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Skuladottir AT, Stefansdottir L, Halldorsson GH, Stefansson OA, Bjornsdottir A, Jonsson P, Palmadottir V, Thorgeirsson TE, Walters GB, Gisladottir RS, Bjornsdottir G, Jonsdottir GA, Sulem P, Gudbjartsson DF, Knowlton KU, Jones DA, Ottas A, Pedersen OB, Didriksen M, Brunak S, Banasik K, Hansen TF, Erikstrup C, Haavik J, Andreassen OA, Rye D, Igland J, Ostrowski SR, Milani LA, Nadauld LD, Stefansson H, Stefansson K. GWAS meta-analysis reveals key risk loci in essential tremor pathogenesis. Commun Biol 2024; 7:504. [PMID: 38671141 PMCID: PMC11053069 DOI: 10.1038/s42003-024-06207-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Essential tremor (ET) is a prevalent neurological disorder with a largely unknown underlying biology. In this genome-wide association study meta-analysis, comprising 16,480 ET cases and 1,936,173 controls from seven datasets, we identify 12 sequence variants at 11 loci. Evaluating mRNA expression, splicing, plasma protein levels, and coding effects, we highlight seven putative causal genes at these loci, including CA3 and CPLX1. CA3 encodes Carbonic Anhydrase III and carbonic anhydrase inhibitors have been shown to decrease tremors. CPLX1, encoding Complexin-1, regulates neurotransmitter release. Through gene-set enrichment analysis, we identify a significant association with specific cell types, including dopaminergic and GABAergic neurons, as well as biological processes like Rho GTPase signaling. Genetic correlation analyses reveals a positive association between ET and Parkinson's disease, depression, and anxiety-related phenotypes. This research uncovers risk loci, enhancing our knowledge of the complex genetics of this common but poorly understood disorder, and highlights CA3 and CPLX1 as potential therapeutic targets.
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Affiliation(s)
- Astros Th Skuladottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
| | | | | | | | | | - Palmi Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Geriatric Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Vala Palmadottir
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Rosa S Gisladottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Icelandic and Comparative Cultural Studies, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, USA
| | - David A Jones
- Precision Genomics, Intermountain Healthcare, Saint George, Utah, UK
| | - Aigar Ottas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ole B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Righospitale, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Righospitalet-Glostrup, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Righospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Aarhus University, Aarhus, Denmark
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Ole A Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - David Rye
- Emory Department of Neurology, Wesley Woods Health Center, Atlanta, GA, USA
| | - Jannicke Igland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Health and Caring sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital, Righospitale, Copenhagen, Denmark
| | - Lili A Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lincoln D Nadauld
- Precision Genomics, Intermountain Healthcare, Saint George, Utah, UK
- Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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2
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Sigurpalsdottir BD, Stefansson OA, Holley G, Beyter D, Zink F, Hardarson MÞ, Sverrisson SÞ, Kristinsdottir N, Magnusdottir DN, Magnusson OÞ, Gudbjartsson DF, Halldorsson BV, Stefansson K. A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes. Genome Biol 2024; 25:69. [PMID: 38468278 DOI: 10.1186/s13059-024-03207-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) and single molecule real-time (SMRT) sequencing developed by Pacific Bioscience (PacBio). In this study, we systematically compare the performance of CpG methylation detection from long-read sequencing. RESULTS We demonstrate that CpG methylation detection from 7179 nanopore-sequenced DNA samples is highly accurate and consistent with 132 oxidative bisulfite-sequenced (oxBS) samples, isolated from the same blood draws. We introduce quality filters for CpGs that further enhance the accuracy of CpG methylation detection from nanopore-sequenced DNA, while removing at most 30% of CpGs. We evaluate the per-site performance of CpG methylation detection across different genomic features and CpG methylation rates and demonstrate how the latest R10.4 flowcell chemistry and base-calling algorithms improve methylation detection from nanopore sequencing. Additionally, we show how the methylation detection of 50 SMRT-sequenced genomes compares to nanopore sequencing and oxBS. CONCLUSIONS This study provides the first systematic comparison of CpG methylation detection tools for long-read sequencing methods. We compare two commonly used computational methods for the detection of CpG methylation in a large number of nanopore genomes, including samples sequenced using the latest R10.4 nanopore flowcell chemistry and 50 SMRT sequenced samples. We provide insights into the strengths and limitations of each sequencing method as well as recommendations for standardization and evaluation of tools designed for genome-scale modified base detection using long-read sequencing.
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Affiliation(s)
- Brynja D Sigurpalsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland.
- School of Technology, Reykjavík University, Reykjavík, Iceland.
| | | | | | - Doruk Beyter
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland
| | - Florian Zink
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland
| | - Marteinn Þ Hardarson
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland
- School of Technology, Reykjavík University, Reykjavík, Iceland
| | | | | | | | | | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland.
- School of Technology, Reykjavík University, Reykjavík, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, Reykjavík, Iceland
- Faculty of Medicine, School of Health Science, University of Iceland, Reykjavík, Iceland
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3
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Thorolfsdottir RB, Jonsdottir AB, Sveinbjornsson G, Aegisdottir HM, Oddsson A, Stefansson OA, Halldorsson GH, Saevarsdottir S, Thorleifsson G, Stefansdottir L, Pedersen OB, Sørensen E, Ghouse J, Raja AA, Zheng C, Silajdzija E, Rand SA, Erikstrup C, Ullum H, Mikkelsen C, Banasik K, Brunak S, Ivarsdottir EV, Sigurdsson A, Beyter D, Sturluson A, Einarsson H, Tragante V, Helgason H, Lund SH, Halldorsson BV, Sigurpalsdottir BD, Olafsson I, Arnar DO, Thorgeirsson G, Knowlton KU, Nadauld LD, Gretarsdottir S, Helgadottir A, Ostrowski SR, Gudbjartssson DF, Jonsdottir I, Bundgaard H, Holm H, Sulem P, Stefansson K. Variants at the Interleukin 1 Gene Locus and Pericarditis. JAMA Cardiol 2024; 9:165-172. [PMID: 38150231 PMCID: PMC10753444 DOI: 10.1001/jamacardio.2023.4820] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 12/28/2023]
Abstract
Importance Recurrent pericarditis is a treatment challenge and often a debilitating condition. Drugs inhibiting interleukin 1 cytokines are a promising new treatment option, but their use is based on scarce biological evidence and clinical trials of modest sizes, and the contributions of innate and adaptive immune processes to the pathophysiology are incompletely understood. Objective To use human genomics, transcriptomics, and proteomics to shed light on the pathogenesis of pericarditis. Design, Setting, and Participants This was a meta-analysis of genome-wide association studies of pericarditis from 5 countries. Associations were examined between the pericarditis-associated variants and pericarditis subtypes (including recurrent pericarditis) and secondary phenotypes. To explore mechanisms, associations with messenger RNA expression (cis-eQTL), plasma protein levels (pQTL), and CpG methylation of DNA (ASM-QTL) were assessed. Data from Iceland (deCODE genetics, 1983-2020), Denmark (Copenhagen Hospital Biobank/Danish Blood Donor Study, 1977-2022), the UK (UK Biobank, 1953-2021), the US (Intermountain, 1996-2022), and Finland (FinnGen, 1970-2022) were included. Data were analyzed from September 2022 to August 2023. Exposure Genotype. Main Outcomes and Measures Pericarditis. Results In this genome-wide association study of 4894 individuals with pericarditis (mean [SD] age at diagnosis, 51.4 [17.9] years, 2734 [67.6%] male, excluding the FinnGen cohort), associations were identified with 2 independent common intergenic variants at the interleukin 1 locus on chromosome 2q14. The lead variant was rs12992780 (T) (effect allele frequency [EAF], 31%-40%; odds ratio [OR], 0.83; 95% CI, 0.79-0.87; P = 6.67 × 10-16), downstream of IL1B and the secondary variant rs7575402 (A or T) (EAF, 45%-55%; adjusted OR, 0.89; 95% CI, 0.85-0.93; adjusted P = 9.6 × 10-8). The lead variant rs12992780 had a smaller odds ratio for recurrent pericarditis (0.76) than the acute form (0.86) (P for heterogeneity = .03) and rs7575402 was associated with CpG methylation overlapping binding sites of 4 transcription factors known to regulate interleukin 1 production: PU.1 (encoded by SPI1), STAT1, STAT3, and CCAAT/enhancer-binding protein β (encoded by CEBPB). Conclusions and Relevance This study found an association between pericarditis and 2 independent sequence variants at the interleukin 1 gene locus. This finding has the potential to contribute to development of more targeted and personalized therapy of pericarditis with interleukin 1-blocking drugs.
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Affiliation(s)
| | | | | | | | | | | | - Gisli H. Halldorsson
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | - Ole B. Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jonas Ghouse
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Anna Axelsson Raja
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Chaoqun Zheng
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Elvira Silajdzija
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Søren Albertsen Rand
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Christina Mikkelsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Hafsteinn Einarsson
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hannes Helgason
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Bjarni V. Halldorsson
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Brynja D. Sigurpalsdottir
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, National University Hospital of Iceland, Reykjavik, Iceland
| | - David O. Arnar
- deCODE genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Kirk U. Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, Utah
- School of Medicine, University of Utah, Salt Lake City
| | - Lincoln D. Nadauld
- Precision Genomics, Intermountain Healthcare, Saint George, Utah
- School of Medicine, Stanford University, Stanford, California
| | | | | | - Sisse R. Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Daniel F. Gudbjartssson
- deCODE genetics, Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Hilma Holm
- deCODE genetics, Amgen, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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4
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Bjornsdottir G, Chalmer MA, Stefansdottir L, Skuladottir AT, Einarsson G, Andresdottir M, Beyter D, Ferkingstad E, Gretarsdottir S, Halldorsson BV, Halldorsson GH, Helgadottir A, Helgason H, Hjorleifsson Eldjarn G, Jonasdottir A, Jonasdottir A, Jonsdottir I, Knowlton KU, Nadauld LD, Lund SH, Magnusson OT, Melsted P, Moore KHS, Oddsson A, Olason PI, Sigurdsson A, Stefansson OA, Saemundsdottir J, Sveinbjornsson G, Tragante V, Unnsteinsdottir U, Walters GB, Zink F, Rødevand L, Andreassen OA, Igland J, Lie RT, Haavik J, Banasik K, Brunak S, Didriksen M, T Bruun M, Erikstrup C, Kogelman LJA, Nielsen KR, Sørensen E, Pedersen OB, Ullum H, Masson G, Thorsteinsdottir U, Olesen J, Ludvigsson P, Thorarensen O, Bjornsdottir A, Sigurdardottir GR, Sveinsson OA, Ostrowski SR, Holm H, Gudbjartsson DF, Thorleifsson G, Sulem P, Stefansson H, Thorgeirsson TE, Hansen TF, Stefansson K. Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura. Nat Genet 2023; 55:1843-1853. [PMID: 37884687 PMCID: PMC10632135 DOI: 10.1038/s41588-023-01538-0] [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: 12/02/2022] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
Migraine is a complex neurovascular disease with a range of severity and symptoms, yet mostly studied as one phenotype in genome-wide association studies (GWAS). Here we combine large GWAS datasets from six European populations to study the main migraine subtypes, migraine with aura (MA) and migraine without aura (MO). We identified four new MA-associated variants (in PRRT2, PALMD, ABO and LRRK2) and classified 13 MO-associated variants. Rare variants with large effects highlight three genes. A rare frameshift variant in brain-expressed PRRT2 confers large risk of MA and epilepsy, but not MO. A burden test of rare loss-of-function variants in SCN11A, encoding a neuron-expressed sodium channel with a key role in pain sensation, shows strong protection against migraine. Finally, a rare variant with cis-regulatory effects on KCNK5 confers large protection against migraine and brain aneurysms. Our findings offer new insights with therapeutic potential into the complex biology of migraine and its subtypes.
