A Cohen
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Ruky Agbahovbe
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Kit S Yeung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ho-Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong, Hong Kong
| | - Nataliya Tkachenko
- Medical Genetics Service, Medical Genetics Center Dr. Jacinto de Magalhães, Porto Hospital Center, Porto, Portugal
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Elena Lopez-Rangel
- Department of Medical Genetics, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
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- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen Brown
- Section of Genetics and Metabolism, Department of Pediatrics, The Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Margarita S Saenz
- Section of Genetics and Metabolism, Department of Pediatrics, The Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shayna Svihovec
- Section of Genetics and Metabolism, Department of Pediatrics, The Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shawn E McCandless
- Section of Genetics and Metabolism, Department of Pediatrics, The Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, California.,Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, California
| | - Aixa Gonzalez Garcia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Michael J Gambello
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | | | | | - Jianghong An
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sanjiv K Bhalla
- Department of Radiology, University of British Columbia, Vancouver, British Columbia, Canada.,Diagnostic and Medical Imaging Services, Surrey Memorial Hospital, Surrey, British Columbia, Canada
| | - Hailey Pinz
- Division of Medical Genetics, Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, Missouri
| | - Stephen R Braddock
- Division of Medical Genetics, Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, Missouri
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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13
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Avela K, Sankila EM, Seitsonen S, Kuuluvainen L, Barton S, Gillies S, Aittomäki K. A founder mutation in CERKL is a major cause of retinal dystrophy in Finland. Acta Ophthalmol 2018; 96:183-191. [PMID: 29068140 DOI: 10.1111/aos.13551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/28/2017] [Indexed: 11/30/2022]
Abstract
PURPOSE To study the genetic aetiology of retinal dystrophies (RD) in Finnish patients. METHODS A targeted next-generation sequencing (NGS) panel of 105 retinal dystrophy genes was used in a cohort of 55 RD patients. RESULTS The overall diagnostic yield was 60% demonstrating the power of this approach. Interestingly, a missense mutation c.375C>G p.(Cys125Trp) in the CERKL gene was found in 18% of the patients in either a homozygous or compound heterozygous state. Data from Exome Aggregation Consortium (ExAC) Browser show that the CERKL c.375C>G p.(Cys125Trp) allele is enriched in the Finnish population and thus is a founder mutation. Furthermore, we report the clinical picture of 18 patients with mutations in the CERKL gene. CERKL mutations cause a macular-onset disease, in which symptoms first become apparent at the second decade. We also detected other novel founder mutations in the CERKL, EYS, RP1, ABCA4 and GUCY2D genes. CONCLUSION Our report indicates that the first diagnostic test for Finnish patients with sporadic or autosomal recessive RD should be a targeted test for founder mutations in the CERKL, EYS, RP1, ABCA4 and GUCY2D genes. These results confirm the utility of NGS-based gene panels as a powerful method for mutation identification in RD, thus enabling improved genetic counselling for these families.
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Affiliation(s)
- Kristiina Avela
- Department of Clinical Genetics; Helsinki University Hospital; Helsinki Finland
| | - Eeva-Marja Sankila
- Department of Ophthalmology; Helsinki University Hospital; Helsinki Finland
| | - Sanna Seitsonen
- Department of Ophthalmology; Helsinki University Hospital; Helsinki Finland
| | - Liina Kuuluvainen
- Department of Clinical Genetics; Helsinki University Hospital; Helsinki Finland
| | - Stephanie Barton
- St Mary's Hospital; Central Manchester University Hospitals and Manchester Centre for Genomic Medicine; Manchester UK
| | - Stuart Gillies
- St Mary's Hospital; Central Manchester University Hospitals and Manchester Centre for Genomic Medicine; Manchester UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics; Helsinki University Hospital; Helsinki Finland
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14
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Piras IS, Mills G, Llaci L, Naymik M, Ramsey K, Belnap N, Balak CD, Jepsen WM, Szelinger S, Siniard AL, Lewis CR, LaFleur M, Richholt RF, De Both MD, Avela K, Rangasamy S, Craig DW, Narayanan V, Järvelä I, Huentelman MJ, Schrauwen I. Exploring genome-wide DNA methylation patterns in Aicardi syndrome. Epigenomics 2017; 9:1373-1386. [PMID: 28967789 DOI: 10.2217/epi-2017-0060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
AIM To explore differential DNA methylation (DNAm) in Aicardi syndrome (AIC), a severe neurodevelopmental disorder with largely unknown etiology. PATIENTS & METHODS We characterized DNAm in AIC female patients and parents using the Illumina 450 K array. Differential DNAm was assessed using the local outlier factor algorithm, and results were validated via qPCR in a larger set of AIC female patients, parents and unrelated young female controls. Functional epigenetic modules analysis was used to detect pathways integrating both genome-wide DNAm and RNA-seq data. RESULTS & CONCLUSION We detected differential methylation patterns in AIC patients in several neurodevelopmental and/or neuroimmunological networks. These networks may be part of the underlying pathogenic mechanisms involved in the disease.
