3
|
Olsson M, Kierczak M, Karlsson Å, Jabłońska J, Leegwater P, Koltookian M, Abadie J, De Citres CD, Thomas A, Hedhammar Å, Tintle L, Lindblad-Toh K, Meadows JRS. Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease. BMC Genomics 2016; 17:299. [PMID: 27107962 PMCID: PMC4841964 DOI: 10.1186/s12864-016-2619-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dissecting the role copy number variants (CNVs) play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory disease with numerous clinical manifestations. One such sign, recurrent fever, was previously shown to be significantly associated with a novel, but unstable CNV (CNV_16.1). Droplet digital PCR (ddPCR) offers a new mechanism for CNV detection via absolute quantification with the promise of added precision and reliability. The aim of this study was to evaluate ddPCR in relation to quantitative PCR (qPCR) and to assess the suitability of the favoured method as a genetic test for Shar-Pei Autoinflammatory Disease (SPAID). RESULTS One hundred and ninety-six individuals were assayed using both PCR methods at two CNV positions (CNV_14.3 and CNV_16.1). The digital method revealed a striking result. The CNVs did not follow a continuum of alleles as previously reported, rather the alleles were stable and pedigree analysis showed they adhered to Mendelian segregation. Subsequent analysis of ddPCR case/control data confirmed that both CNVs remained significantly associated with the subphenotype of fever, but also to the encompassing SPAID complex (p < 0.001). In addition, harbouring CNV_16.1 allele five (CNV_16.1|5) resulted in a four-fold increase in the odds for SPAID (p < 0.001). The inclusion of a genetic marker for CNV_16.1 in a genome-wide association test revealed that this variant explained 9.7 % of genetic variance and 25.8 % of the additive genetic heritability of this autoinflammatory disease. CONCLUSIONS This data shows the utility of the ddPCR method to resolve cryptic copy number inheritance patterns and so open avenues of genetic testing. In its current form, the ddPCR test presented here could be used in canine breeding to reduce the number of homozygote CNV_16.1|5 individuals and thereby to reduce the prevalence of disease in this breed.
Collapse
Affiliation(s)
- M Olsson
- Department of Medicine, Rheumatology Unit, Karolinska Institute, Stockholm, Sweden
| | - M Kierczak
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Å Karlsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - J Jabłońska
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P Leegwater
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
| | - M Koltookian
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - J Abadie
- LUNAM University, Oniris, AMaROC Unit, Nantes, F-44307, France
| | | | - A Thomas
- ANTAGENE Animal Genetics Laboratory, La Tour de Salvagny, Lyon, 69, France
| | - Å Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L Tintle
- Wurtsboro Veterinary Clinic, Wurtsboro, New York, USA
| | - K Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Boston, MA, USA
| | - J R S Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
7
|
Fernandez-Cuesta L, Peifer M, Lu X, Sun R, Ozretić L, Seidal D, Zander T, Leenders F, George J, Müller C, Dahmen I, Pinther B, Bosco G, Konrad K, Altmüller J, Nürnberg P, Achter V, Lang U, Schneider PM, Bogus M, Soltermann A, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Ansén S, Stoelben E, Wright GM, Russell P, Wainer Z, Solomon B, Field JK, Hyde R, Davies MPA, Heukamp LC, Petersen I, Perner S, Lovly C, Cappuzzo F, Travis WD, Wolf J, Vingron M, Brambilla E, Haas SA, Buettner R, Thomas RK. Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Nat Commun 2014; 5:3518. [PMID: 24670920 PMCID: PMC4132974 DOI: 10.1038/ncomms4518] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 02/26/2014] [Indexed: 02/07/2023] Open
Abstract
Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n=44) and transcriptome (n=69) sequencing of pulmonary carcinoids and observe frequent mutations in chromatin-remodelling genes. Covalent histone modifiers and subunits of the SWI/SNF complex are mutated in 40 and 22.2% of the cases, respectively, with MEN1, PSIP1 and ARID1A being recurrently affected. In contrast to small-cell lung cancer and large-cell neuroendocrine lung tumours, TP53 and RB1 mutations are rare events, suggesting that pulmonary carcinoids are not early progenitor lesions of the highly aggressive lung neuroendocrine tumours but arise through independent cellular mechanisms. These data also suggest that inactivation of chromatin-remodelling genes is sufficient to drive transformation in pulmonary carcinoids.
Collapse
Affiliation(s)
- Lynnette Fernandez-Cuesta
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Xin Lu
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Ruping Sun
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Luka Ozretić
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
| | - Danila Seidal
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
| | - Thomas Zander
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Frauke Leenders
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
| | - Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Christian Müller
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Berit Pinther
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Graziella Bosco
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Kathryn Konrad
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, 50931 Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, 50931 Cologne, Germany
- Department of Informatics, University of Cologne, 50931 Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Magdalena Bogus
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Alex Soltermann
- Institute for Surgical Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Odd Terje Brustugun
- Institute of clinical medicine, Faculty of Medicine, University of Oslo, N-0424 Oslo, Norway
- Department of oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Åslaug Helland
- Institute of clinical medicine, Faculty of Medicine, University of Oslo, N-0424 Oslo, Norway
- Department of oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Steinar Solberg
- Department of Thoracic Surgery, Rikshospitalet, Oslo University Hospital, N-0027 Oslo, Norway
| | - Marius Lund-Iversen
- Department of pathology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Sascha Ansén
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
| | - Erich Stoelben
- Thoracic Surgery, Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH, 51109 Cologne, Germany
| | - Gavin M. Wright
- University of Melbourne Department of Surgery, St Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Prudence Russell
- Department of Pathology, St. Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Zoe Wainer
- University of Melbourne Department of Surgery, St Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Benjamin Solomon
- Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, 3002 Victoria, Australia
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Russell Hyde
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Michael PA. Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Lukas C Heukamp
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Iver Petersen
- Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Sven Perner
- Department of Prostate Cancer Research, Institute of Pathology, University Hospital of Bonn, 53127 Bonn, Germany
| | | | - Federico Cappuzzo
- Department of Medical Oncology, Istituto Toscano Tumouri, 57100 Livorno, Italy
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York 10065, USA
| | - Jürgen Wolf
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Martin Vingron
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Elisabeth Brambilla
- Department of Pathology, CHU Grenoble INSERM U823, Institute Albert Bonniot 38043 CS10217 Grenoble, France
| | - Stefan A. Haas
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Reinhard Buettner
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
| |
Collapse
|