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Affiliation(s)
| | - Mona A Chalmer
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Copenhagen, Denmark
| | | | | | | | | | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Reykjavik University, School of Technology, Reykjavik, Iceland
| | - Gisli H Halldorsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Sigrun H Lund
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Physical Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | - Linn Rødevand
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jannicke Igland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Health and Social Science, Centre for Evidence-Based Practice, Western Norway University of Applied Science, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Mie T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine Health, Aarhus University, Aarhus, Denmark
| | - Lisette J A Kogelman
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Copenhagen, Denmark
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ole B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Copenhagen, Denmark
| | - Petur Ludvigsson
- Department of Pediatrics, Landspitali University Hostpital, Reykjavik, Iceland
| | - Olafur Thorarensen
- Department of Pediatrics, Landspitali University Hostpital, Reykjavik, Iceland
| | | | | | - Olafur A Sveinsson
- Laeknasetrid Clinic, Reykjavik, Iceland
- Department of Neurology, Landspitali University Hospital, Reykjavik, Iceland
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Thomas F Hansen
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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5
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Westergaard D, Steinthorsdottir V, Stefansdottir L, Rohde PD, Wu X, Geller F, Tyrmi J, Havulinna AS, Navais PS, Flatley C, Ostrowski SR, Pedersen OB, Erikstrup C, Sørensen E, Mikkelsen C, Brun MT, Jensen BA, Brodersen T, Ullum H, Magnus P, Andreassen OA, Njolstad PR, Kolte AM, Krebs L, Nyegaard M, Hansen TF, Fenstra B, Daly M, Lindgren CM, Thorleifsson G, Stefansson OA, Sveinbjornsson G, Gudbjartsson DF, Thorsteinsdottir U, Banasik K, Jacobsson B, Laisk T, Laivuori H, Stefansson K, Brunak S, Nielsen HS. Pregnancy-Associated Bleeding and Genetics: Five Sequence Variants in the Myometrium and Progesterone Signaling Pathway are associated with postpartum hemorrhage. medRxiv 2023:2023.08.10.23293932. [PMID: 37645979 PMCID: PMC10462219 DOI: 10.1101/2023.08.10.23293932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severity of these complications in maternal-fetal health. Here, we investigated the genetic variation underlying aspects of pregnancy-associated bleeding and identified five loci associated with PPH through a meta-analysis of 21,512 cases and 259,500 controls. Functional annotation analysis indicated candidate genes, HAND2, TBX3, and RAP2C/FRMD7, at three loci and showed that at each locus, associated variants were located within binding sites for progesterone receptors (PGR). Furthermore, there were strong genetic correlations with birth weight, gestational duration, and uterine fibroids. Early bleeding during pregnancy (28,898 cases and 302,894 controls) yielded no genome-wide association signals, but showed strong genetic correlation with a variety of human traits, indicative of polygenic and pleiotropic effects. Our results suggest that postpartum bleeding is related to myometrium dysregulation, whereas early bleeding is a complex trait related to underlying health and possibly socioeconomic status.
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Affiliation(s)
- David Westergaard
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | | | | | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Xiaoping Wu
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jaakko Tyrmi
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare - THL, Helsinki, Finland
| | - Pol Sole Navais
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Flatley
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Sisse Rye Ostrowski
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Pedersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christina Mikkelsen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mie Topholm Brun
- Clinical Immunological Research Unit, Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Thorsten Brodersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
| | - Henrik Ullum
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Per Magnus
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Pål R Njolstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Astrid Marie Kolte
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Lone Krebs
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Headache Center, Department of neurology, Copenhagen University Hospital, Glostrup, Denmark
| | - Bjarke Fenstra
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mark Daly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Big Data Institute Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Karina Banasik
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynaecology, Tampere University Hospital, Tampere, Finland
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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6
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Publisher Correction: Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3923. [PMID: 37400429 PMCID: PMC10318025 DOI: 10.1038/s41467-023-39492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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7
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Kristmundsdottir S, Jonsson H, Hardarson MT, Palsson G, Beyter D, Eggertsson HP, Gylfason A, Sveinbjornsson G, Holley G, Stefansson OA, Halldorsson GH, Olafsson S, Arnadottir GA, Olason PI, Eiriksson O, Masson G, Thorsteinsdottir U, Rafnar T, Sulem P, Helgason A, Gudbjartsson DF, Halldorsson BV, Stefansson K. Sequence variants affecting the genome-wide rate of germline microsatellite mutations. Nat Commun 2023; 14:3855. [PMID: 37386006 PMCID: PMC10310707 DOI: 10.1038/s41467-023-39547-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9-65.4) microsatellite de novo mutations (mDNMs) per offspring per generation, excluding one bp repeats motifs (homopolymers) the estimate is 48.2 mDNMs (95% CI: 46.7-49.6). Paternal mDNMs occur at longer repeats than maternal ones, which are in turn larger with a mean size of 3.4 bp vs 3.1 bp for paternal ones. mDNMs increase by 0.97 (95% CI: 0.90-1.04) and 0.31 (95% CI: 0.25-0.37) per year of father's and mother's age at conception, respectively. Here, we find two independent coding variants that associate with the number of mDNMs transmitted to offspring; The minor allele of a missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.
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Affiliation(s)
- Snaedis Kristmundsdottir
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | - Marteinn T Hardarson
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | - Doruk Beyter
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
| | | | | | | | | | | | - Gisli H Halldorsson
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Gudny A Arnadottir
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Gisli Masson
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Agnar Helgason
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics / Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics / Amgen Inc., Reykjavik, Iceland.
- School of Technology, Reykjavik University, Reykjavik, Iceland.
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8
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3453. [PMID: 37301908 PMCID: PMC10257723 DOI: 10.1038/s41467-023-38951-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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9
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Aegisdottir HM, Thorolfsdottir RB, Sveinbjornsson G, Stefansson OA, Gunnarsson B, Tragante V, Thorleifsson G, Stefansdottir L, Thorgeirsson TE, Ferkingstad E, Sulem P, Norddahl G, Rutsdottir G, Banasik K, Christensen AH, Mikkelsen C, Pedersen OB, Brunak S, Bruun MT, Erikstrup C, Jacobsen RL, Nielsen KR, Sørensen E, Frigge ML, Hjorleifsson KE, Ivarsdottir EV, Helgadottir A, Gretarsdottir S, Steinthorsdottir V, Oddsson A, Eggertsson HP, Halldorsson GH, Jones DA, Anderson JL, Knowlton KU, Nadauld LD, Haraldsson M, Thorgeirsson G, Bundgaard H, Arnar DO, Thorsteinsdottir U, Gudbjartsson DF, Ostrowski SR, Holm H, Stefansson K. Genetic variants associated with syncope implicate neural and autonomic processes. Eur Heart J 2023; 44:1070-1080. [PMID: 36747475 DOI: 10.1093/eurheartj/ehad016] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 11/22/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023] Open
Abstract
AIMS Syncope is a common and clinically challenging condition. In this study, the genetics of syncope were investigated to seek knowledge about its pathophysiology and prognostic implications. METHODS AND RESULTS This genome-wide association meta-analysis included 56 071 syncope cases and 890 790 controls from deCODE genetics (Iceland), UK Biobank (United Kingdom), and Copenhagen Hospital Biobank Cardiovascular Study/Danish Blood Donor Study (Denmark), with a follow-up assessment of variants in 22 412 cases and 286 003 controls from Intermountain (Utah, USA) and FinnGen (Finland). The study yielded 18 independent syncope variants, 17 of which were novel. One of the variants, p.Ser140Thr in PTPRN2, affected syncope only when maternally inherited. Another variant associated with a vasovagal reaction during blood donation and five others with heart rate and/or blood pressure regulation, with variable directions of effects. None of the 18 associations could be attributed to cardiovascular or other disorders. Annotation with regard to regulatory elements indicated that the syncope variants were preferentially located in neural-specific regulatory regions. Mendelian randomization analysis supported a causal effect of coronary artery disease on syncope. A polygenic score (PGS) for syncope captured genetic correlation with cardiovascular disorders, diabetes, depression, and shortened lifespan. However, a score based solely on the 18 syncope variants performed similarly to the PGS in detecting syncope risk but did not associate with other disorders. CONCLUSION The results demonstrate that syncope has a distinct genetic architecture that implicates neural regulatory processes and a complex relationship with heart rate and blood pressure regulation. A shared genetic background with poor cardiovascular health was observed, supporting the importance of a thorough assessment of individuals presenting with syncope.