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Affiliation(s)
- Ignazio S Piras
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Gabrielle Mills
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Lorida Llaci
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Chris D Balak
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Wayne M Jepsen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Ashley L Siniard
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Candace R Lewis
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Madison LaFleur
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Ryan F Richholt
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Matt D De Both
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Hospital, Meilahdentie 2, FI-00029 Helsinki, Finland
| | - Sampathkumar Rangasamy
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - David W Craig
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,University of Southern California, Keck School of Medicine, Department of Translational Genomics, Los Angeles, NRT 1450 Biggy Street, CA 90033, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Haartmaninkatu 8, 00251 Helsinki, Finland
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Neurogenomics Division, Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, USA.,Center for Statistical Genetics, Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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15
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Paulussen ADC, Steyls A, Vanoevelen J, van Tienen FHJ, Krapels IPC, Claes GRF, Chocron S, Velter C, Tan-Sindhunata GM, Lundin C, Valenzuela I, Nagy B, Bache I, Maroun LL, Avela K, Brunner HG, Smeets HJM, Bakkers J, van den Wijngaard A. Rare novel variants in the ZIC3 gene cause X-linked heterotaxy. Eur J Hum Genet 2016; 24:1783-1791. [PMID: 27406248 PMCID: PMC5117940 DOI: 10.1038/ejhg.2016.91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/25/2016] [Accepted: 05/20/2016] [Indexed: 02/08/2023] Open
Abstract
Variants in the ZIC3 gene are rare, but have demonstrated their profound clinical significance in X-linked heterotaxy, affecting in particular male patients with abnormal arrangement of thoracic and visceral organs. Several reports have shown relevance of ZIC3 gene variants in both familial and sporadic cases and with a predominance of mutations detected in zinc-finger domains. No studies so far have assessed the functional consequences of ZIC3 variants in an in vivo model organism. A study population of 348 patients collected over more than 10 years with a large variety of congenital heart disease including heterotaxy was screened for variants in the ZIC3 gene. Functional effects of three variants were assessed both in vitro and in vivo in the zebrafish. We identified six novel pathogenic variants (1,7%), all in either male patients with heterotaxy (n=5) or a female patient with multiple male deaths due to heterotaxy in the family (n=1). All variants were located within the zinc-finger domains or leading to a truncation before these domains. Truncating variants showed abnormal trafficking of mutated ZIC3 proteins, whereas the missense variant showed normal trafficking. Overexpression of wild-type and mutated ZIC protein in zebrafish showed full non-functionality of the two frame-shift variants and partial activity of the missense variant compared with wild-type, further underscoring the pathogenic character of these variants. Concluding, we greatly expanded the number of causative variants in ZIC3 and delineated the functional effects of three variants using in vitro and in vivo model systems.
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Affiliation(s)
- Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jo Vanoevelen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Florence HJ van Tienen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Godelieve RF Claes
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Chocron
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gita M Tan-Sindhunata
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Catarina Lundin
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Irene Valenzuela
- Department of Clinical Genetics and Cytogenetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Balint Nagy
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Leth Maroun
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hubert J M Smeets
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Bakkers
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
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16
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Vulto-van Silfhout AT, Nakagawa T, Bahi-Buisson N, Haas SA, Hu H, Bienek M, Vissers LELM, Gilissen C, Tzschach A, Busche A, Müsebeck J, Rump P, Mathijssen IB, Avela K, Somer M, Doagu F, Philips AK, Rauch A, Baumer A, Voesenek K, Poirier K, Vigneron J, Amram D, Odent S, Nawara M, Obersztyn E, Lenart J, Charzewska A, Lebrun N, Fischer U, Nillesen WM, Yntema HG, Järvelä I, Ropers HH, de Vries BBA, Brunner HG, van Bokhoven H, Raymond FL, Willemsen MAAP, Chelly J, Xiong Y, Barkovich AJ, Kalscheuer VM, Kleefstra T, de Brouwer APM. Variants in CUL4B are associated with cerebral malformations. Hum Mutat 2015; 36:106-17. [PMID: 25385192 DOI: 10.1002/humu.22718] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022]
Abstract
Variants in cullin 4B (CUL4B) are a known cause of syndromic X-linked intellectual disability. Here, we describe an additional 25 patients from 11 families with variants in CUL4B. We identified nine different novel variants in these families and confirmed the pathogenicity of all nontruncating variants. Neuroimaging data, available for 15 patients, showed the presence of cerebral malformations in ten patients. The cerebral anomalies comprised malformations of cortical development (MCD), ventriculomegaly, and diminished white matter volume. The phenotypic heterogeneity of the cerebral malformations might result from the involvement of CUL-4B in various cellular pathways essential for normal brain development. Accordingly, we show that CUL-4B interacts with WDR62, a protein in which variants were previously identified in patients with microcephaly and a wide range of MCD. This interaction might contribute to the development of cerebral malformations in patients with variants in CUL4B.
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Affiliation(s)
- Anneke T Vulto-van Silfhout
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
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17
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Avela K, Hirvinen H, Ben Amor M, Rauch F. Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly in a Finnish woman: first confirmation of a duplication in RUNX2 as pathogenic variant. Eur J Med Genet 2015; 57:617-20. [PMID: 25311905 DOI: 10.1016/j.ejmg.2014.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/24/2014] [Indexed: 12/25/2022]
Abstract
Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly (MDMHB) is an autosomal-dominant bone dysplasia that until now has only been reported in French Canadian individuals. We have recently identified an intragenic duplication in RUNX2, encompassing exons 3 to 5, as a cause of MDMHB in French Canadian families. Here we describe a 20-year-old Finnish woman who had typical clinical and radiological signs of MDMHB, the first reported individual with MDMHB who is not of French-Canadian origin. Copy number variant assays based on quantitative PCR of genomic DNA showed the presence of three copies within a part of RUNX2. Sequencing RUNX2 cDNA from the skin fibroblasts revealed a duplication of exons 3 to 5. The results demonstrated that the intronic breakpoints of the duplication differed from those previously found in the French Canadian family, but that the consequences on RUNX2 transcript were identical. These findings demonstrate that the MDMHB phenotype results from an intragenic duplication of RUNX2 exons 3 to 5 also outside of the community where the disorder was first identified.
