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Klemenzdottir EO, Arnadottir GA, Jensson BO, Jonasdottir A, Katrinardottir H, Fridriksdottir R, Jonasdottir A, Sigurdsson A, Gudjonsson SA, Jonsson JJ, Stefansdottir V, Danielsen R, Palsdottir A, Jonsson H, Helgason A, Magnusson OT, Thorsteinsdottir U, Bjornsson HT, Stefansson K, Sulem P. A population-based survey of FBN1 variants in Iceland reveals underdiagnosis of Marfan syndrome. Eur J Hum Genet 2024; 32:44-51. [PMID: 37684520 PMCID: PMC10772070 DOI: 10.1038/s41431-023-01455-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Marfan syndrome (MFS) is an autosomal dominant condition characterized by aortic aneurysm, skeletal abnormalities, and lens dislocation, and is caused by variants in the FBN1 gene. To explore causes of MFS and the prevalence of the disease in Iceland we collected information from all living individuals with a clinical diagnosis of MFS in Iceland (n = 32) and performed whole-genome sequencing of those who did not have a confirmed genetic diagnosis (27/32). Moreover, to assess a potential underdiagnosis of MFS in Iceland we attempted a genotype-based approach to identify individuals with MFS. We interrogated deCODE genetics' database of 35,712 whole-genome sequenced individuals to search for rare sequence variants in FBN1. Overall, we identified 15 pathogenic or likely pathogenic variants in FBN1 in 44 individuals, only 22 of whom were previously diagnosed with MFS. The most common of these variants, NM_000138.4:c.8038 C > T p.(Arg2680Cys), is present in a multi-generational pedigree, and was found to stem from a single forefather born around 1840. The p.(Arg2680Cys) variant associates with a form of MFS that seems to have an enrichment of abdominal aortic aneurysm, suggesting that this may be a particularly common feature of p.(Arg2680Cys)-associated MFS. Based on these combined genetic and clinical data, we show that MFS prevalence in Iceland could be as high as 1/6,600 in Iceland, compared to 1/10,000 based on clinical diagnosis alone, which indicates underdiagnosis of this actionable genetic disorder.
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Affiliation(s)
| | - Gudny Anna Arnadottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | - Jon Johannes Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Genetics, Landspitali Universtity Hospital, Reykjavik, Iceland
| | | | - Ragnar Danielsen
- Department of Cardiology, Landspitali University Hospital, Reykjavik, Iceland
| | - Astridur Palsdottir
- Institute for Experimental Pathology at Keldur, University of Iceland, 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, University of Iceland, Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Department of Pediatrics, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Genetics, Landspitali Universtity Hospital, Reykjavik, Iceland
- McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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Jónsson H, Sulem P, Arnadottir GA, Pálsson G, Eggertsson HP, Kristmundsdottir S, Zink F, Kehr B, Hjorleifsson KE, Jensson BÖ, Jonsdottir I, Marelsson SE, Gudjonsson SA, Gylfason A, Jonasdottir A, Jonasdottir A, Stacey SN, Magnusson OT, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K. Multiple transmissions of de novo mutations in families. Nat Genet 2018; 50:1674-1680. [DOI: 10.1038/s41588-018-0259-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 09/19/2018] [Indexed: 11/09/2022]
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Jónsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir A, Jonasdottir A, Rafnar T, Frigge M, Stacey SN, Th Magnusson O, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature 2017; 549:519-522. [PMID: 28959963 DOI: 10.1038/nature24018] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/20/2017] [Indexed: 12/20/2022]
Abstract
The characterization of mutational processes that generate sequence diversity in the human genome is of paramount importance both to medical genetics and to evolutionary studies. To understand how the age and sex of transmitting parents affect de novo mutations, here we sequence 1,548 Icelanders, their parents, and, for a subset of 225, at least one child, to 35× genome-wide coverage. We find 108,778 de novo mutations, both single nucleotide polymorphisms and indels, and determine the parent of origin of 42,961. The number of de novo mutations from mothers increases by 0.37 per year of age (95% CI 0.32-0.43), a quarter of the 1.51 per year from fathers (95% CI 1.45-1.57). The number of clustered mutations increases faster with the mother's age than with the father's, and the genomic span of maternal de novo mutation clusters is greater than that of paternal ones. The types of de novo mutation from mothers change substantially with age, with a 0.26% (95% CI 0.19-0.33%) decrease in cytosine-phosphate-guanine to thymine-phosphate-guanine (CpG>TpG) de novo mutations and a 0.33% (95% CI 0.28-0.38%) increase in C>G de novo mutations per year, respectively. Remarkably, these age-related changes are not distributed uniformly across the genome. A striking example is a 20 megabase region on chromosome 8p, with a maternal C>G mutation rate that is up to 50-fold greater than the rest of the genome. The age-related accumulation of maternal non-crossover gene conversions also mostly occurs within these regions. Increased sequence diversity and linkage disequilibrium of C>G variants within regions affected by excess maternal mutations indicate that the underlying mutational process has persisted in humans for thousands of years. Moreover, the regional excess of C>G variation in humans is largely shared by chimpanzees, less by gorillas, and is almost absent from orangutans. This demonstrates that sequence diversity in humans results from evolving interactions between age, sex, mutation type, and genomic location.