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Affiliation(s)
- Hildur M Aegisdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | | | | | | | | | | | | | | | | | - Egil Ferkingstad
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Alex Hoerby Christensen
- The Unit for Inherited Cardiac Diseases, Department of Cardiology, The Heart Centre, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
- Department of Cardiology, Herlev-Gentofte Hospital, Copenhagen University Hospital, Borgmester Ib Juuls Vej 1, Herlev 2730, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Christina Mikkelsen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Ole Birger Pedersen
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- Department of Clinical Immunology, Zealand University Hospital - Køge, Lykkebækvej 1, Køge 4600, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, J. B. Winsløws Vej 4, Odense 5000, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus 8200, Denmark
- Department of Clinical Medicine, Aarhus University, Nordre Ringgade 1, Aarhus 8000, Denmark
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Urbansgade 32, Aalborg 9000, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Michael L Frigge
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Anna Helgadottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Asmundur Oddsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - David A Jones
- Precision Genomics, Intermountain Healthcare, 600 S. Medical Center Drive, Saint George, UT 84790, USA
| | - Jeffrey L Anderson
- Intermountain Medical Center, Intermountain Heart Institute, 5171 S. Cottonwood Street Building 1, Salt Lake City, UT 84107, USA
- Department of Internal Medicine, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, 5171 S. Cottonwood Street Building 1, Salt Lake City, UT 84107, USA
- School of Medicine, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - Lincoln D Nadauld
- Precision Genomics, Intermountain Healthcare, 600 S. Medical Center Drive, Saint George, UT 84790, USA
- School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA 94305, USA
| | | | - Magnus Haraldsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Psychiatry, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Henning Bundgaard
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- The Capital Regions Unit for Inherited Cardiac Diseases, Department of Cardiology, The Heart Centre, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Hjardarhagi 4, Reykjavik 107, Iceland
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
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10
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Styrkarsdottir U, Stefansdottir L, Thorleifsson G, Stefansson OA, Saevarsdottir S, Lund SH, Rafnar T, Hoshijima K, Novak K, Oreiro N, Rego-Perez I, Hansen C, Kazmers N, Kiemeney LA, Blanco FJ, Barker T, Kloppenburg M, Jurynec MJ, Gudbjartsson DF, Jonsson H, Thorsteinsdottir U, Stefansson K. Meta-analysis of erosive hand osteoarthritis identifies four common variants that associate with relatively large effect. Ann Rheum Dis 2023; 82:873-880. [PMID: 36931692 DOI: 10.1136/ard-2022-223468] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/25/2023] [Indexed: 03/19/2023]
Abstract
OBJECTIVES Erosive hand osteoarthritis (EHOA) is a severe subset of hand osteoarthritis (OA). It is unclear if EHOA is genetically different from other forms of OA. Sequence variants at ten loci have been associated with hand OA but none with EHOA. METHODS We performed meta-analysis of EHOA in 1484 cases and 550 680 controls, from 5 populations. To identify causal genes, we performed eQTL and plasma pQTL analyses, and developed one zebrafish mutant. We analysed associations of variants with other traits and estimated shared genetics between EHOA and other traits. RESULTS Four common sequence variants associated with EHOA, all with relatively high effect. Rs17013495 (SPP1/MEPE, OR=1.40, p=8.4×10-14) and rs11243284 (6p24.3, OR=1.35, p=4.2×10-11) have not been associated with OA, whereas rs11631127 (ALDH1A2, OR=1.46, p=7.1×10-18), and rs1800801 (MGP, OR=1.37, p=3.6×10-13) have previously been associated with hand OA. The association of rs1800801 (MGP) was consistent with a recessive mode of inheritance in contrast to its additive association with hand OA (OR homozygotes vs non-carriers=2.01, 95% CI 1.71 to 2.37). All four variants associated nominally with finger OA, although with substantially lower effect. We found shared genetic components between EHOA and other OA measures, grip strength, urate levels and gout, but not rheumatoid arthritis. We identified ALDH1A2, MGP and BMP6 as causal genes for EHOA, with loss-of-function Bmp6 zebrafish mutants displaying EHOA-like phenotypes. CONCLUSIONS We report on significant genetic associations with EHOA. The results support the view of EHOA as a form of severe hand OA and partly separate it from OA in larger joints.
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Affiliation(s)
| | | | | | | | - Saedis Saevarsdottir
- Population Genomics, deCODE genetics / Amgen Inc, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigrun H Lund
- Statistics, deCODE genetics / Amgen Inc, Reykjavik, Iceland
| | - Thorunn Rafnar
- Population Genomics, deCODE genetics / Amgen Inc, Reykjavik, Iceland
| | - Kazuyuki Hoshijima
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Kendra Novak
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, USA
| | - Natividad Oreiro
- Rheumatology Division, A Coruna University Hospital, A Coruna, Spain
| | | | - Channing Hansen
- Enterprise Analytics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Nikolas Kazmers
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, USA
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Science, Radboud University, Nijmegen, The Netherlands
| | - Francisco J Blanco
- Rheumatology Division, A Coruna University Hospital, A Coruna, Spain.,Department of Phisiotherapy, Medicine and Biomedical Sciences, A Coruna University Hospital, A Coruna, Spain
| | - Tyler Barker
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, USA.,Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA.,Nutrition and Integrative Physiology, University of Utah, Salt Lake City, Utah, USA
| | - Margreet Kloppenburg
- Department of Rheumatology, Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michael J Jurynec
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel F Gudbjartsson
- Statistics, deCODE genetics / Amgen Inc, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Helgi Jonsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- Population Genomics, deCODE genetics / Amgen Inc, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland .,deCODE genetics / Amgen Inc, Reykjavik, Capital, Iceland
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11
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Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO, Kristmundsdottir S, Sigurpalsdottir BD, Stefansson OA, Beyter D, Holley G, Tragante V, Gylfason A, Olason PI, Zink F, Asgeirsdottir M, Sverrisson ST, Sigurdsson B, Gudjonsson SA, Sigurdsson GT, Halldorsson GH, Sveinbjornsson G, Norland K, Styrkarsdottir U, Magnusdottir DN, Snorradottir S, Kristinsson K, Sobech E, Jonsson H, Geirsson AJ, Olafsson I, Jonsson P, Pedersen OB, Erikstrup C, Brunak S, Ostrowski SR, Thorleifsson G, Jonsson F, Melsted P, Jonsdottir I, Rafnar T, Holm H, Stefansson H, Saemundsdottir J, Gudbjartsson DF, Magnusson OT, Masson G, Thorsteinsdottir U, Helgason A, Jonsson H, Sulem P, Stefansson K. The sequences of 150,119 genomes in the UK Biobank. Nature 2022; 607:732-740. [PMID: 35859178 PMCID: PMC9329122 DOI: 10.1038/s41586-022-04965-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank3. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.
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Affiliation(s)
- Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland. .,School of Technology, Reykjavik University, Reykjavik, Iceland.
| | | | | | | | | | - Magnus O Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Marteinn T Hardarson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | - Snaedis Kristmundsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Brynja D Sigurpalsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Helgi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Palmi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Christian Erikstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Clinical Sciences, Copenhagen University, Copenhagen, Denmark
| | | | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
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12
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Steinthorsdottir V, McGinnis R, Williams NO, Stefansdottir L, Thorleifsson G, Shooter S, Fadista J, Sigurdsson JK, Auro KM, Berezina G, Borges MC, Bumpstead S, Bybjerg-Grauholm J, Colgiu I, Dolby VA, Dudbridge F, Engel SM, Franklin CS, Frigge ML, Frisbaek Y, Geirsson RT, Geller F, Gretarsdottir S, Gudbjartsson DF, Harmon Q, Hougaard DM, Hegay T, Helgadottir A, Hjartardottir S, Jääskeläinen T, Johannsdottir H, Jonsdottir I, Juliusdottir T, Kalsheker N, Kasimov A, Kemp JP, Kivinen K, Klungsøyr K, Lee WK, Melbye M, Miedzybrodska Z, Moffett A, Najmutdinova D, Nishanova F, Olafsdottir T, Perola M, Pipkin FB, Poston L, Prescott G, Saevarsdottir S, Salimbayeva D, Scaife PJ, Skotte L, Staines-Urias E, Stefansson OA, Sørensen KM, Thomsen LCV, Tragante V, Trogstad L, Simpson NAB, Aripova T, Casas JP, Dominiczak AF, Walker JJ, Thorsteinsdottir U, Iversen AC, Feenstra B, Lawlor DA, Boyd HA, Magnus P, Laivuori H, Zakhidova N, Svyatova G, Stefansson K, Morgan L. Genetic predisposition to hypertension is associated with preeclampsia in European and Central Asian women. Nat Commun 2020; 11:5976. [PMID: 33239696 PMCID: PMC7688949 DOI: 10.1038/s41467-020-19733-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [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: 09/18/2019] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
Preeclampsia is a serious complication of pregnancy, affecting both maternal and fetal health. In genome-wide association meta-analysis of European and Central Asian mothers, we identify sequence variants that associate with preeclampsia in the maternal genome at ZNF831/20q13 and FTO/16q12. These are previously established variants for blood pressure (BP) and the FTO variant has also been associated with body mass index (BMI). Further analysis of BP variants establishes that variants at MECOM/3q26, FGF5/4q21 and SH2B3/12q24 also associate with preeclampsia through the maternal genome. We further show that a polygenic risk score for hypertension associates with preeclampsia. However, comparison with gestational hypertension indicates that additional factors modify the risk of preeclampsia.
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Affiliation(s)
| | | | | | | | | | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | | | - Kirsi M Auro
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Galina Berezina
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan
| | - Maria-Carolina Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | | | - Vivien A Dolby
- Leeds Institute of Medical Research (LIMR), School of Medicine, University of Leeds, Leeds, UK
| | - Frank Dudbridge
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Yr Frisbaek
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Quaker Harmon
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - David Michael Hougaard
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Tatyana Hegay
- Institute of immunology and human genomics, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | | | - Sigrun Hjartardottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Tiina Jääskeläinen
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Abdumadjit Kasimov
- Institute of immunology and human genomics, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | - John P Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Katja Kivinen
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Kari Klungsøyr
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Wai K Lee
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Zosia Miedzybrodska
- Division of Applied Medicine, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Dilbar Najmutdinova
- Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology, Tashkent, Uzbekistan
| | - Firuza Nishanova
- Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology, Tashkent, Uzbekistan
| | - Thorunn Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Lucilla Poston
- Department of Women and Children's Health, King's College London, London, UK
| | - Gordon Prescott
- Division of Applied Medicine, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
- Lancashire Clinical Trials Unit, University of Central Lancashire, Preston, UK
| | | | - Damilya Salimbayeva
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan
| | | | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Eleonora Staines-Urias
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Liv Cecilie Vestrheim Thomsen
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vinicius Tragante
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Lill Trogstad
- Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
| | - Nigel A B Simpson
- Division of Womens and Children's Health, School of Medicine, University of Leeds, Leeds, UK
| | - Tamara Aripova
- Institute of immunology and human genomics, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | - Juan P Casas
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anna F Dominiczak
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - James J Walker
- Leeds Institute of Medical Research (LIMR), School of Medicine, University of Leeds, Leeds, UK
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ann-Charlotte Iversen
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Heather Allison Boyd
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital and Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Nodira Zakhidova
- Institute of immunology and human genomics, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | - Gulnara Svyatova
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Linda Morgan
- School of Life Sciences, University of Nottingham, Nottingham, UK
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13
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Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, Sigurdsson A, Eggertsson HP, Melsted P, Halldorsson BV, Lund SH, Styrkarsdottir U, Steinthorsdottir V, Gudmundsson J, Holm H, Tragante V, Asselbergs FW, Thorsteinsdottir U, Gudbjartsson DF, Jonsdottir K, Rafnar T, Stefansson K. Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank. Commun Biol 2020; 3:129. [PMID: 32184442 PMCID: PMC7078216 DOI: 10.1038/s42003-020-0857-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 08/07/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
Pelvic organ prolapse (POP) is a downward descent of one or more of the pelvic organs, resulting in a protrusion of the vaginal wall and/or uterus. We performed a genome-wide association study of POP using data from Iceland and the UK Biobank, a total of 15,010 cases with hospital-based diagnosis code and 340,734 female controls, and found eight sequence variants at seven loci associating with POP (P < 5 × 10-8); seven common (minor allele frequency >5%) and one with minor allele frequency of 4.87%. Some of the variants associating with POP also associated with traits of similar pathophysiology. Of these, rs3820282, which may alter the estrogen-based regulation of WNT4, also associates with leiomyoma of uterus, gestational duration and endometriosis. Rs3791675 at EFEMP1, a gene involved in connective tissue homeostasis, also associates with hernias and carpal tunnel syndrome. Our results highlight the role of connective tissue metabolism and estrogen exposure in the etiology of POP.
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Affiliation(s)
| | | | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | - Helga Medek
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Karl Olafsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Orri Ingthorsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Valur Gudmundsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Pall Melsted
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, 101, Reykjavik, Iceland
| | - Sigrun H Lund
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Vinicius Tragante
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Kristin Jonsdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.