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18
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Gripp KW, Robbins KM, Sobreira NL, Witmer PD, Bird LM, Avela K, Makitie O, Alves D, Hogue JS, Zackai EH, Doheny KF, Stabley DL, Sol-Church K. Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome. Am J Med Genet A 2015; 167A:271-81. [PMID: 25394726 PMCID: PMC5589071 DOI: 10.1002/ajmg.a.36863] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/15/2014] [Indexed: 12/30/2022]
Abstract
Lateral meningocele syndrome (LMS, OMIM%130720), also known as Lehman syndrome, is a very rare skeletal disorder with facial anomalies, hypotonia and meningocele-related neurologic dysfunction. The characteristic lateral meningoceles represent the severe end of the dural ectasia spectrum and are typically most severe in the lower spine. Facial features of LMS include hypertelorism and telecanthus, high arched eyebrows, ptosis, midfacial hypoplasia, micrognathia, high and narrow palate, low-set ears and a hypotonic appearance. Hyperextensibility, hernias and scoliosis reflect a connective tissue abnormality, and aortic dilation, a high-pitched nasal voice, wormian bones and osteolysis may be present. Lateral meningocele syndrome has phenotypic overlap with Hajdu-Cheney syndrome. We performed exome resequencing in five unrelated individuals with LMS and identified heterozygous truncating NOTCH3 mutations. In an additional unrelated individual Sanger sequencing revealed a deleterious variant in the same exon 33. In total, five novel de novo NOTCH3 mutations were identified in six unrelated patients. One had a 26 bp deletion (c.6461_6486del, p.G2154fsTer78), two carried the same single base pair insertion (c.6692_93insC, p.P2231fsTer11), and three individuals had a nonsense point mutation at c.6247A > T (pK2083*), c.6663C > G (p.Y2221*) or c.6732C > A, (p.Y2244*). All mutations cluster into the last coding exon, resulting in premature termination of the protein and truncation of the negative regulatory proline-glutamate-serine-threonine rich PEST domain. Our results suggest that mutant mRNA products escape nonsense mediated decay. The truncated NOTCH3 may cause gain-of-function through decreased clearance of the active intracellular product, resembling NOTCH2 mutations in the clinically related Hajdu-Cheney syndrome and contrasting the NOTCH3 missense mutations causing CADASIL.
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Affiliation(s)
- Karen W. Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, and Sidney Kimmel Medical School at T. Jefferson University, Philadelphia, Pennsylvania
| | - Katherine M. Robbins
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
- Department of Biological Sciences, University of Delaware, Newark, Delaware
| | - Nara L. Sobreira
- Johns Hopkins University School of Medicine, Institute of Genetic Medicine, Baltimore, Maryland
| | - P. Dane Witmer
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lynne M. Bird
- University of California San Diego and Rady Children's Hospital, San Diego, California
| | - Kristiina Avela
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Outi Makitie
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Daniela Alves
- Neurogenetics Unit, Department of Medical Genetics, Centro Hospitalar de São João, Porto, Portugal
| | | | - Elaine H. Zackai
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kimberly F. Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deborah L. Stabley
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
| | - Katia Sol-Church
- Department of Biomedical Research, A.I. duPont Hospital for Children, Wilmington, Delaware
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19
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Siggberg L, Ala-Mello S, Linnankivi T, Avela K, Scheinin I, Kristiansson K, Lahermo P, Hietala M, Metsähonkala L, Kuusinen E, Laaksonen M, Saarela J, Knuutila S. Erratum to: High-resolution SNP array analysis of patients with developmental disorder and normal array CGH result. BMC Med Genet 2014; 15:124. [PMID: 25928284 PMCID: PMC4429685 DOI: 10.1186/s12881-014-0124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Linda Siggberg
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland.
| | - Sirpa Ala-Mello
- Rinnekoti Foundation, Rehabilitation Home for Children, Espoo, Finland.
| | - Tarja Linnankivi
- Department of Pediatric Neurology, Helsinki University Central Hospital, Helsinki, Finland.
| | - Kristiina Avela
- Department of Medical Genetics, Väestöliitto, The Family Federation of Finland, Helsinki, Finland.
| | - Ilari Scheinin
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland. .,Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands. .,Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Kati Kristiansson
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland. .,Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Päivi Lahermo
- Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Marja Hietala
- Department of Clinical Genetics, Turku University Hospital and Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland.
| | - Liisa Metsähonkala
- Department of Pediatric Neurology, Helsinki University Central Hospital, Helsinki, Finland.
| | - Esa Kuusinen
- Department of Pediatrics, Satakunta Hospital District, Pori, Finland.
| | - Maarit Laaksonen
- Population Health Unit, Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 21, 00014, Helsinki, Finland.
| | - Janna Saarela
- Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland.
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20
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Mantere T, Haanpää M, Hanenberg H, Schleutker J, Kallioniemi A, Kähkönen M, Parto K, Avela K, Aittomäki K, von Koskull H, Hartikainen JM, Kosma VM, Laasanen SL, Mannermaa A, Pylkäs K, Winqvist R. Finnish Fanconi anemia mutations and hereditary predisposition to breast and prostate cancer. Clin Genet 2014; 88:68-73. [PMID: 24989076 DOI: 10.1111/cge.12447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/13/2014] [Accepted: 06/19/2014] [Indexed: 01/07/2023]
Abstract
Mutations in downstream Fanconi anemia (FA) pathway genes, BRCA2, PALB2, BRIP1 and RAD51C, explain part of the hereditary breast cancer susceptibility, but the contribution of other FA genes has remained questionable. Due to FA's rarity, the finding of recurrent deleterious FA mutations among breast cancer families is challenging. The use of founder populations, such as the Finns, could provide some advantage in this. Here, we have resolved complementation groups and causative mutations of five FA patients, representing the first mutation confirmed FA cases in Finland. These patients belonged to complementation groups FA-A (n = 3), FA-G (n = 1) and FA-I (n = 1). The prevalence of the six FA causing mutations was then studied in breast (n = 1840) and prostate (n = 565) cancer cohorts, and in matched controls (n = 1176 females, n = 469 males). All mutations were recurrent, but no significant association with cancer susceptibility was observed for any: the prevalence of FANCI c.2957_2969del and c.3041G>A mutations was even highest in healthy males (1.7%). This strengthens the exclusive role of downstream genes in cancer predisposition. From a clinical point of view, current results provide fundamental information of the mutations to be tested first in all suspected FA cases in Finland.
