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Novak W, Berner J, Svaton M, Jimenez-Heredia R, Segarra-Roca A, Frohne A, Guiliani S, Rouhani D, Eder SK, Rottal A, Trapin D, Scheuchenstuhl A, Pickl WF, Simonitsch-Klupp I, Kager L, Boztug K. Evans syndrome caused by a deleterious mutation affecting the adaptor protein SASH3. Br J Haematol 2023; 203:678-683. [PMID: 37646304 DOI: 10.1111/bjh.19061] [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: 04/23/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023]
Abstract
Increasing evidence suggests multilineage cytopenias (also known as Evans syndrome) may be caused by inborn errors of immunity (IEI) with immune dysregulation. We studied a patient with autoimmune haemolytic anaemia and immune thrombocytopenia and identified a germline mutation in SASH3 (c.862C>T;p.Arg288Ter), indicating a recently identified IEI. Immunohistochemistry performed after clinically indicated splenectomy revealed severe hypoplasia/absence of germinal centres. The autoimmune phenotype was associated with an increased CD21low T-bet+ CD11c+ subset along with decreased regulatory T cells, impaired T-cell proliferation and T-cell exhaustion. The younger brother carries the same SASH3 mutation and shares immunophenotypic features but is currently clinical asymptomatic, indicating heterogeneity of SASH3 deficiency.
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Affiliation(s)
- Wolfgang Novak
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
| | - Jakob Berner
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Dermatology, Venerology and Allergology, Klinik Landstrasse, Vienna, Austria
| | - Michael Svaton
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raul Jimenez-Heredia
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Anna Segarra-Roca
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Alexandra Frohne
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sarah Guiliani
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - David Rouhani
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
| | - Sebastian K Eder
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Arno Rottal
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Doris Trapin
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Anja Scheuchenstuhl
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Winfried F Pickl
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | | | - Leo Kager
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Kaan Boztug
- St. Anna Children's Hospital, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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2
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Panzer M, Viveiros A, Schaefer B, Baumgartner N, Seppi K, Djamshidian A, Todorov T, Griffiths WJH, Schott E, Schuelke M, Eurich D, Stättermayer AF, Bomford A, Foskett P, Vodopiutz J, Stauber R, Pertler E, Morell B, Tilg H, Müller T, Kiechl S, Jimenez-Heredia R, Weiss KH, Hahn SH, Janecke A, Ferenci P, Zoller H. Synonymous mutation in adenosine triphosphatase copper-transporting beta causes enhanced exon skipping in Wilson disease. Hepatol Commun 2022; 6:1611-1619. [PMID: 35271763 PMCID: PMC9234614 DOI: 10.1002/hep4.1922] [Citation(s) in RCA: 3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 12/21/2022] Open
Abstract
Wilson disease (WD) is caused by biallelic pathogenic variants in adenosine triphosphatase copper-transporting beta (ATP7B); however, genetic testing identifies only one or no pathogenic ATP7B variant in a number of patients with WD. Synonymous single-nucleotide sequence variants have been recognized as pathogenic in individual families. The aim of the present study was to evaluate the prevalence and disease mechanism of the synonymous variant c.2292C>T (p.Phe764=) in WD. A cohort of 280 patients with WD heterozygous for a single ATP7B variant was investigated for the presence of c.2292C>T (p.Phe764=). In this cohort of otherwise genetically unexplained WD, the allele frequency of c.2292C>T (p.Phe764=) was 2.5% (14 of 560) compared to 7.1 × 10-6 in the general population (2 of 280,964 in the Genome Aggregation Database; p < 10-5 ; Fisher exact test). In an independent United Kingdom (UK) cohort, 2 patients with WD homozygous for p.Phe764= were identified. RNA analysis of ATP7B transcripts from patients homozygous or heterozygous for c.2292C>T and control fibroblasts showed that this variant caused high expression of an ATP7B transcript variant lacking exon 8. Conclusion: The synonymous ATP7B variant c.2292C>T (p.Phe764=) causes abnormal messenger RNA processing of ATP7B transcripts and is associated with WD in compound heterozygotes and homozygotes.