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14
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Olafsdottir TA, Theodors F, Bjarnadottir K, Bjornsdottir US, Agustsdottir AB, Stefansson OA, Ivarsdottir EV, Sigurdsson JK, Benonisdottir S, Eyjolfsson GI, Gislason D, Gislason T, Guðmundsdóttir S, Gylfason A, Halldorsson BV, Halldorsson GH, Juliusdottir T, Kristinsdottir AM, Ludviksdottir D, Ludviksson BR, Masson G, Norland K, Onundarson PT, Olafsson I, Sigurdardottir O, Stefansdottir L, Sveinbjornsson G, Tragante V, Gudbjartsson DF, Thorleifsson G, Sulem P, Thorsteinsdottir U, Norddahl GL, Jonsdottir I, Stefansson K. Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis. Nat Commun 2020; 11:393. [PMID: 31959851 PMCID: PMC6971247 DOI: 10.1038/s41467-019-14144-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/05/2019] [Indexed: 12/28/2022] Open
Abstract
Asthma is one of the most common chronic diseases affecting both children and adults. We report a genome-wide association meta-analysis of 69,189 cases and 702,199 controls from Iceland and UK biobank. We find 88 asthma risk variants at 56 loci, 19 previously unreported, and evaluate their effect on other asthma and allergic phenotypes. Of special interest are two low frequency variants associated with protection against asthma; a missense variant in TNFRSF8 and 3‘ UTR variant in TGFBR1. Functional studies show that the TNFRSF8 variant reduces TNFRSF8 expression both on cell surface and in soluble form, acting as loss of function. eQTL analysis suggests that the TGFBR1 variant acts through gain of function and together with an intronic variant in a downstream gene, SMAD3, points to defective TGFβR1 signaling as one of the biological perturbations increasing asthma risk. Our results increase the number of asthma variants and implicate genes with known role in T cell regulation, inflammation and airway remodeling in asthma pathogenesis. Asthma is a common allergic airway disease with significant inter-individual heterogeneity. Here, Olafsdottir et al. report a genome-wide meta-analysis of two large population-based cohorts to identify sequence variants that associate with asthma risk and perform follow-up functional analyses on a protective loss-of-function variant in TNFRSF8.
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Affiliation(s)
- Thorunn A Olafsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Unnur Steina Bjornsdottir
- Department of Medicine, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland.,The Medical Center Mjodd, Reykjavik, Iceland
| | | | | | - Erna V Ivarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - David Gislason
- The Medical Center Mjodd, Reykjavik, Iceland.,Department of Respiratory Medicine and Sleep, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Thorarinn Gislason
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Sleep, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavík, Iceland
| | | | | | | | - Dora Ludviksdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Respiratory Medicine and Sleep, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjorn R Ludviksson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Immunology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | - Pall T Onundarson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Laboratory Hematology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Olof Sigurdardottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Clinical Biochemistry, Akureyri Hospital, Akureyri, Iceland
| | | | | | - Vinicius Tragante
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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15
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Stefansson OA, Hilmarsdottir H, Olafsdottir K, Tryggvadottir L, Sverrisdottir A, Johannsson OT, Jonasson JG, Eyfjord JE, Sigurdsson S. BRCA1 Promoter Methylation Status in 1031 Primary Breast Cancers Predicts Favorable Outcomes Following Chemotherapy. JNCI Cancer Spectr 2019; 4:pkz100. [PMID: 32175521 PMCID: PMC7061679 DOI: 10.1093/jncics/pkz100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/28/2019] [Accepted: 12/07/2019] [Indexed: 11/28/2022] Open
Abstract
Background Breast Cancer 1 gene (BRCA1) is known to be inactivated in breast tumors by promoter methylation. Tumor cells in patients carrying a germline mutation in BRCA1 are sensitive to cytotoxic drugs that cause DNA double strand breaks. However, very little is known on whether patients with BRCA1 promoter methylated tumors are similarly sensitive to cytotoxic drugs. In this study, we address this by making use of extensive follow-up data on patients treated with cyclophosphamide, methotrexate, and fluorouracil in Iceland between 1976 and 2007. Methods We analyzed BRCA1 promoter methylation by pyrosequencing DNA from tumor samples from 1031 patients with primary breast cancer. Of those, 965 were sporadic cases, 61 were BRCA2, and five were BRCA1 germline mutation carriers. All cases were examined with respect to clinicopathological parameters and breast cancer–specific survival in patients treated with cytotoxic drugs. Information on chemotherapy treatment in noncarriers was available for 26 BRCA1 methylated tumors and 857 unmethylated tumors. Results BRCA1 was promoter methylated in 29 sporadic tumors or in 3.0% of cases (29 of 965), whereas none of the tumors derived from BRCA germline mutation carriers were promoter methylated. Important to note, patients with BRCA1 promoter methylation receiving chemotherapeutic drug treatment show highly improved breast cancer–specific survival compared with unmethylated controls (hazard ratio = 0.10, 95% confidence interval = 0.01 to 0.75, two-sided P = .02). Conclusions BRCA1 promoter methylation is predictive of improved disease outcome in patients receiving cyclophosphamide, methotrexate, and fluorouracil drug treatment. Our results support the use of markers indicative of “BRCAness” in sporadic breast cancers to identify patients that are likely to benefit from the use of DNA-damaging agents.
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Affiliation(s)
- Olafur A Stefansson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Cancer Research Laboratory, Biomedical Center, University of Iceland, Reykjavik, Iceland.,Current affiliation deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland
| | | | | | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
| | | | - Oskar T Johannsson
- Department of Oncology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jon G Jonasson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jorunn E Eyfjord
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Cancer Research Laboratory, Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Stefan Sigurdsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Cancer Research Laboratory, Biomedical Center, University of Iceland, Reykjavik, Iceland
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16
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Styrkarsdottir U, Stefansson OA, Gunnarsdottir K, Thorleifsson G, Lund SH, Stefansdottir L, Juliusson K, Agustsdottir AB, Zink F, Halldorsson GH, Ivarsdottir EV, Benonisdottir S, Jonsson H, Gylfason A, Norland K, Trajanoska K, Boer CG, Southam L, Leung JCS, Tang NLS, Kwok TCY, Lee JSW, Ho SC, Byrjalsen I, Center JR, Lee SH, Koh JM, Lohmander LS, Ho-Pham LT, Nguyen TV, Eisman JA, Woo J, Leung PC, Loughlin J, Zeggini E, Christiansen C, Rivadeneira F, van Meurs J, Uitterlinden AG, Mogensen B, Jonsson H, Ingvarsson T, Sigurdsson G, Benediktsson R, Sulem P, Jonsdottir I, Masson G, Holm H, Norddahl GL, Thorsteinsdottir U, Gudbjartsson DF, Stefansson K. GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures. Nat Commun 2019; 10:2054. [PMID: 31053729 PMCID: PMC6499783 DOI: 10.1038/s41467-019-09860-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 08/31/2018] [Accepted: 04/03/2019] [Indexed: 12/12/2022] Open
Abstract
Bone area is one measure of bone size that is easily derived from dual-energy X-ray absorptiometry (DXA) scans. In a GWA study of DXA bone area of the hip and lumbar spine (N ≥ 28,954), we find thirteen independent association signals at twelve loci that replicate in samples of European and East Asian descent (N = 13,608 - 21,277). Eight DXA area loci associate with osteoarthritis, including rs143384 in GDF5 and a missense variant in COL11A1 (rs3753841). The strongest DXA area association is with rs11614913[T] in the microRNA MIR196A2 gene that associates with lumbar spine area (P = 2.3 × 10-42, β = -0.090) and confers risk of hip fracture (P = 1.0 × 10-8, OR = 1.11). We demonstrate that the risk allele is less efficient in repressing miR-196a-5p target genes. We also show that the DXA area measure contributes to the risk of hip fracture independent of bone density.
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Affiliation(s)
| | | | | | | | - Sigrun H Lund
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | | | | | - Florian Zink
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
| | | | | | | | | | | | | | - Katerina Trajanoska
- Department of Epidemiology, ErasmusMC, 3015 GD, Rotterdam, The Netherlands
- Department of Internal Medicine, ErasmusMC, 3015 GD, Rotterdam, the Netherlands
| | - Cindy G Boer
- Department of Internal Medicine, ErasmusMC, 3015 GD, Rotterdam, the Netherlands
| | - Lorraine Southam
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jason C S Leung
- Jockey Club Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L S Tang
- Faculty of Medicine, Department of Chemical Pathology and Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences,, The Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Timothy C Y Kwok
- Jockey Club Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
| | - Jenny S W Lee
- Faculty of Medicine, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine, Alice Ho Miu Ling Nethersole Hospital and Tai Po Hospital, Hong Kong, China
| | - Suzanne C Ho
- JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Jacqueline R Center
- Bone Biology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- School of Medicine Sydney, University of Notre Dame Australia, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Seung Hun Lee
- Division of Endocrinology and Metabolism, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Jung-Min Koh
- Division of Endocrinology and Metabolism, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - L Stefan Lohmander
- Orthopaedics, Department of Clinical Sciences Lund, Lund University, SE-22 100, Lund, Sweden
| | - Lan T Ho-Pham
- Bone and Muscle Research Lab, Ton Duc Thang University, Ho Chi Minh City, 700000, Vietnam
| | - Tuan V Nguyen
- Bone Biology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - John A Eisman
- Bone Biology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- School of Medicine Sydney, University of Notre Dame Australia, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- Clinical Translation and Advanced Education, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Jean Woo
- Faculty of Medicine, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ping-C Leung
- Jockey Club Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - John Loughlin
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, 85764, München, Germany
| | | | - Fernando Rivadeneira
- Department of Epidemiology, ErasmusMC, 3015 GD, Rotterdam, The Netherlands
- Department of Internal Medicine, ErasmusMC, 3015 GD, Rotterdam, the Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, ErasmusMC, 3015 GD, Rotterdam, the Netherlands
| | | | - Brynjolfur Mogensen
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Emergengy Medicine, Landspitali, The National University Hospital of Iceland, 101, Reykjavik, Iceland
- Research Institute in Emergency Medicine, Landspitali, The National University Hospital of Iceland, and University of Iceland, 101, Reykjavik, Iceland
| | - Helgi Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Medicine, Landspitali-The National University Hospital of Iceland, 101, Reykjavik, Iceland
| | - Thorvaldur Ingvarsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Orthopedic Surgery, Akureyri Hospital, 600, Akureyri, Iceland
- Institution of Health Science, University of Akureyri, 600, Akureyri, Iceland
| | - Gunnar Sigurdsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Research Service Center, Reykjavik, 201, Iceland
- Department of Endocrinology and Metabolism, Landspitali, The National University Hospital of Iceland, 101, Reykjavik, Iceland
| | - Rafn Benediktsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Endocrinology and Metabolism, Landspitali, The National University Hospital of Iceland, 101, Reykjavik, Iceland
| | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Immunology, Landspitali-The National University Hospital of Iceland, 101, Reykjavik, Iceland
| | - Gisli Masson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
| | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 107, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.
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17
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Halldorsson BV, Palsson G, Stefansson OA, Jonsson H, Hardarson MT, Eggertsson HP, Gunnarsson B, Oddsson A, Halldorsson GH, Zink F, Gudjonsson SA, Frigge ML, Thorleifsson G, Sigurdsson A, Stacey SN, Sulem P, Masson G, Helgason A, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 2019; 363:363/6425/eaau1043. [DOI: 10.1126/science.aau1043] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/16/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022]
Abstract
Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.