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Affiliation(s)
- T Mantere
- Department of Clinical Chemistry and Biocenter Oulu, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland.,Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - M Haanpää
- Department of Clinical Chemistry and Biocenter Oulu, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland.,Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - H Hanenberg
- Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University School of Medicine, Duesseldorf, Germany
| | - J Schleutker
- BioMediTech and FimLab Laboratories, University of Tampere, Tampere, Finland.,Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland
| | - A Kallioniemi
- BioMediTech and FimLab Laboratories, University of Tampere, Tampere, Finland
| | - M Kähkönen
- FimLab Laboratories, Laboratory of Clinical Genetics, Tampere, Finland
| | - K Parto
- Pediatric Oncology, Tampere University Hospital, Tampere, Finland
| | - K Avela
- Department of Clinical Genetics, University of Helsinki, Helsinki University Central Hospital, Helsinki, Finland
| | - K Aittomäki
- Department of Clinical Genetics, University of Helsinki, Helsinki University Central Hospital, Helsinki, Finland
| | - H von Koskull
- Department of Clinical Genetics, University of Helsinki, Helsinki University Central Hospital, Helsinki, Finland
| | - J M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine; Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - V-M Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine; Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - S-L Laasanen
- Department of Pediatrics, Genetics Outpatient Clinic, and Department of Dermatology, Tampere University Hospital, Tampere, Finland
| | - A Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine; Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - K Pylkäs
- Department of Clinical Chemistry and Biocenter Oulu, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland.,Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - R Winqvist
- Department of Clinical Chemistry and Biocenter Oulu, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland.,Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Avela K, Toiviainen-Salo S, Karttunen-Lewandowski P, Kauria L, Valanne L, Salonen-Kajander R. Frontotemporal pachygyria-two new patients. Eur J Med Genet 2012; 55:753-7. [PMID: 23022981 DOI: 10.1016/j.ejmg.2012.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 09/22/2012] [Indexed: 11/16/2022]
Abstract
We describe two Finnish brothers with frontotemporal pachygyria, intellectual deficiency and mild dysmorphisms. Previously, only a few cases of similar frontotemporal pachygyria have been reported. This report provides further evidence about frontotemporal pachygyria being a distinct genetic entity inherited as an autosomal recessive trait.
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Affiliation(s)
- Kristiina Avela
- Department of Clinical Genetics, Helsinki University Central Hospital, 00029 HUS, Finland.
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23
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Avela K, Mäkitie O. Response to “Lateral Meningocele Syndrome and Hajdu-Cheney Syndrome: Different Disorders With Overlapping Phenotypes” by Gripp. Am J Med Genet A 2011. [DOI: 10.1002/ajmg.a.34085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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Avela K, Aktan-Collan K, Horelli-Kuitunen N, Knuutila S, Somer M. A microduplication on chromosome 17p13.1p13.3 including the PAFAH1B1 (LIS1) gene. Am J Med Genet A 2011; 155A:875-9. [PMID: 21595003 DOI: 10.1002/ajmg.a.33944] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 12/10/2010] [Indexed: 11/10/2022]
Abstract
Recently, three children with a microduplication in 17p13 including the PAFAH1B1 gene that encodes LIS1 were reported. LIS1 overexpression has earlier been shown to affect brain development by causing migrational defects and reductions in brain volume [Bi et al., 2009]. Here, we report an additional patient with a microduplication on chromosome 17p13.1p13.3 including the PAFAH1B1 gene, that was inserted into the long arm of chromosome 4. The patient had psychomotor and growth retardation, dysmorphic features, small ventricular septal defect (VSD), and immunoglobulin abnormality. Only subtle abnormalities in brain MRI scan were seen. Interestingly, the facial features of our patient closely resemble those previously reported in 17p trisomy patients.
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Affiliation(s)
- Kristiina Avela
- Vaestoliitto, The Family Federation of Finland, Department of Medical Genetics, Helsinki, Finland.
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25
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Abstract
Hajdu-Cheney syndrome (HCS) is an autosomal dominant condition comprising osteolysis of the terminal phalanges, characteristic craniofacial abnormalities, dental anomalies, and proportionate short stature. The clinical and radiological findings develop and progress with age. Here, we report on a HCS patient with severe scoliosis and exceptionally massive dural ectasia. Congenital scoliosis and dural ectasia have not been reported previously in HCS.
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Affiliation(s)
- Kristiina Avela
- Väestöliitto, The Family Federation of Finland, Department of Medical Genetics, Helsinki, Finland.