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Affiliation(s)
| | | | - Birte Kehr
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland
| | | | - Florian Zink
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland
| | | | | | | | | | | | - Lucas D Ward
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland
| | | | | | | | | | | | | | | | - Mike Frigge
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland
| | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Gisli Masson
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland
| | - Augustine Kong
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, 101 Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., 101 Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland
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Sveinbjornsson G, Gudbjartsson DF, Halldorsson BV, Kristinsson KG, Gottfredsson M, Barrett JC, Gudmundsson LJ, Blondal K, Gylfason A, Gudjonsson SA, Helgadottir HT, Jonasdottir A, Jonasdottir A, Karason A, Kardum LB, Knežević J, Kristjansson H, Kristjansson M, Love A, Luo Y, Magnusson OT, Sulem P, Kong A, Masson G, Thorsteinsdottir U, Dembic Z, Nejentsev S, Blondal T, Jonsdottir I, Stefansson K. HLA class II sequence variants influence tuberculosis risk in populations of European ancestry. Nat Genet 2016; 48:318-22. [PMID: 26829749 PMCID: PMC5081101 DOI: 10.1038/ng.3498] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [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: 05/06/2015] [Accepted: 01/04/2016] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis infections cause 9 million new tuberculosis cases and 1.5 million deaths annually. To identify variants conferring risk of tuberculosis, we tested 28.3 million variants identified through whole-genome sequencing of 2,636 Icelanders for association with tuberculosis (8,162 cases and 277,643 controls), pulmonary tuberculosis (PTB) and M. tuberculosis infection. We found association of three variants in the region harboring genes encoding the class II human leukocyte antigens (HLAs): rs557011[T] (minor allele frequency (MAF) = 40.2%), associated with M. tuberculosis infection (odds ratio (OR) = 1.14, P = 3.1 × 10(-13)) and PTB (OR = 1.25, P = 5.8 × 10(-12)), and rs9271378[G] (MAF = 32.5%), associated with PTB (OR = 0.78, P = 2.5 × 10(-12))--both located between HLA-DQA1 and HLA-DRB1--and a missense variant encoding p.Ala210Thr in HLA-DQA1 (MAF = 19.1%, rs9272785), associated with M. tuberculosis infection (P = 9.3 × 10(-9), OR = 1.14). We replicated association of these variants with PTB in samples of European ancestry from Russia and Croatia (P < 5.9 × 10(-4)). These findings show that the HLA class II region contributes to genetic risk of tuberculosis, possibly through reduced presentation of protective M. tuberculosis antigens to T cells.
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Affiliation(s)
- Gardar Sveinbjornsson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Daniel F. Gudbjartsson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V. Halldorsson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavík, Iceland
| | - Karl G. Kristinsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Clinical Microbiology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Magnus Gottfredsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Infectious Diseases, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Kai Blondal
- Division of Communicable Disease Prevention and Control, Primary Health Care of the Capital Area, Reykjavik, Iceland
| | | | | | | | | | | | - Ari Karason
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
| | - Ljiljana Bulat Kardum
- Department of Pulmology, Clinic of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Jelena Knežević
- Laboratory of Molecular Genetics, Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Helgi Kristjansson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Mar Kristjansson
- Department of Infectious Diseases, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Arthur Love
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Virology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Yang Luo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Patrick Sulem
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
| | - Augustine Kong
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
| | - Gisli Masson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Zlatko Dembic
- Laboratory of Molecular Genetics, Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Thorsteinn Blondal
- Division of Communicable Disease Prevention and Control, Primary Health Care of the Capital Area, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics / Amgen Inc., Sturlugata 8, 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
| | - Kari Stefansson
- deCODE genetics / Amgen Inc., Sturlugata 8, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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Lund SH, Sigurdsson A, Gudjonsson SA, Gudmundsson J, Gudbjartsson DF, Rafnar T, Stefansson K, Stefansson G. The effect of SNPs on expression levels in Nimblegen RNA expression microarrays. INT J DATA MIN BIOIN 2015; 12:1-13. [PMID: 26489138 DOI: 10.1504/ijdmb.2015.068949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper the effect of SNPs on expression levels in Nimblegen RNA expression microarrays is investigated. A vast number of replicates of probe pairs representing both alleles of SNPs on 14 loci allows accurate estimation of the difference in signal intensities both within and between probe pairs. The majority of probe-pairs with sufficiently high expression have significant differences in expression levels within the pair and the difference shows concordance with the genotype of the samples. With two or more replicates of each probe, the allele-to-allele variance dominates the error in estimating the difference within the probe-pair, ten replicates are needed for adequate power in calling a true difference within a single probe-pair. Using the expression level of the probe within the probe-pair that has the higher value gives more accurate estimates. When using probes at loci containing known SNP's one should use probes containing both alleles of the SNP.
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Lund SH, Gudbjartsson DF, Rafnar T, Sigurdsson A, Gudjonsson SA, Gudmundsson J, Stefansson K, Stefansson G. A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PLoS One 2014; 9:e99899. [PMID: 24937006 PMCID: PMC4061049 DOI: 10.1371/journal.pone.0099899] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 01/29/2014] [Accepted: 05/20/2014] [Indexed: 01/08/2023] Open
Abstract
Long non-coding ribonucleic acids (lncRNAs) have been proposed as biomarkers in prostate cancer. This paper proposes a selection method which uses data from tiled microarrays to identify relatively long regions of moderate expression independent of the microarray platform and probe design. The method is used to search for candidate long non-coding ribonucleic acids (lncRNAs) at locus 8q24 and is run on three independent experiments which all use samples from prostate cancer patients. The robustness of the method is tested by utilizing repeated copies of tiled probes. The method shows high consistency between experiments that used the same samples, but different probe layout. There also is statistically significant consistency when comparing experiments with different samples. The method selected the long non-coding ribonucleic acid PCNCR1 in all three experiments.
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Affiliation(s)
- Sigrun Helga Lund
- Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland
- * E-mail:
| | | | | | | | | | | | | | - Gunnar Stefansson
- Faculty of Physical Sciences, University of Iceland, Reykjavik, Iceland
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