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18
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 2019; 566:E1. [DOI: 10.1038/s41586-019-0883-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Kristjansson RP, Benonisdottir S, Davidsson OB, Oddsson A, Tragante V, Sigurdsson JK, Stefansdottir L, Jonsson S, Jensson BO, Arthur JG, Arnadottir GA, Sulem G, Halldorsson BV, Gunnarsson B, Halldorsson GH, Stefansson OA, Oskarsson GR, Deaton AM, Olafsson I, Eyjolfsson GI, Sigurdardottir O, Onundarson PT, Gislason D, Gislason T, Ludviksson BR, Ludviksdottir D, Olafsdottir TA, Rafnar T, Masson G, Zink F, Bjornsdottir G, Magnusson OT, Bjornsdottir US, Thorleifsson G, Norddahl GL, Gudbjartsson DF, Thorsteinsdottir U, Jonsdottir I, Sulem P, Stefansson K. A loss-of-function variant in ALOX15 protects against nasal polyps and chronic rhinosinusitis. Nat Genet 2019; 51:267-276. [PMID: 30643255 DOI: 10.1038/s41588-018-0314-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Abstract
Nasal polyps (NP) are lesions on the nasal and paranasal sinus mucosa and are a risk factor for chronic rhinosinusitis (CRS). We performed genome-wide association studies on NP and CRS in Iceland and the UK (using UK Biobank data) with 4,366 NP cases, 5,608 CRS cases, and >700,000 controls. We found 10 markers associated with NP and 2 with CRS. We also tested 210 markers reported to associate with eosinophil count, yielding 17 additional NP associations. Of the 27 NP signals, 7 associate with CRS and 13 with asthma. Most notably, a missense variant in ALOX15 that causes a p.Thr560Met alteration in arachidonate 15-lipoxygenase (15-LO) confers large genome-wide significant protection against NP (P = 8.0 × 10-27, odds ratio = 0.32; 95% confidence interval = 0.26, 0.39) and CRS (P = 1.1 × 10-8, odds ratio = 0.64; 95% confidence interval = 0.55, 0.75). p.Thr560Met, carried by around 1 in 20 Europeans, was previously shown to cause near total loss of 15-LO enzymatic activity. Our findings identify 15-LO as a potential target for therapeutic intervention in NP and CRS.
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Affiliation(s)
| | | | | | | | - Vinicius Tragante
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | | | | | | | | | | | | | | | - Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | - Pall T Onundarson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Laboratory Hematology, Landspítali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - David Gislason
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Thorarinn Gislason
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Sleep, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjorn R Ludviksson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Immunology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Dora Ludviksdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Respiratory Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Unnur S Bjornsdottir
- Department of Medicine, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland.,The Medical Center Mjodd, Reykjavik, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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20
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Ferkingstad E, Oddsson A, Gretarsdottir S, Benonisdottir S, Thorleifsson G, Deaton AM, Jonsson S, Stefansson OA, Norddahl GL, Zink F, Arnadottir GA, Gunnarsson B, Halldorsson GH, Helgadottir A, Jensson BO, Kristjansson RP, Sveinbjornsson G, Sverrisson DA, Masson G, Olafsson I, Eyjolfsson GI, Sigurdardottir O, Holm H, Jonsdottir I, Olafsson S, Steingrimsdottir T, Rafnar T, Bjornsson ES, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K. Genome-wide association meta-analysis yields 20 loci associated with gallstone disease. Nat Commun 2018; 9:5101. [PMID: 30504769 PMCID: PMC6269469 DOI: 10.1038/s41467-018-07460-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023] Open
Abstract
Gallstones are responsible for one of the most common diseases in the Western world and are commonly treated with cholecystectomy. We perform a meta-analysis of two genome-wide association studies of gallstone disease in Iceland and the UK, totaling 27,174 cases and 736,838 controls, uncovering 21 novel gallstone-associated variants at 20 loci. Two distinct low frequency missense variants in SLC10A2, encoding the apical sodium-dependent bile acid transporter (ASBT), associate with an increased risk of gallstone disease (Pro290Ser: OR = 1.36 [1.25-1.49], P = 2.1 × 10-12, MAF = 1%; Val98Ile: OR = 1.15 [1.10-1.20], P = 1.8 × 10-10, MAF = 4%). We demonstrate that lower bile acid transport by ASBT is accompanied by greater risk of gallstone disease and highlight the role of the intestinal compartment of the enterohepatic circulation of bile acids in gallstone disease susceptibility. Additionally, two low frequency missense variants in SERPINA1 and HNF4A and 17 common variants represent novel associations with gallstone disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Florian Zink
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | | | | | | | | | | | | | | | | | - Gisli Masson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspítali University Hospital, Reykjavik, 101, Iceland
| | | | - Olof Sigurdardottir
- Department of Clinical Biochemistry, Akureyri Hospital, Akureyri, 600, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Sigurdur Olafsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | | | - Einar S Bjornsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Patrick Sulem
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.
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21
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Rafnar T, Gunnarsson B, Stefansson OA, Sulem P, Ingason A, Frigge ML, Stefansdottir L, Sigurdsson JK, Tragante V, Steinthorsdottir V, Styrkarsdottir U, Stacey SN, Gudmundsson J, Arnadottir GA, Oddsson A, Zink F, Halldorsson G, Sveinbjornsson G, Kristjansson RP, Davidsson OB, Salvarsdottir A, Thoroddsen A, Helgadottir EA, Kristjansdottir K, Ingthorsson O, Gudmundsson V, Geirsson RT, Arnadottir R, Gudbjartsson DF, Masson G, Asselbergs FW, Jonasson JG, Olafsson K, Thorsteinsdottir U, Halldorsson BV, Thorleifsson G, Stefansson K. Variants associating with uterine leiomyoma highlight genetic background shared by various cancers and hormone-related traits. Nat Commun 2018; 9:3636. [PMID: 30194396 PMCID: PMC6128903 DOI: 10.1038/s41467-018-05428-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/02/2018] [Indexed: 01/12/2023] Open
Abstract
Uterine leiomyomas are common benign tumors of the myometrium. We performed a meta-analysis of two genome-wide association studies of leiomyoma in European women (16,595 cases and 523,330 controls), uncovering 21 variants at 16 loci that associate with the disease. Five variants were previously reported to confer risk of various malignant or benign tumors (rs78378222 in TP53, rs10069690 in TERT, rs1800057 and rs1801516 in ATM, and rs7907606 at OBFC1) and four signals are located at established risk loci for hormone-related traits (endometriosis and breast cancer) at 1q36.12 (CDC42/WNT4), 2p25.1 (GREB1), 20p12.3 (MCM8), and 6q26.2 (SYNE1/ESR1). Polygenic score for leiomyoma, computed using UKB data, is significantly correlated with risk of cancer in the Icelandic population. Functional annotation suggests that the non-coding risk variants affect multiple genes, including ESR1. Our results provide insights into the genetic background of leiomyoma that are shared by other benign and malignant tumors and highlight the role of hormones in leiomyoma growth. Uterine leiomyomas are common benign tumors. Here, a meta-analysis of two European leiomyoma GWAS uncovers 21 leiomyoma risk variants at 16 loci, providing evidence of genetic overlap between leiomyoma and various benign and malignant tumors and highlighting the role of estrogen in tumor growth.
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Affiliation(s)
- Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.
| | | | | | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Andres Ingason
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Vinicius Tragante
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, 3584 CX, Utrecht, The Netherlands
| | | | | | - Simon N Stacey
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Florian Zink
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | | | - Anna Salvarsdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Asgeir Thoroddsen
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Elisabet A Helgadottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Katrin Kristjansdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Orri Ingthorsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Valur Gudmundsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Ragnheidur Arnadottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Gisli Masson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, 3584 CX, Utrecht, The Netherlands.,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, 3501 DG, Utrecht, The Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, WC1E 6HX, UK.,Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Jon G Jonasson
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.,Department of Pathology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Karl Olafsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, 101, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.
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22
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Stefansson OA, Hilmarsdottir H, Olafsdottir K, Tryggvadottir L, Sverrisdottir A, Jonasson JG, Eyfjord JE, Sigurdsson S. Abstract 3307: BRCA1 promoter methylation analyzed in 1032 primary breast cancers predicts favorable response to chemotherapy independently of p53 mutations. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Individuals with germline mutations in the breast cancer susceptibility gene, BRCA1, are at increased risk of developing breast- and ovarian cancer. BRCA1 is involved in DNA double strand break repair (DSB) by homologous recombination (HR), an error-free DNA repair pathway that uses an intact sister chromatid for the repair. BRCA1 mutated tumors are therefore HR deficient and sensitive to drugs that stall DNA replication forks, resulting in DSBs. Tumor cells lacking the protein are characterized by genomic instability and a pattern of specific genome-wide mutation signature as a consequence of dependence on alternative error prone repair pathways. BRCA1 can also be inactivated epigenetically by CpG promoter hypermethylation. These BRCA1 epigenetically silenced tumors are more likely to be of the basal-like subtype and are strongly associated with this pattern of mutational signature characteristic for individuals with germline mutations in BRCA1. This suggests that the tumorigenesis in the sporadic cancer cases is similar to tumors where germline mutations are present, highlighting the importance of epigenetic silencing of BRCA1. The aim of the study was to examine the clinical significance of epigenetic silencing of BRCA1 in primary breast cancer, focusing on the response to chemotherapy. DNA methylation analysis of the BRCA1 promoter was performed by pyrosequencing tumor samples from 1032 patients with primary breast cancer of which 966 were sporadic, 61 were BRCA2 germline mutation carriers and 5 were BRCA1 mutation carriers. The p53 mutational status was also studied in the same primary tumors by DNA sequencing. We analysed the methylation status of BRCA1 in tumors derived from 1032 patients and found BRCA1 to be promoter hypermethylated in 29 sporadic tumors (29 out of 966, 3.0 %) whereas none of the tumors derived from BRCA mutation carriers were BRCA1 promoter hypermethylated. Patients with BRCA1 promoter hypermethylation receiving chemotherapeutic drug treatment show significantly better breast cancer specific survival (P=0.0192). The trend is opposite in patients not receiving chemotherapeutic treatment, were patients with BRCA1 hypermethylated tumors show worse survival (P=0.074). The impact of BRCA1 methylation with respect to survival in chemotherapy treated patients was found to be independent of p53 mutational status, ER status, tumorsize, lymph node status, year- and age at diagnosis (HR = 0.108; 95% CI = 0.015-0.794; P = 0.0288). BRCA1 promoter hypermethylation predicts improved disease outcome in anti-cancer drug treated patients. Therefore, BRCA1 promoter methylation status in primary breast cancer is an important factor to be considered when deciding treatment options.
Citation Format: Olafur A. Stefansson, Holmfridur Hilmarsdottir, Kristrun Olafsdottir, Laufey Tryggvadottir, Asgerdur Sverrisdottir, Jon G. Jonasson, Jorunn E. Eyfjord, Stefan Sigurdsson. BRCA1 promoter methylation analyzed in 1032 primary breast cancers predicts favorable response to chemotherapy independently of p53 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3307.