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26
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Avela K, Alen R, Huttunen M, Pärssinen O. Megalocornea – Urticaria pigmentosa syndrome – A new syndrome? Eur J Med Genet 2009; 52:430-2. [DOI: 10.1016/j.ejmg.2009.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 08/15/2009] [Indexed: 11/29/2022]
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27
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Avela K, Mikkola T, Orpana A, Viinikka L, Ylikorkala O. Effects of Labetalol on the Releas of Prostacyclin and Endothelin-1 by Cultured Human Umbilical Vein Endothelial Cells and on the Excretion of Prostacyclin and Thromboxane Metabolites in Preeclamptic Patients. Hypertens Pregnancy 2009. [DOI: 10.3109/10641959509015682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Gylling A, Ridanpää M, Vierimaa O, Aittomäki K, Avela K, Kääriäinen H, Laivuori H, Pöyhönen M, Sallinen SL, Wallgren-Pettersson C, Järvinen HJ, Mecklin JP, Peltomäki P. Large genomic rearrangements and germline epimutations in Lynch syndrome. Int J Cancer 2009; 124:2333-40. [PMID: 19173287 DOI: 10.1002/ijc.24230] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In one-third of families fulfilling the Amsterdam criteria for hereditary nonpolyposis colorectal cancer/Lynch syndrome, and a majority of those not fulfilling these criteria point mutations in DNA mismatch repair (MMR) genes are not found. The role of large genomic rearrangements and germline epimutations in MLH1, MSH2 and MSH6 was evaluated in 2 such cohorts. All 45 index patients were mutation-negative by genomic sequencing and testing for a prevalent population-specific founder mutation, and selectively lacked MMR protein expression in tumor tissue. Eleven patients ("research cohort") represented 11 mutation-negative families among 81 verified or putative Lynch syndrome families from the nation-wide Hereditary Colorectal Cancer Registry of Finland. Thirty-four patients from 33 families ("clinic-based cohort") represented suspected Lynch syndrome patients tested for MMR gene mutations in a diagnostic laboratory during 2004-2007. Multiplex ligation-dependent probe amplification (MLPA) and methylation-specific (MS)-MLPA were used to detect rearrangements and epimutations, respectively. Large genomic deletions occurred in 12/45 patients (27%), being present in 3/25 (12%), 9/16 (56%) and 0/4 (0%) among index patients lacking MLH1, MSH2 or MSH6 expression, respectively. Germline epimutations of MLH1, one of which coexisted with a genomic deletion, occurred in 2 patients (4%) and were accompanied by monoallelic expression in mRNA. Large genomic deletions (mainly MSH2) and germline epimutations (MLH1) together explain a significant fraction of point mutation-negative families suspected of Lynch syndrome and are associated with characteristic clinical and family features. Our findings have important implications in the diagnosis and management of such families.
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Affiliation(s)
- Annette Gylling
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland.
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29
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Hämäläinen RH, Avela K, Lambert JA, Kallijärvi J, Eyaid W, Gronau J, Ignaszewski AP, McFadden D, Sorge G, Lipsanen-Nyman M, Lehesjoki AE. Novel mutations in theTRIM37gene in Mulibrey Nanism. Hum Mutat 2004; 23:522. [PMID: 15108285 DOI: 10.1002/humu.9233] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mulibrey nanism is an autosomal recessive prenatal-onset growth disorder of unknown pathogenesis. The main clinical features are pre- and postnatal growth failure, characteristic dysmorphic craniofacial features, heart disease, and hepatomegaly. Five truncating mutations in the TRIM37 gene have previously been reported in Mulibrey nanism patients. The TRIM37 protein encodes a novel protein of unknown function. It contains a tripartite motif (TRIM, also denoted the RING-B-box-Coiled-coil or RBCC domain) and a TRAF (tumor necrosis factor-receptor associated factor) domain. TRIM37 localizes to peroxisomes classifying Mulibrey nanism as a peroxisomal disorder. Here we have characterized the genomic structure of the TRIM37 gene, which has 24 exons spanning approximately 109 kb of genomic DNA. Further, we report six novel disease-associated mutations, five of which predict a truncated protein: c.745C>T (p.Gln249X), c.1411C>T (p.Arg471X), c.2056C>T (p.Arg686X), and an 8.6 kb genomic deletion (c.1314+507_1668-207del resulting in p.Arg439fsX4). The sixth mutation (c.965G>T) is the first missense mutation (p.Gly322Val) associated with Mulibrey nanism. It affects the TRAF domain of TRIM37 and results in altered subcellular localization of the mutant TRIM37 protein, further suggesting that it is pathogenic.
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Affiliation(s)
- Riikka H Hämäläinen
- The Folkhälsan Institute of Genetics and Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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30
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Savander M, Ropponen A, Avela K, Weerasekera N, Cormand B, Hirvioja ML, Riikonen S, Ylikorkala O, Lehesjoki AE, Williamson C, Aittomäki K. Genetic evidence of heterogeneity in intrahepatic cholestasis of pregnancy. Gut 2003; 52:1025-9. [PMID: 12801961 PMCID: PMC1773695 DOI: 10.1136/gut.52.7.1025] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS The aim of this study was to investigate the genetic aetiology of intrahepatic cholestasis of pregnancy (ICP) and the impact of known cholestasis genes (BSEP, FIC1, and MDR3) on the development of this disease. PATIENTS AND METHODS Sixty nine Finnish ICP patients were prospectively interviewed for a family history of ICP, and clinical features were compared in patients with familial ICP (patients with a positive family history, n=11) and sporadic patients (patients with no known family history of ICP, n=58). For molecular genetic analysis, 16 individuals from two independently ascertained Finnish ICP families were genotyped for the flanking markers for BSEP, FIC1, and MDR3. RESULTS The pedigree structures in 16% (11/69) of patients suggested dominant inheritance. Patients with familial ICP had higher serum aminotransferase levels and a higher recurrence risk (92% v 40%). Both segregation of haplotypes and multipoint linkage analysis excluded BSEP, FIC1, and MDR3 genes in the studied pedigrees. Additionally, the MDR3 gene, previously shown to harbour mutations in ICP patients, was negative for mutations when sequenced in four affected individuals from the two families. CONCLUSIONS These results support the hypothesis that the aetiology of ICP is heterogeneous and that ICP is due to a genetic predisposition in a proportion of patients. The results of molecular genetic analysis further suggest that the previously identified three cholestasis genes are not likely to be implicated in these Finnish ICP families with dominant inheritance.