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Affiliation(s)
- Marlene Panzer
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria.,VASCage Research Center on Vascular Ageing and StrokeInnsbruckAustria
| | - André Viveiros
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria
| | - Benedikt Schaefer
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria
| | - Nadja Baumgartner
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria
| | - Klaus Seppi
- Department of NeurologyMedical University of InnsbruckInnsbruckAustria
| | - Atbin Djamshidian
- Department of NeurologyMedical University of InnsbruckInnsbruckAustria
| | - Theodor Todorov
- Department of Medical Genetics and Molecular BiologyUniversity Hospital LozenetzSofiaBulgaria
| | - William J H Griffiths
- Cambridge Liver UnitCambridge University Hospitals National Health Service (NHS) Foundation TrustCambridgeUK
| | - Eckart Schott
- Helios Klinikum Emil von Behring GmbHKlinik für Innere Medizin IIBerlinGermany
| | - Markus Schuelke
- Department of NeuropediatricsCharité University Medical Center BerlinBerlinGermany
| | - Dennis Eurich
- Department of SurgeryCharité University Medical Center BerlinBerlinGermany
| | - Albert Friedrich Stättermayer
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University ViennaViennaAustria
| | - Adrian Bomford
- Institute of Liver StudiesKing's College Hospital NHS Foundation TrustLondonUK
| | - Pierre Foskett
- Institute of Liver StudiesKing's College Hospital NHS Foundation TrustLondonUK
| | - Julia Vodopiutz
- Division of Pediatric Pulmology, Allergology, and EndocrinologyDepartment of Pediatrics and Adolescent MedicineComprehensive Center for PediatricsMedical University of ViennaViennaAustria
| | - Rudolf Stauber
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria
| | - Elke Pertler
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria.,Christian Doppler Laboratory on Iron and Phosphate BiologyInnsbruckAustria
| | - Bernhard Morell
- Department of Gastroenterology and HepatologyUniversity Hospital ZurichZurichSwitzerland
| | - Herbert Tilg
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria
| | - Thomas Müller
- Department of Pediatrics IMedical University of InnsbruckInnsbruckAustria
| | - Stefan Kiechl
- Department of NeurologyMedical University of InnsbruckInnsbruckAustria
| | - Raul Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria.,Department of Pediatrics and Adolescent MedicineMedical University of ViennaViennaAustria.,St. Anna Children's Cancer Research InstituteViennaAustria
| | - Karl Heinz Weiss
- Internal MedicineKrankenhaus Salem der Evangelischen StadtmissionHeidelbergGermany
| | - Si Houn Hahn
- University of Washington School of MedicineSeattle Children's HospitalSeattleWashingtonUSA
| | - Andreas Janecke
- Department of Pediatrics IMedical University of InnsbruckInnsbruckAustria
| | - Peter Ferenci
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine IIIMedical University ViennaViennaAustria
| | - Heinz Zoller
- Department of Medicine IMedical University of InnsbruckInnsbruckAustria.,Christian Doppler Laboratory on Iron and Phosphate BiologyInnsbruckAustria
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Müller H, Jimenez-Heredia R, Krolo A, Hirschmugl T, Dmytrus J, Boztug K, Bock C. VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data. Nucleic Acids Res 2019; 45:W567-W572. [PMID: 28520890 PMCID: PMC5570181 DOI: 10.1093/nar/gkx425] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 02/28/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023] Open
Abstract
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.
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Affiliation(s)
- Heiko Müller
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria.,Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Raul Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria
| | - Tatjana Hirschmugl
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria
| | - Jasmin Dmytrus
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria.,St. Anna Kinderspital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
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4
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Zoghi S, Ziaee V, Hirschmugl T, Jimenez-Heredia R, Krolo A, Boztug K, Rezaei N. Exome sequencing revealed C1Q homozygous mutation in Pediatric Systemic Lupus Erythematosus. Allergol Immunopathol (Madr) 2018; 46:594-598. [PMID: 29739689 DOI: 10.1016/j.aller.2018.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 12/23/2022]
Abstract
INTRODUCTION AND OBJECTIVES Pediatric Systemic Lupus Erythematosus (pSLE) is an autoimmune disorder of children. Early disease onset raises the probability of genetic etiology and it is more severe than adult SLE. PATIENTS AND METHODS Herein an eight-year-old girl with pSLE from consanguineous parents is reported. RESULTS Although she was diagnosed as pSLE since the age of two years, Whole Exome Sequencing (WES) revealed a rare stop-gained C>T mutation in C1QA gene. The variant was validated and segregated in patient and the family. Furthermore, serum levels of the C1q protein were measured and found to be much lower than normal ranges. CONCLUSIONS This study indicated that C1Q deficiency should be considered as a differential diagnosis of pSLE. Therefore, measurement of C1q should be recommended in all cases with pSLE.
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Weinberger J, Jimenez-Heredia R, Schaller S, Suessner S, Sunzenauer J, Reindl-Schwaighofer R, Weiss R, Winkler S, Gabriel C, Danzer M, Oberbauer R. Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood. PLoS One 2015; 10:e0143125. [PMID: 26600245 PMCID: PMC4658119 DOI: 10.1371/journal.pone.0143125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 05/23/2015] [Accepted: 10/30/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data. We used Biomed-2 primer panels and ImmunExplorer software to sequence, analyze and compare complementarity determining regions and V-(D)-J elements. While generally an individual's renal receptor repertoire is different from the repertoire present in blood, 94% (30/32) of the lymphocytes with clonal expansion in kidney can also be traced in blood however, not all of these clonotypes are equally abundant. Summarizing the data of all analyzed patients, 68% of highly expanded T cell clonotypes and 30% of the highly expanded B cell clonotypes that have infiltrated the kidney can be found amongst the five most abundant clonotypes in blood. In addition, complementarity determining region 3 sequences of the immunoglobulin heavy chains are on average more diverse than T cell receptor beta chains. Immune repertoire analysis of tissue infiltrating B and T cells adds new approaches to the assessment of adaptive immune response in kidney diseases. Our data suggest that expanded clonotypes in the tissues might be traceable in blood samples in the course of treatment or the natural history of the disease.
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Affiliation(s)
- Johannes Weinberger
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Raul Jimenez-Heredia
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Susanne Suessner
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Judith Sunzenauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Richard Weiss
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Stephan Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Christian Gabriel
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Martin Danzer
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
- * E-mail: (MD); (RO)
| | - Rainer Oberbauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- * E-mail: (MD); (RO)
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Schaller S, Weinberger J, Jimenez-Heredia R, Danzer M, Oberbauer R, Gabriel C, Winkler SM. ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data. BMC Bioinformatics 2015; 16:252. [PMID: 26264428 PMCID: PMC4531494 DOI: 10.1186/s12859-015-0687-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information. Results We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported. Conclusion IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0687-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanne Schaller
- University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. .,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria.
| | - Raul Jimenez-Heredia
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. .,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria.
| | - Martin Danzer
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria.
| | - Rainer Oberbauer
- Elisabethinen Hospital, Fadingerstrasse 1, Linz, 4020, Austria. .,Medical University of Vienna, Department of Nephrology, Spitalgasse 23, Vienna, 1090, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria.
| | - Stephan M Winkler
- University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria.
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