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23
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Helgadottir A, Thorleifsson G, Gretarsdottir S, Stefansson OA, Tragante V, Thorolfsdottir RB, Jonsdottir I, Bjornsson T, Steinthorsdottir V, Verweij N, Nielsen JB, Zhou W, Folkersen L, Martinsson A, Heydarpour M, Prakash S, Oskarsson G, Gudbjartsson T, Geirsson A, Olafsson I, Sigurdsson EL, Almgren P, Melander O, Franco-Cereceda A, Hamsten A, Fritsche L, Lin M, Yang B, Hornsby W, Guo D, Brummett CM, Abecasis G, Mathis M, Milewicz D, Body SC, Eriksson P, Willer CJ, Hveem K, Newton-Cheh C, Smith JG, Danielsen R, Thorgeirsson G, Thorsteinsdottir U, Gudbjartsson DF, Holm H, Stefansson K. Genome-wide analysis yields new loci associating with aortic valve stenosis. Nat Commun 2018; 9:987. [PMID: 29511194 PMCID: PMC5840367 DOI: 10.1038/s41467-018-03252-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Aortic valve stenosis (AS) is the most common valvular heart disease, and valve replacement is the only definitive treatment. Here we report a large genome-wide association (GWA) study of 2,457 Icelandic AS cases and 349,342 controls with a follow-up in up to 4,850 cases and 451,731 controls of European ancestry. We identify two new AS loci, on chromosome 1p21 near PALMD (rs7543130; odds ratio (OR) = 1.20, P = 1.2 × 10−22) and on chromosome 2q22 in TEX41 (rs1830321; OR = 1.15, P = 1.8 × 10−13). Rs7543130 also associates with bicuspid aortic valve (BAV) (OR = 1.28, P = 6.6 × 10−10) and aortic root diameter (P = 1.30 × 10−8), and rs1830321 associates with BAV (OR = 1.12, P = 5.3 × 10−3) and coronary artery disease (OR = 1.05, P = 9.3 × 10−5). The results implicate both cardiac developmental abnormalities and atherosclerosis-like processes in the pathogenesis of AS. We show that several pathways are shared by CAD and AS. Causal analysis suggests that the shared risk factors of Lp(a) and non-high-density lipoprotein cholesterol contribute substantially to the frequent co-occurence of these diseases. Aortic valve stenosis (AS) is the most common valvular heart disease. Here the authors identify two new AS loci that also associate with bicuspid aortic valve, aortic root diameter and/or coronary artery disease implicating both developmental abnormalities and atherosclerosis-like processes in AS.
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Affiliation(s)
| | | | | | | | | | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | | | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Lasse Folkersen
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, 17176, Sweden.,Department of Bioinformatics, Technical University of Denmark, Copenhagen, 2800, Denmark
| | - Andreas Martinsson
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, 22185, Sweden
| | - Mahyar Heydarpour
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Siddharth Prakash
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Gylfi Oskarsson
- Childrens Hospital, Landspitali National University Hospital of Iceland, Reykjavik, 101, Iceland
| | - Tomas Gudbjartsson
- Department of Surgery and Cardiothoracic Surgery, Landspitali National University Hospital, Reykjavik, 101, Iceland
| | - Arnar Geirsson
- Section of Cardiac Surgery, Department of Surgery, Yale University School of Medicine, New Haven, 06510, CT, USA
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali National University Hospital, Reykjavik, 101, Iceland
| | - Emil L Sigurdsson
- Heilsugaeslan Solvangi, Hafnarfjördur, 220, Iceland.,Department of Family Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Peter Almgren
- Department of Clinical Sciences, Lund University, Malmö, 22185, Sweden.,Department of Internal Medicine, Skåne University Hospital, Malmö, 22185, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, 22185, Sweden.,Department of Internal Medicine, Skåne University Hospital, Malmö, 22185, Sweden
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, 17176, Sweden
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, 17176, Sweden
| | - Lars Fritsche
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7491, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Maoxuan Lin
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, 48105, USA.,Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Whitney Hornsby
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dongchuan Guo
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael Mathis
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Dianna Milewicz
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston, Houston, 77030, TX, USA.,Medicine Services, Texas Heart Institute, St. Luke's Episcopal Hospital, Houston, TX, 77030, USA
| | - Simon C Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Per Eriksson
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, 17176, Sweden
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, 48109, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA.,Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7491, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Christopher Newton-Cheh
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.,Massachusetts General Hospital, Harvard Medical School, Broad Institute of Harvard and MIT, Boston, MA, 02114, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, 22185, Sweden
| | - Ragnar Danielsen
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.,Department of Internal Medicine, Division of Cardiology, Landspitali National University Hospital of Iceland, Reykjavik, 101, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.,Department of Internal Medicine, Division of Cardiology, Landspitali National University Hospital of Iceland, Reykjavik, 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, 101, Iceland. .,Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.
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Crujeiras AB, Diaz-Lagares A, Stefansson OA, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Moran S, Jonasson JG, Tryggvadottir L, Olafsdottir E, Tinahones FJ, Carreira MC, Casanueva FF, Esteller M. Obesity and menopause modify the epigenomic profile of breast cancer. Endocr Relat Cancer 2017; 24:351-363. [PMID: 28442560 DOI: 10.1530/erc-16-0565] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Received: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumors were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern. Intriguingly, the DNA methylation pattern identified in association with the high-risk group (postmenopausal women with high BMI (>25) and premenopausal women with normal or low BMI < 25) exclusively characterized by hypermethylation of 1287 CpG sites as compared with the low-risk group. These CpG sites included the promoter region of fourteen protein-coding genes of which CpG methylation over the ZNF577 promoter region represents the top scoring associated event. In an independent cohort, the ZNF577 promoter methylation remained statistically significant in association with the high-risk group. Additionally, the impact of ZNF577 promoter methylation on mRNA expression levels was demonstrated in breast cancer cell lines after treatment with a demethylating agent (5-azacytidine). In conclusion, the epigenome of breast tumors is affected by a complex interaction between BMI and menopausal status. The ZNF577 methylation quantification is clearly relevant for the development of novel biomarkers of precision therapy in breast cancer.
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Affiliation(s)
- Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Cancer Research LaboratoryFaculty of Medicine, University of Iceland, Reykjavic, Iceland
| | - Manuel Macias-Gonzalez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Juan Cueva
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Jon G Jonasson
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Elinborg Olafsdottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Marcos C Carreira
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Felipe F Casanueva
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences IISchool of Medicine, University of Barcelona and Instituto Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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25
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Thorvaldsdottir B, Aradottir M, Stefansson OA, Bodvarsdottir SK, Eyfjörd JE. Telomere Length Is Predictive of Breast Cancer Risk in BRCA2 Mutation Carriers. Cancer Epidemiol Biomarkers Prev 2017; 26:1248-1254. [PMID: 28235830 DOI: 10.1158/1055-9965.epi-16-0946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Germline BRCA2 mutations increase risk of breast cancer and other malignancies. BRCA2 has been shown to play a role in telomere protection and maintenance. Telomere length (TL) has been studied as a modifying factor for various diseases, including breast cancer. Previous research on TL in BRCA mutation carriers has produced contradicting results.Methods: We measured blood TL, using a high-throughput monochrome multiplex qPCR method, in a well-defined Icelandic cohort of female BRCA2 mutation carriers (n = 169), sporadic breast cancer patients (n = 561), and healthy controls (n = 537).Results: Breast cancer cases had significantly shorter TL than unaffected women (P < 0.0001), both BRCA2 mutation carriers (P = 0.0097) and noncarriers (P = 0.00006). Using exclusively samples acquired before breast cancer diagnosis, we found that shorter telomeres were significantly associated with increased breast cancer risk in BRCA2 mutation carriers [HR, 3.60; 95% confidence interval (CI), 1.17-11.28; P, 0.025] but not in non-carriers (HR,1.40; 95% CI, 0.89-2.22; P, 0.15). We found no association between TL and breast cancer-specific survival.Conclusions: Blood TL is predictive of breast cancer risk in BRCA2 mutation carriers. Breast cancer cases have significantly shorter TL than unaffected women, regardless of BRCA2 status, indicating that samples taken after breast cancer diagnosis should not be included in evaluations of TL and breast cancer risk.Impact: Our study is built on a well-defined cohort, highly accurate methods, and long follow-up and can therefore help to clarify some previously published, contradictory results. Our findings also suggest that BRCA2 has an important role in telomere maintenance, even in normal blood cells. Cancer Epidemiol Biomarkers Prev; 26(8); 1248-54. ©2017 AACR.
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Affiliation(s)
- Birna Thorvaldsdottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Margret Aradottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Olafur A Stefansson
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sigridur K Bodvarsdottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jorunn E Eyfjörd
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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26
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 2016; 534:47-54. [PMID: 27135926 PMCID: PMC4910866 DOI: 10.1038/nature17676] [Citation(s) in RCA: 1421] [Impact Index Per Article: 177.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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Affiliation(s)
- Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Ludmil B. Alexandrov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Young Seok Ju
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Arie B Brinkman
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Miriam R. Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole Christian Lingjærde
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sung-Min Ahn
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sandrine Boyault
- Translational Research Lab, Centre Léon Bérard, 28, rue Laënnec, 69373 Lyon Cedex 08, France
| | - Jane E. Brock
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Annegien Broeks
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Serge Dronov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - John A. Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gerrit KJ Hooijer
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - David R. Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Tari A. King
- Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, United States
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - Jeong-Yeon Lee
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, South Korea
| | - Yilong Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Stuart McLaren
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah O’Meara
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Iris Pauporté
- Institut National du Cancer, Research Division, Clinical Research Department, 52 avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Xavier Pivot
- University Hospital of Minjoz, INSERM UMR 1098, Bd Fleming, Besançon 25000, France
| | - Colin A. Purdie
- Pathology Department, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - F. Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Gilles Romieu
- Oncologie Sénologie, ICM Institut Régional du Cancer, Montpellier, France
| | - Anieta M. Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Peter T Simpson
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
| | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Olafur A Stefansson
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jon Teague
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Isabelle Treilleux
- Department of Pathology, Centre Léon Bérard, 28 rue Laënnec, 69373 Lyon Cédex 08, France
| | - Gert G. Van den Eynden
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Peter Vermeulen
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Lucy Yates
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Laura van’t Veer
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Andrew Tutt
- Breast Cancer Now Toby Research Unit, King’s College London
- Breast Cancer Now Toby Robin’s Research Centre, Institute of Cancer Research, London
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Benita Kiat Tee Tan
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610
- Singapore General Hospital, Outram Road, Singapore 169608
| | - Jos Jonkers
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Naoto T Ueno
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Alain Viari
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Av. de l’Europe, 38330 Montbonnot-Saint Martin, France
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - P. Andrew Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Van Laere
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sunil R Lakhani
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane, Australia
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Alastair M. Thompson
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, 1400 Pressler Street,Houston, Texas 77030
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - John W.M. Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
- Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
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27
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Aradottir M, Reynisdottir ST, Stefansson OA, Jonasson JG, Sverrisdottir A, Tryggvadottir L, Eyfjord JE, Bodvarsdottir SK. Aurora A is a prognostic marker for breast cancer arising in BRCA2 mutation carriers. J Pathol Clin Res 2014; 1:33-40. [PMID: 27499891 PMCID: PMC4858119 DOI: 10.1002/cjp2.6] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/07/2014] [Indexed: 12/20/2022]
Abstract
Overexpression of the Aurora A kinase has been shown to have prognostic value in breast cancer. Previously, we showed a significant association between AURKA gene amplification and BRCA2 mutation in breast cancer. The aim of this study was to assess the prognostic impact of Aurora A overexpression on breast cancer arising in BRCA2 mutation carriers. Aurora A expression was evaluated by immunohistochemistry on breast tumour tissue microarrays from 107 BRCA2 999del5 mutation carriers and 284 of sporadic origin. Prognostic value of Aurora A nuclear staining was estimated in relation to clinical markers and adjuvant treatment, using multivariate Cox's proportional hazards ratio regression model. BRCA2 wild‐type allele loss was measured by TaqMan in BRCA2 mutated tumour samples. All statistical tests were two sided. Multivariate analysis of breast cancer‐specific survival, including proliferative markers and treatment, indicated independent prognostic value of Aurora A nuclear staining for BRCA2 mutation carriers (hazards ratio = 7.06; 95% confidence interval = 1.23–40.6; p = 0.028). Poor breast cancer‐specific survival of BRCA2 mutation carriers was found to be significantly associated with combined Aurora A nuclear expression and BRCA2 wild type allele loss in tumours (p < 0.001). Multivariate analysis indicated independent prognostic value of both positive Aurora A nuclear staining (hazards ratio = 10.09; 95% confidence interval = 1.19–85.4, p = 0.034) and BRCA2 wild type allele loss (hazards ratio = 9.63; 95% confidence interval = 1.81–51.0, p = 0.008) for BRCA2 mutation carriers. Aurora A nuclear expression was found to be a significant prognostic marker for BRCA2 mutation carriers, independent of clinical parameters and adjuvant treatment. Our conclusion is that treatment benefits for BRCA2 mutation carriers and sporadic breast cancer patients with Aurora A positive tumours may be enhanced by giving attention to Aurora A targeted treatment.