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Affiliation(s)
- M Savander
- Department of Medical Genetics and Folkhälsan Institute of Genetics, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Kallijärvi J, Avela K, Lipsanen-Nyman M, Ulmanen I, Lehesjoki AE. The TRIM37 gene encodes a peroxisomal RING-B-box-coiled-coil protein: classification of mulibrey nanism as a new peroxisomal disorder. Am J Hum Genet 2002; 70:1215-28. [PMID: 11938494 PMCID: PMC447596 DOI: 10.1086/340256] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2001] [Accepted: 02/11/2002] [Indexed: 12/31/2022] Open
Abstract
Mulibrey nanism is a rare growth disorder of prenatal onset caused by mutations in the TRIM37 gene, which encodes a RING-B-box-coiled-coil protein. The pathogenetic mechanisms of mulibrey nanism are unknown. We have used transiently transfected cells and antibodies raised against the predicted TRIM37 protein to characterize the TRIM37 gene product and to determine its intracellular localization. We show that the human TRIM37 cDNA encodes a peroxisomal protein with an apparent molecular weight of 130 kD. Peroxisomal localization is compromised in mutant protein representing the major Finnish TRIM37 mutation but is retained in the protein representing the minor Finnish mutation. Colocalization of endogenous TRIM37 with peroxisomal markers was observed by double immunofluorescence staining in HepG2 and human intestinal smooth muscle cell lines. In human tissue sections, TRIM37 shows a granular cytoplasmic pattern. Endogenous TRIM37 is not imported into peroxisomes in peroxin 1 (PEX1(-/-)) and peroxin 5 (PEX5(-/-)) mutant fibroblasts but is imported normally in peroxin 7 (PEX7(-/-)) deficient fibroblasts, giving further evidence for a peroxisomal localization of TRIM37. Fibroblasts derived from patients with mulibrey nanism lack C-terminal TRIM37 immunoreactivity but stain normally for both peroxisomal matrix and membrane markers, suggesting apparently normal peroxisome biogenesis in patient fibroblasts. Taken together, this molecular evidence unequivocally indicates that TRIM37 is located in the peroxisomes, and Mulibrey nanism thus can be classified as a new peroxisomal disorder.
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Affiliation(s)
- Jukka Kallijärvi
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, Biomedicum Helsinki, Department of Molecular Medicine, National Public Health Institute, Biomedicum Helsinki, The Hospital for Children and Adolescents, and Helsinki University Central Hospital, University of Helsinki, Helsinki
| | - Kristiina Avela
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, Biomedicum Helsinki, Department of Molecular Medicine, National Public Health Institute, Biomedicum Helsinki, The Hospital for Children and Adolescents, and Helsinki University Central Hospital, University of Helsinki, Helsinki
| | - Marita Lipsanen-Nyman
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, Biomedicum Helsinki, Department of Molecular Medicine, National Public Health Institute, Biomedicum Helsinki, The Hospital for Children and Adolescents, and Helsinki University Central Hospital, University of Helsinki, Helsinki
| | - Ismo Ulmanen
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, Biomedicum Helsinki, Department of Molecular Medicine, National Public Health Institute, Biomedicum Helsinki, The Hospital for Children and Adolescents, and Helsinki University Central Hospital, University of Helsinki, Helsinki
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, Biomedicum Helsinki, Department of Molecular Medicine, National Public Health Institute, Biomedicum Helsinki, The Hospital for Children and Adolescents, and Helsinki University Central Hospital, University of Helsinki, Helsinki
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Monni O, Barlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner ML, Kallioniemi A. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci U S A 2001; 98:5711-6. [PMID: 11331760 PMCID: PMC33278 DOI: 10.1073/pnas.091582298] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biological significance of DNA amplification in cancer is thought to be due to the selection of increased expression of a single or few important genes. However, systematic surveys of the copy number and expression of all genes within an amplified region of the genome have not been performed. Here we have used a combination of molecular, genomic, and microarray technologies to identify target genes for 17q23, a common region of amplification in breast cancers with poor prognosis. Construction of a 4-Mb genomic contig made it possible to define two common regions of amplification in breast cancer cell lines. Analysis of 184 primary breast tumors by fluorescence in situ hybridization on tissue microarrays validated these results with the highest amplification frequency (12.5%) observed for the distal region. Based on GeneMap'99 information, 17 known genes and 26 expressed sequence tags were localized to the contig. Analysis of genomic sequence identified 77 additional transcripts. A comprehensive analysis of expression levels of these transcripts in six breast cancer cell lines was carried out by using complementary DNA microarrays. The expression patterns varied from one cell line to another, and several overexpressed genes were identified. Of these, RPS6KB1, MUL, APPBP2, and TRAP240 as well as one uncharacterized expressed sequence tag were located in the two common amplified regions. In summary, comprehensive analysis of the 17q23 amplicon revealed a limited number of highly expressed genes that may contribute to the more aggressive clinical course observed in breast cancer patients with 17q23-amplified tumors.
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Affiliation(s)
- O Monni
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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33
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Avela K, Lipsanen-Nyman M, Idänheimo N, Seemanová E, Rosengren S, Mäkelä TP, Perheentupa J, Chapelle AD, Lehesjoki AE. Gene encoding a new RING-B-box-Coiled-coil protein is mutated in mulibrey nanism. Nat Genet 2000; 25:298-301. [PMID: 10888877 DOI: 10.1038/77053] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mulibrey nanism (for muscle-liver-brain-eye nanism, MUL; MIM 253250) is an autosomal recessive disorder that involves several tissues of mesodermal origin, implying a defect in a highly pleiotropic gene. Characteristic features include severe growth failure of prenatal onset and constrictive pericardium with consequent hepatomegaly. In addition, muscle hypotonia, J-shaped sella turcica, yellowish dots in the ocular fundi, typical dysmorphic features and hypoplasia of various endocrine glands causing hormonal deficiency are common. About 4% of MUL patients develop Wilms' tumour. MUL is enriched in the Finnish population, but is rare elsewhere. We previously assigned MUL to chromosome 17q22-q23 and constructed a physical contig over the critical MUL region. The region has now been further refined by haplotype analysis and new positional candidate genes have been localized. We identified a gene with four independent MUL-associated mutations that all cause a frameshift and predict a truncated protein. MUL is ubiquitously expressed and encodes a new member of the RING-B-box-Coiled-coil (RBCC) family of zinc-finger proteins, whose members are involved in diverse cellular functions such as developmental patterning and oncogenesis.
