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http://hdl.handle.net/10668/1328| Title: | Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC. |
| Authors: | Caboux, Elodie Lallemand, Christophe Ferro, Gilles Hémon, Bertrand Mendy, Maimuna Biessy, Carine Sims, Matt Wareham, Nick Britten, Abigail Boland, Anne Hutchinson, Amy Siddiq, Afshan Vineis, Paolo Riboli, Elio Romieu, Isabelle Rinaldi, Sabina Gunter, Marc J Peeters, Petra H M van der Schouw, Yvonne T Travis, Ruth Bueno-de-Mesquita, H Bas Canzian, Federico Sánchez, Maria-José Skeie, Guri Olsen, Karina Standahl Lund, Eiliv Bilbao, Roberto Sala, Núria Barricarte, Aurelio Palli, Domenico Navarro, Carmen Panico, Salvatore Redondo, Maria Luisa Polidoro, Silvia Dossus, Laure Boutron-Ruault, Marie Christine Clavel-Chapelon, Françoise Trichopoulou, Antonia Trichopoulos, Dimitrios Lagiou, Pagona Boeing, Heiner Fisher, Eva Tumino, Rosario Agnoli, Claudia Hainaut, Pierre |
| metadata.dc.contributor.authoraffiliation: | [Caboux,E; Lallemand,C; Ferro,G; Hémon,B; Mendy,M; Biessy,C; Romieu,I; Rinaldi,S] International Agency for Research on Cancer, Lyon, France. [Sims,M; Wareham,N; Britten,A] Medical Research Council (MRC) Epidemiology Unit, Addenbrooke’s Hospital, Cambridge, United Kingdom. [Boland,A] Centre National de Génotypage, Institut Génomique, Commissariat à l’énergie Atomique, Evry, France. [Hutchinson,A] Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America. [Siddiq,A; Vineis,P; Riboli,E; Gunter,MJ; Peeters,PHM] Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom. [Peeters,PHM; Schouw,T] Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands. [Travis,R[ Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom. [Bueno-de-Mesquita,HB] National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands. Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands. [Canzian,F] Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany. [Sánchez,M] Andalusian School of Public Health, Granada (Spain) and CIBER de Epidemiología y Salud Pública (CIBERESP), Granada, Spain. [Skeie,G; Olsen,KS; Lund,E] Institute of Community Medicine, University of Tromsø, Tromsø, Norway. [Bilbao,R] Fundación Vasca de Innovación e Investigación Sanitarias, Sondika, Bizkaia, Spain. [Sala,N] Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology (ICO)-IDIBELL, Barcelona, Spain. [Barricarte,A] Navarre Public Health Institute, Pamplona, Spain. [Barricarte,A; Navarro,C] Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública-CIBERESP), Madrid, Spain. [Hainaut,P] International Prevention Research Institute, Lyon, France. [Palli,D] Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute – ISPO, Florence, Italy. [Navarro,C] Department of Epidemiology, Regional Health Authority, Murcia, Spain. [Panico,S] Department of clinical and experimental medicine, Federico ii University, Naples, Italy. [Redondo,ML] Public Health Directorate, Asturias, Spain. [Polidoro,S] Human Genetics Foundation-HuGeF, Turin, Italy. [Dossus,L; Boutron-Ruault,MC; Clavel-Chapelon,F] INSERM U1018, Gustave Roussy Institute, Paris South University, Villejuif, France. [Trichopoulou,A; Lagiou,P] Department of Hygiene, Epidemiology and Medical Statistics, Medical School, World Health Organization (WHO) Collaborating Center for Food and Nutrition Policies, University of Athens, Goudi, Athens, Greece. [Trichopoulou,A; Trichopoulos,D] Hellenic Health Foundation, Athens, Greece. [Trichopoulos,D; Lagiou,P] Department of Epidemiology, Harvard School of Public Health, Massachusetts, Boston, United States of America. Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece. [Boeing,H] Potsdam-Rehbrücke Department of Epidemiology, German Institute of Human Nutrition (DIfE), Nuthetal, Germany. [Fisher,E] Administrative Office of the Commission on Genetic Testing Robert Koch-Institute, Berlin, Germany. [Tumino,R] Cancer Registry and Histopathology Unit, ‘‘Civile M. P. Arezzo’’ Hospital, Ragusa, Italy. [Agnoli,C] Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy. |
| Keywords: | Factores de Edad;Anciano;Índice de Masa Corporal;ADN |
| metadata.dc.subject.mesh: | Medical Subject Headings::Health Care::Health Care Quality, Access, and Evaluation::Quality of Health Care::Epidemiologic Factors::Age Factors Medical Subject Headings::Named Groups::Persons::Age Groups::Adult::Aged Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Physical Examination::Body Constitution::Body Weights and Measures::Body Mass Index Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Case-Control Studies Medical Subject Headings::Chemicals and Drugs::Nucleic Acids, Nucleotides, and Nucleosides::Nucleic Acids::DNA Medical Subject Headings::Anatomy::Cells::Blood Cells::Erythrocytes Medical Subject Headings::Check Tags::Female Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Genotyping Techniques Medical Subject Headings::Diseases::Pathological Conditions, Signs and Symptoms::Pathologic Processes::Hemolysis Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans Medical Subject Headings::Anatomy::Cells::Blood Cells::Leukocytes::Leukocytes, Mononuclear Medical Subject Headings::Check Tags::Male Medical Subject Headings::Named Groups::Persons::Age Groups::Adult::Middle Aged Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Errors::Observer Variation Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Cohort Studies::Longitudinal Studies::Prospective Studies Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Research Design::Reproducibility of Results Medical Subject Headings::Health Care::Health Care Quality, Access, and Evaluation::Quality of Health Care::Epidemiologic Factors::Sex Factors Medical Subject Headings::Psychiatry and Psychology::Behavior and Behavior Mechanisms::Behavior::Habits::Smoking Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Clinical Laboratory Techniques::Specimen Handling Medical Subject Headings::Named Groups::Persons::Age Groups::Adult |
| Issue Date: | 13-Jul-2012 |
| Publisher: | Public Library of Science |
| Citation: | Caboux E, Lallemand C, Ferro G, Hémon B, Mendy M, Biessy C, et al. Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC. PLoS ONE; 7(7):e39821 |
| Abstract: | The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies. |
| Description: | Journal Article; Multicenter Study; Research Support, Non-U.S. Gov't; |
| URI: | http://hdl.handle.net/10668/1328 |
| metadata.dc.relation.publisherversion: | http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039821 |
| metadata.dc.identifier.doi: | 10.1371/journal.pone.0039821 |
| ISSN: | 1932-6203 (Online) |
| Appears in Collections: | 01- Artículos - EASP. Escuela Andaluza de Salud Pública |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| Caboux_SourcesOfPre.pdf | 183,41 kB | Adobe PDF | View/Open |
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