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Affiliation(s)
- Margret Aradottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland Reykjavik Iceland
| | - Sigridur T Reynisdottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland Reykjavik Iceland
| | - Olafur A Stefansson
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland Reykjavik Iceland
| | - Jon G Jonasson
- Faculty of MedicineSchool of Health Sciences, University of IcelandReykjavikIceland; Icelandic Cancer RegistryIcelandic Cancer SocietyReykjavikIceland; Department of PathologyNational University HospitalReykjavikIceland
| | | | - Laufey Tryggvadottir
- Faculty of MedicineSchool of Health Sciences, University of IcelandReykjavikIceland; Icelandic Cancer RegistryIcelandic Cancer SocietyReykjavikIceland
| | - Jorunn E Eyfjord
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland Reykjavik Iceland
| | - Sigridur K Bodvarsdottir
- Cancer Research Laboratory, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland Reykjavik Iceland
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Stefansson OA, Moran S, Gomez A, Sayols S, Arribas-Jorba C, Sandoval J, Hilmarsdottir H, Olafsdottir E, Tryggvadottir L, Jonasson JG, Eyfjord J, Esteller M. A DNA methylation-based definition of biologically distinct breast cancer subtypes. Mol Oncol 2014; 9:555-68. [PMID: 25468711 PMCID: PMC5528700 DOI: 10.1016/j.molonc.2014.10.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 10/06/2014] [Accepted: 10/29/2014] [Indexed: 01/12/2023] Open
Abstract
In cancer, epigenetic states are deregulated and thought to be of significance in cancer development and progression. We explored DNA methylation‐based signatures in association with breast cancer subtypes to assess their impact on clinical presentation and patient prognosis. DNA methylation was analyzed using Infinium 450K arrays in 40 tumors and 17 normal breast samples, together with DNA copy number changes and subtype‐specific markers by tissue microarrays. The identified methylation signatures were validated against a cohort of 212 tumors annotated for breast cancer subtypes by the PAM50 method (The Cancer Genome Atlas). Selected markers were pyrosequenced in an independent validation cohort of 310 tumors and analyzed with respect to survival, clinical stage and grade. The results demonstrate that DNA methylation patterns linked to the luminal‐B subtype are characterized by CpG island promoter methylation events. In contrast, a large fraction of basal‐like tumors are characterized by hypomethylation events occurring within the gene body. Based on these hallmark signatures, we defined two DNA methylation‐based subtypes, Epi‐LumB and Epi‐Basal, and show that they are associated with unfavorable clinical parameters and reduced survival. Our data show that distinct mechanisms leading to changes in CpG methylation states are operative in different breast cancer subtypes. Importantly, we show that a few selected proxy markers can be used to detect the distinct DNA methylation‐based subtypes thereby providing valuable information on disease prognosis. We describe distinct signatures associated with luminal‐B and basal‐like subtypes. The signatures identified show differences in genes, but also in the CpG context. A selected set of proxy markers for each signature revealed their clinical relevance.
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Affiliation(s)
- Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | - Carlos Arribas-Jorba
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain
| | | | | | | | - Jon G Jonasson
- The Icelandic Cancer Registry, Reykjavik, Iceland; Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jorunn Eyfjord
- The Cancer Research Laboratory, Medical Faculty, University of Iceland, Reykjavik, Iceland
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia 08908, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Carmona FJ, Davalos V, Vidal E, Gomez A, Heyn H, Hashimoto Y, Vizoso M, Martinez-Cardus A, Sayols S, Ferreira HJ, Sánchez-Mut JV, Morán S, Margelí M, Castella E, Berdasco M, Stefansson OA, Eyfjord JE, Gonzalez-Suarez E, Dopazo J, Orozco M, Gut IG, Esteller M. A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition. Cancer Res 2014; 74:5608-19. [PMID: 25106427 DOI: 10.1158/0008-5472.can-13-3659] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a plastic process in which fully differentiated epithelial cells are converted into poorly differentiated, migratory and invasive mesenchymal cells, and it has been related to the metastasis potential of tumors. This is a reversible process and cells can also eventually undergo mesenchymal-to-epithelial transition. The existence of a dynamic EMT process suggests the involvement of epigenetic shifts in the phenotype. Herein, we obtained the DNA methylomes at single-base resolution of Madin-Darby canine kidney cells undergoing EMT and translated the identified differentially methylated regions to human breast cancer cells undergoing a gain of migratory and invasive capabilities associated with the EMT phenotype. We noticed dynamic and reversible changes of DNA methylation, both on promoter sequences and gene-bodies in association with transcription regulation of EMT-related genes. Most importantly, the identified DNA methylation markers of EMT were present in primary mammary tumors in association with the epithelial or the mesenchymal phenotype of the studied breast cancer samples.
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Affiliation(s)
- F Javier Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Veronica Davalos
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Yutaka Hashimoto
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Miguel Vizoso
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Jose V Sánchez-Mut
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Sebastián Morán
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | | | - Eva Castella
- Pathology Department, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Maria Berdasco
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Jorunn E Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, Reykjavik, Iceland. Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Eva Gonzalez-Suarez
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain
| | - Joaquín Dopazo
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain. CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. Functional Genomics Node (INB) at CIPF, Valencia, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. Joint IRB-BSC Research Program on Computational Biology, Barcelona, Spain. Barcelona Supercomputing Center, Barcelona, Spain. Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Ivo G Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Stefansson OA, Esteller M. CARM1 and BAF155: an example of how chromatin remodeling factors can be relocalized and contribute to cancer. Breast Cancer Res 2014; 16:307. [PMID: 25927994 PMCID: PMC4053224 DOI: 10.1186/bcr3657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In a recent article, Wang and colleagues reported the discovery of a mechanism by which CARM1 regulates the genomic localization of BAF155 (a SWI/SNF subunit involved in chromatin remodeling) through post-translational methylation at R1064 arginine residues. This modification leads to the relocalization of BAF155-containing SWI/SNF complexes to regions containing genes involved in the Myc oncogenic pathway. The results presented are evidence that these interactions constitute a mechanism by which the BAF155 chromatin remodeling factor contributes to cancer.
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Affiliation(s)
- Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, L'Hospitalet del Llobregat, Barcelona, Catalonia, 08908, Spain. .,Cancer Research Laboratory, Faculty of Medicine, University of Iceland, Sæmundargötu 2, 101, Reykjavík, Iceland.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, L'Hospitalet del Llobregat, Barcelona, Catalonia, 08908, Spain. .,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, 08908, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain.
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Stefansson OA, Esteller M. Epigenetic Modifications in Breast Cancer and Their Role in Personalized Medicine. The American Journal of Pathology 2013; 183:1052-1063. [DOI: 10.1016/j.ajpath.2013.04.033] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/04/2013] [Accepted: 04/29/2013] [Indexed: 12/14/2022]
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Tryggvadottir L, Olafsdottir EJ, Olafsdottir GH, Sigurdsson H, Johannsson OT, Bjorgvinsson E, Alexiusdottir K, Stefansson OA, Agnarsson BA, Narod SA, Eyfjord JE, Jonasson JG. Tumour diploidy and survival in breast cancer patients with BRCA2 mutations. Breast Cancer Res Treat 2013; 140:375-84. [PMID: 23857704 DOI: 10.1007/s10549-013-2637-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
It is not well known to what extent carrying a BRCA2 mutation affects the survival of women with breast cancer and prognostic factors among BRCA2-positive women warrant investigation. Using a record linkage approach we compared the long-term survival in carriers and noncarriers of an inherited BRCA2 founder mutation (999del5), and sought to identify prognostic factors among the BRCA2 mutation-positive subset, including markers of genetic instability (aneuploidy) and mitotic activity (S-phase fraction). We established the genetic status of 2,967 Icelandic breast cancer patients (215 mutation carriers and 2,752 noncarriers) diagnosed from 1955 to 2004, representing 72 % of all cases diagnosed in the country during this period. Tumour ploidy and S-phase fraction were assessed on tumour cells by DNA flow cytometry. Prognostic factors were assessed blindly with respect to mutation status. Univariate and multivariate hazard ratios (HR) were estimated for breast cancer-specific survival by BRCA2 status, using Cox regression. After a median follow-up of 9.5 years, BRCA2 mutation carriers had a higher risk of death from breast cancer than noncarriers (HR 1.64, 95 % CI 1.24-2.16, p < 0.001). The risk increase was restricted to women with diploid tumours (HR 3.03, 95 % CI 1.91-4.79, p < 0.001). Among breast cancer patients with aneuploid tumours, survival of carriers was similar to that of noncarriers (HR 0.76, 95 % CI 0.41-1.41, p = 0.38). Increased tumour size and a positive nodal status predicted worse prognosis in all patients, whereas the highly correlated prognostic factors diploidy, low proliferative activity and a positive estrogen receptor status had reverse effects in mutation carriers and noncarriers. Breast cancer patients who carry the Icelandic founder BRCA2 mutation have inferior long-term survival than noncarriers, but the adverse prognosis is restricted to mutation carriers with diploid, slowly proliferating tumours.
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Affiliation(s)
- Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Skogarhlid 8, P.O. Box 5420, 125, Reykjavik, Iceland.