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Affiliation(s)
- K Avela
- Folkhälsan Institute of Genetics, Helsinki, Finland.
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34
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Paavola P, Avela K, Horelli-Kuitunen N, Bärlund M, Kallioniemi A, Idänheimo N, Kyttälä M, de la Chapelle A, Palotie A, Lehesjoki AE, Peltonen L. High-resolution physical and genetic mapping of the critical region for Meckel syndrome and Mulibrey Nanism on chromosome 17q22-q23. Genome Res 1999; 9:267-76. [PMID: 10077533 PMCID: PMC310730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Previously, we assigned the genes for two autosomal recessive disorders, Meckel syndrome (MKS; MIM 249000) and Mulibrey Nanism [MUL (muscle-liver-brain-eye Nanism); MIM 253250] that are enriched in the Finnish population, to overlapping genomic regions on chromosome 17q. Now, we report the construction of a bacterial clone contig over the critical region for both disorders. Several novel CA-repeat markers were isolated from these clones, which allowed refined mapping of the MKS and MUL loci using haplotype and linkage disequilibrium analysis. The localization of the MKS locus was narrowed to <1 cM between markers D17S1290 and 132-CA, within an approximately 800-kb region. The MUL locus was refined into an approximately 1400-kb interval between markers D17S1290 and 52-CA. The whole MKS region falls within the MUL region. In the common critical region, the conserved haplotypes were different in MKS and MUL patients. A trancript map was constructed by assigning expressed sequence tags (ESTs) and genes, derived from the human gene map, to the bacterial clone contig. Altogether, four genes and a total of 20 ESTs were precisely localized. These data provide the molecular tools for the final identification of the MKS and the MUL genes.
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Affiliation(s)
- P Paavola
- National Public Health Institute, Department of Human Molecular Genetics, 00300 Helsinki, Finland
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35
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Paavola P, Avela K, Horelli-Kuitunen N, Bärlund M, Kallioniemi A, Idänheimo N, Kyttälä M, de la Chapelle A, Palotie A, Lehesjoki AE, Peltonen L. High-Resolution Physical and Genetic Mapping of the Critical Region for Meckel Syndrome and Mulibrey Nanism on Chromosome 17q22–q23. Genome Res 1999. [DOI: 10.1101/gr.9.3.267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Previously, we assigned the genes for two autosomal recessive disorders, Meckel syndrome (MKS; MIM 249000) and Mulibrey Nanism [MUL (muscle–liver–brain–eye Nanism); MIM 253250] that are enriched in the Finnish population, to overlapping genomic regions on chromosome 17q. Now, we report the construction of a bacterial clone contig over the critical region for both disorders. Several novel CA-repeat markers were isolated from these clones, which allowed refined mapping of the MKS and MUL loci using haplotype and linkage disequilibrium analysis. The localization of the MKS locus was narrowed to <1 cM between markers D17S1290 and 132-CA, within an ∼800-kb region. The MUL locus was refined into an ∼1400-kb interval between markers D17S1290 and 52-CA. The whole MKS region falls within the MUL region. In the common critical region, the conserved haplotypes were different in MKS and MUL patients. A trancript map was constructed by assigning expressed sequence tags (ESTs) and genes, derived from the human gene map, to the bacterial clone contig. Altogether, four genes and a total of 20 ESTs were precisely localized. These data provide the molecular tools for the final identification of the MKS and the MUL genes.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. G42608–G42611,G42376–G42388, and G42200–G42250. The online supplement for primer sequences and PCR product sizes, as well as the STS-content table, are available at http://www.cshl.org/gr.]
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36
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Cormand B, Avela K, Pihko H, Santavuori P, Talim B, Topaloglu H, de la Chapelle A, Lehesjoki AE. Assignment of the muscle-eye-brain disease gene to 1p32-p34 by linkage analysis and homozygosity mapping. Am J Hum Genet 1999; 64:126-35. [PMID: 9915951 PMCID: PMC1377710 DOI: 10.1086/302206] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Muscle-eye-brain disease (MEB) is an autosomal recessive disease of unknown etiology characterized by severe mental retardation, ocular abnormalities, congenital muscular dystrophy, and a polymicrogyria-pachygyria-type neuronal migration disorder of the brain. A similar combination of muscle and brain involvement is also seen in Walker-Warburg syndrome (WWS) and Fukuyama congenital muscular dystrophy (FCMD). Whereas the gene underlying FCMD has been mapped and cloned, the genetic location of the WWS gene is still unknown. Here we report the assignment of the MEB gene to chromosome 1p32-p34 by linkage analysis and homozygosity mapping in eight families with 12 affected individuals. After a genomewide search for linkage in four affected sib pairs had pinpointed the assignment to 1p, the MEB locus was more precisely assigned to a 9-cM interval flanked by markers D1S200 proximally and D1S211 distally. Multipoint linkage analysis gave a maximum LOD score of 6.17 at locus D1S2677. These findings provide a starting point for the positional cloning of the disease gene, which may play an important role in muscle function and brain development. It also provides an opportunity to test other congenital muscular dystrophy phenotypes, in particular WWS, for linkage to the same locus.
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Affiliation(s)
- B Cormand
- Department of Medical Genetics, University of Helsinki, Finland
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37
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Avela K, Lipsanen-Nyman M, Perheentupa J, Wallgren-Pettersson C, Marchand S, Fauré S, Sistonen P, de la Chapelle A, Lehesjoki AE. Assignment of the mulibrey nanism gene to 17q by linkage and linkage-disequilibrium analysis. Am J Hum Genet 1997; 60:896-902. [PMID: 9106536 PMCID: PMC1712467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mulibrey nanism (MUL) is an autosomal recessive disorder with unknown basic metabolic defect. It is characterized by growth failure of prenatal onset, characteristic dysmorphic features, constrictive pericardium, hepatomegaly as a consequence of constrictive pericardium, yellowish dots in the ocular fundi, and J-shaped sella turcica. Hypoplasia of various endocrine glands, causing hormone deficiencies, is common. Here we report the assignment of the MUL gene, by linkage analysis in Finnish families, to a 7-cM region flanked by D17S1799 and D17S948 on chromosome 17q. Multipoint linkage analysis gave a maximum LOD score of 5.01 at loci D17S1606-D17S1853 and at D17S1604. The estimate of the critical MUL region was further narrowed to within approximately 250 kb of marker D17S1853 by linkage disequilibrium analysis. Positional candidate genes that belong to the growth hormone and homeobox B gene clusters were excluded. These data confirm the autosomal recessive inheritance of MUL and allow highly focused attempts to clone the gene.
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Affiliation(s)
- K Avela
- Department of Medical Genetics, University of Helsinki, Folkhälsan Institute of Genetics, Finland
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38
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Orpana AK, Avela K, Ranta V, Viinikka L, Ylikorkala O. The calcium-dependent nitric oxide production of human vascular endothelial cells in preeclampsia. Am J Obstet Gynecol 1996; 174:1056-60. [PMID: 8633636 DOI: 10.1016/s0002-9378(96)70350-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Nitric oxide is an important vasodilator, and in this study we studied whether the calcium-dependent nitric oxide production capacity of human umbilical vein endothelial cells was affected by preeclampsia. STUDY DESIGN Human umbilical vein endothelial cells were isolated from 11 preeclamptic and 10 normotensive pregnancies. The maximal calcium ionophore A23187-stimulated nitric oxide production capacity was measured as accumulation of nitrate and nitrite into the culture medium, and it was related to the number of viable endothelial cells by measurement of their mitochondrial dehydrogenase activity. RESULTS The cell number-related nitric oxide production capacity was similar in preeclamptic and normotensive pregnancies. The total nitric oxide production of cells from preeclamptic pregnancies was significantly lower (p <0.001). This difference, however, was mainly caused by larger amount of viable endothelial cells recovered from normotensive pregnancies. CONCLUSION The maximal calcium-dependent nitric oxide production capacity of individual human umbilical vein endothelial cells is not affected by preeclampsia.
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Affiliation(s)
- A K Orpana
- Department of Obstetrics and Gynecology, University of Helsinki, Finland
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39
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Wallgren-Pettersson C, Avela K, Marchand S, Kolehmainen J, Tahvanainen E, Hansen FJ, Muntoni F, Dubowitz V, De Visser M, Van Langen IM. A gene for autosomal recessive nemaline myopathy assigned to chromosome 2q by linkage analysis. Neuromuscul Disord 1995; 5:441-3. [PMID: 8580725 DOI: 10.1016/0960-8966(95)00022-f] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Clinical genetic evidence suggests the existence of an autosomal recessive form of congenital nemaline myopathy in addition to the autosomal dominant one(s). One mutation in an Australian kindred has been identified as causing an autosomal dominant form of the disease. This mutation in the alpha-tropomyosin gene TPM3 has previously been excluded as causing autosomal recessive nemaline myopathy. We searched systematically for genetic linkage to autosomal recessive nemaline myopathy (NEM2) by studying microsatellite marker alleles in seven multiplex families from Finland, Denmark, Wales, England and The Netherlands. Significant evidence of linkage was found to markers of chromosome 2q, the highest multipoint lod score value being 5.34 for the marker D2S151. Recombinant genotypes in affected individuals demarcate the the region in which the NEM2 gene is likely to reside as a 13 cM region between the markers D2S150 and D2S142. These results confirm the existence of at least one distinctive form of autosomal recessive nemaline myopathy and provide a basis for the identification of its gene.
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Mikkola T, Turunen P, Avela K, Orpana A, Viinikka L, Ylikorkala O. 17 beta-estradiol stimulates prostacyclin, but not endothelin-1, production in human vascular endothelial cells. J Clin Endocrinol Metab 1995; 80:1832-6. [PMID: 7775630 DOI: 10.1210/jcem.80.6.7775630] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The exact mechanisms by which estrogens protect against occlusive vascular disorders are not known. One possibility could be an effect on vascular endothelial vasoactive compounds, such as vasodilatory prostacyclin (PGI2) and vasoconstrictory endothelin (ET-1). Here we report on the effect of 17 beta-estradiol on the synthesis of PGI2 and ET-1 in cultured human umbilical vein endothelial cells. These cells were incubated in the absence (control) and presence of 17 beta-estradiol (0.001-1 mumol/L) for 3-24 h with serum (10%) or without serum. The release of PGI2, as assessed by its metabolite 6-keto-prostaglandin F1 alpha, and that of ET-1, were assessed by RIA. 17 beta-Estradiol (0.01-0.1 mumol/L) predissolved in ethanol (final concentration, 0.01%) increased PGI2 production by 26-30% in endothelial cells incubated without serum. This increase in PGI2 production was enhanced up to 66% when 17 beta-estradiol (1 mumol/L) was encapsulated within beta-cyclodextrin. The stimulation of PGI2 production was detectable after 12 h of incubation. The 17 beta-estradiol-induced stimulation of PGI2 production was blocked in dose-dependent manner by antiestrogenic tamoxifen. 17 beta-Estradiol failed to affect the production of PGI2 if the endothelial cells were incubated with serum and had no effect on ET-1 production under any conditions. 17 beta-Estradiol-induced stimulation of vasodilatory and antiaggregatory PGI2 production without a concomitant change in vasoconstrictory ET-1 production may provide one explanation for the ability of estradiol to maintain vascular health and protect against vascular disorders.
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Affiliation(s)
- T Mikkola
- Department of Obstetrics and Gynecology, University of Helsinki, Finland
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