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Stefansson OA, Moran S, Gomez A, Puig SS, Eyfjord J, Esteller M. Abstract 2018: Genome-wide analysis of DNA methylation and copy number changes in breast cancers. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic modifications are known to be critical in regulating normal developmental processes and cellular differentiation. DNA methylation of CpG dinucleotides is a well-characterized epigenetic marker frequently associated with transcriptional silencing. CpG dinucleotides are non-randomly distributed throughout the genome with regions enriched for CpGs being known as CpG islands. It is now well established that epigenetic inactivation of tumor suppressor genes can occur by CpG island promoter methylation. For example, BRCA1 promoter methylation occurs in approximately 10 - 15% of all breast cancers and is associated with gene silencing. Recent technological advances have enabled DNA methylation to be profiled genome-wide. Using the Infinium 450 thousand probe arrays, we have studied DNA methylation and copy number changes to discover new markers of potential clinical relevance in breast cancer. Expression analyses by immunohistochemisty on tissue arrays for subtype-specific markers (ER, PR, HER2, Ki-67, EGFR, CK5/6, CK8, CK18, MUC1 and Claudin-3) carried out previously were used to establish DNA methylation markers of breast cancer subtypes. This integrated approach is presented in clinical context with available data on histological grade, disease stage and breast cancer-specific survival outcomes.
Citation Format: Olafur A. Stefansson, Sebastian Moran, Antonio Gomez, Sergi Sayols Puig, Jorunn Eyfjord, Manel Esteller. Genome-wide analysis of DNA methylation and copy number changes in breast cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2018. doi:10.1158/1538-7445.AM2013-2018
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Affiliation(s)
- Olafur A. Stefansson
- 1Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sebastian Moran
- 1Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Gomez
- 1Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sergi Sayols Puig
- 1Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jorunn Eyfjord
- 2University of Iceland, Faculty of Medicine, Reykjavik, Iceland
| | - Manel Esteller
- 1Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
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Stefansson OA, Villanueva A, Vidal A, Martí L, Esteller M. BRCA1 epigenetic inactivation predicts sensitivity to platinum-based chemotherapy in breast and ovarian cancer. Epigenetics 2012; 7:1225-9. [PMID: 23069641 PMCID: PMC3499323 DOI: 10.4161/epi.22561] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Germline mutations in the BRCA1 or BRCA2 genes are associated with an increased risk of breast and ovarian cancer development. Both genes are involved in DNA repair, and tumors harboring genetic defects in them are thought to be more sensitive to DNA-damaging agents used in chemotherapy. However, as only a minority of breast and ovarian cancer patients carry BRCA1 or BRCA2 mutations, few patients are likely to benefit from these pharmacogenetic biomarkers. Herein, we show that, in cancer cell lines and xenografted tumors, BRCA1 CpG island promoter hypermethylation-associated silencing also predicts enhanced sensitivity to platinum-derived drugs to the same extent as BRCA1 mutations. Most importantly, BRCA1 hypermethylation proves to be a predictor of longer time to relapse and improved overall survival in ovarian cancer patients undergoing chemotherapy with cisplatin.
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Affiliation(s)
- Olafur A Stefansson
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Catalonia Spain
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Heyn H, Carmona FJ, Gomez A, Ferreira HJ, Bell JT, Sayols S, Ward K, Stefansson OA, Moran S, Sandoval J, Eyfjord JE, Spector TD, Esteller M. DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker. Carcinogenesis 2012; 34:102-8. [PMID: 23054610 PMCID: PMC3534196 DOI: 10.1093/carcin/bgs321] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Using whole blood from 15 twin pairs discordant for breast cancer and high-resolution (450K) DNA methylation analysis, we identified 403 differentially methylated CpG sites including known and novel potential breast cancer genes. Confirming the results in an independent validation cohort of 21 twin pairs determined the docking protein DOK7 as a candidate for blood-based cancer diagnosis. DNA hypermethylation of the promoter region was also seen in primary breast cancer tissues and cancer cell lines. Hypermethylation of DOK7 occurs years before tumor diagnosis, suggesting a role as a powerful epigenetic blood-based biomarker as well as providing insights into breast cancer pathogenesis.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia 08907, Spain
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Stefansson OA, Villanueva A, Vidal A, Martí L, Esteller M. Re: A DNA repair pathway-focused score for prediction of outcomes in ovarian cancer treated with platinum-based chemotherapy. J Natl Cancer Inst 2012; 104:1514; author reply 1514-5. [PMID: 22923512 DOI: 10.1093/jnci/djs363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stefansson OA, Jonasson JG, Olafsdottir K, Bjarnason H, Th Johannsson O, Bodvarsdottir SK, Valgeirsdottir S, Eyfjord JE. Genomic and phenotypic analysis of BRCA2 mutated breast cancers reveals co-occurring changes linked to progression. Breast Cancer Res 2011; 13:R95. [PMID: 21958427 PMCID: PMC3262207 DOI: 10.1186/bcr3020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 07/12/2011] [Accepted: 09/29/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Inherited mutations in the BRCA2 gene greatly increase the risk of developing breast cancer. Consistent with an important role for BRCA2 in error-free DNA repair, complex genomic changes are frequently observed in tumors derived from BRCA2 mutation carriers. Here, we explore the impact of DNA copy-number changes in BRCA2 tumors with respect to phenotype and clinical staging of the disease. METHODS Breast tumors (n = 33) derived from BRCA2 999del5 mutation carriers were examined in terms of copy-number changes with high-resolution aCGH (array comparative genomic hybridization) containing 385 thousand probes (about one for each 7 kbp) and expression of phenotypic markers on TMAs (tissue microarrays). The data were examined with respect to clinical parameters including TNM staging, histologic grade, S phase, and ploidy. RESULTS Tumors from BRCA2 carriers of luminal and basal/triple-negative phenotypes (TNPs) differ with respect to patterns of DNA copy-number changes. The basal/TNP subtype was characterized by lack of pRb (RB1) coupled with high/intense expression of p16 (CDKN2A) gene products. We found increased proportions of Ki-67-positive cells to be significantly associated with loss of the wild-type (wt) BRCA2 allele in luminal types, whereas BRCA2wt loss was less frequent in BRCA2 tumors displaying basal/TNP phenotypes. Furthermore, we show that deletions at 13q13.1, involving the BRCA2wt allele, represents a part of a larger network of co-occurring genetic changes, including deletions at 6q22.32-q22.33, 11q14.2-q24.1, and gains at 17q24.1. Importantly, copy-number changes at these BRCA2-linked networking regions coincide with those associated with advanced progression, involving the capacity to metastasize to the nodes or more-distant sites at diagnosis. CONCLUSIONS The results presented here demonstrate divergent paths of tumor evolution in BRCA2 carriers and that deletion of the wild-type BRCA2 allele, together with co-occurring changes at 6 q, 11 q, and 17 q, are important events in progression toward advanced disease.
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Affiliation(s)
- Olafur A Stefansson
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
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Birgisdottir V, Stefansson OA, Bodvarsdottir SK, Hilmarsdottir H, Jonasson JG, Eyfjord JE. Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer. Breast Cancer Res 2007; 8:R38. [PMID: 16846527 PMCID: PMC1779478 DOI: 10.1186/bcr1522] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 06/16/2006] [Accepted: 06/26/2006] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION BRCA1 or BRCA2 germline mutations increase the risk of developing breast cancer. Tumour cells from germline mutation carriers have frequently lost the wild-type allele. This is predicted to result in genomic instability where cell survival depends upon dysfunctional checkpoint mechanisms. Tumorigenic potential could then be acquired through further genomic alterations. Surprisingly, somatic BRCA mutations are not found in sporadic breast tumours. BRCA1 methylation has been shown to occur in sporadic breast tumours and to be associated with reduced gene expression. We examined the frequency of BRCA1 methylation in 143 primary sporadic breast tumours along with BRCA1 copy number alterations and tumour phenotype. METHODS Primary sporadic breast tumours were analysed for BRCA1alpha promoter methylation by methylation specific PCR and for allelic imbalance (AI) at BRCA1 and BRCA2 loci by microsatellite analysis and TP53 (also known as p53) mutations by constant denaturing gel electrophoresis. The BRCA1 methylated tumours were analysed for BRCA1 copy alterations by fluorescence in situ hybridisation and BRCA1 expression by immunostaining. RESULTS BRCA1 methylation was found in 13/143 (9.1%) sporadic breast tumours. The BRCA1 methylated tumours were significantly associated with estrogen receptor (ER) negativity (P = 0.0475) and displayed a trend for BRCA1 AI (P = 0.0731) as well as young-age at diagnosis (< or = 55; P = 0.0898). BRCA1 methylation was not associated with BRCA2 AI (P = 0.5420), although a significant association was found between BRCA1 AI and BRCA2 AI (P < 0.0001).Absent/markedly reduced BRCA1 expression was observed in 9/13 BRCA1 methylated tumours, most of which had BRCA1 deletion. An elevated TP53 mutation frequency was found among BRCA1 methylated tumours (38.5%) compared with non-methylated tumours (17.2%). The BRCA1 methylated tumours were mainly of tumour grade 3 (7/13) and infiltrating ductal type (12/13). Only one methylated tumour was of grade 1. CONCLUSION BRCA1 methylation is frequent in primary sporadic breast tumours. We found an indication for BRCA1 methylation to be associated with AI at the BRCA1 locus. Almost all BRCA1 methylated tumours with absent/markedly reduced BRCA1 expression (8/9) displayed BRCA1 deletion. Thus, epigenetic silencing and deletion of the BRCA1 gene might serve as Knudson's two 'hits' in sporadic breast tumorigenesis. We observed phenotypic similarities between BRCA1 methylated and familial BRCA1 tumours, based on BRCA1 deletion, TP53 mutations, ER status, young age at diagnosis and tumour grade.
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Affiliation(s)
- Valgerdur Birgisdottir
- The Icelandic Cancer Society, Molecular and Cell Biology Research Laboratory, Reykjavik, Iceland
- University of Iceland Department of Medicine, Reykjavik, Iceland
| | - Olafur A Stefansson
- The Icelandic Cancer Society, Molecular and Cell Biology Research Laboratory, Reykjavik, Iceland
- University of Iceland Department of Medicine, Reykjavik, Iceland
| | - Sigridur K Bodvarsdottir
- The Icelandic Cancer Society, Molecular and Cell Biology Research Laboratory, Reykjavik, Iceland
- University of Iceland Department of Medicine, Reykjavik, Iceland
| | - Holmfridur Hilmarsdottir
- The Icelandic Cancer Society, Molecular and Cell Biology Research Laboratory, Reykjavik, Iceland
- University of Iceland Department of Medicine, Reykjavik, Iceland
| | - Jon G Jonasson
- University of Iceland Department of Medicine, Reykjavik, Iceland
- The Icelandic Cancer Registry, Reykjavik, Iceland
- University Hospital Department of Pathology, Reykjavik, Iceland
| | - Jorunn E Eyfjord
- The Icelandic Cancer Society, Molecular and Cell Biology Research Laboratory, Reykjavik, Iceland
- University of Iceland Department of Medicine, Reykjavik, Iceland
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