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Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

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dc.contributor.authorCaboux, Elodie
dc.contributor.authorLallemand, Christophe
dc.contributor.authorFerro, Gilles
dc.contributor.authorHémon, Bertrand
dc.contributor.authorMendy, Maimuna
dc.contributor.authorBiessy, Carine
dc.contributor.authorSims, Matt
dc.contributor.authorWareham, Nick
dc.contributor.authorBritten, Abigail
dc.contributor.authorBoland, Anne
dc.contributor.authorHutchinson, Amy
dc.contributor.authorSiddiq, Afshan
dc.contributor.authorVineis, Paolo
dc.contributor.authorRiboli, Elio
dc.contributor.authorRomieu, Isabelle
dc.contributor.authorRinaldi, Sabina
dc.contributor.authorGunter, Marc J
dc.contributor.authorPeeters, Petra H M
dc.contributor.authorvan der Schouw, Yvonne T
dc.contributor.authorTravis, Ruth
dc.contributor.authorBueno-de-Mesquita, H Bas
dc.contributor.authorCanzian, Federico
dc.contributor.authorSanchez-Perez, Maria-Jose
dc.contributor.authorSkeie, Guri
dc.contributor.authorOlsen, Karina Standahl
dc.contributor.authorLund, Eiliv
dc.contributor.authorBilbao, Roberto
dc.contributor.authorSala, Núria
dc.contributor.authorBarricarte, Aurelio
dc.contributor.authorPalli, Domenico
dc.contributor.authorNavarro, Carmen
dc.contributor.authorPanico, Salvatore
dc.contributor.authorRedondo, Maria Luisa
dc.contributor.authorPolidoro, Silvia
dc.contributor.authorDossus, Laure
dc.contributor.authorBoutron-Ruault, Marie Christine
dc.contributor.authorClavel-Chapelon, Françoise
dc.contributor.authorTrichopoulou, Antonia
dc.contributor.authorTrichopoulos, Dimitrios
dc.contributor.authorLagiou, Pagona
dc.contributor.authorBoeing, Heiner
dc.contributor.authorFisher, Eva
dc.contributor.authorTumino, Rosario
dc.contributor.authorAgnoli, Claudia
dc.contributor.authorHainaut, Pierre
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.es
dc.contributor.funderFunding: The study was funded by European Commission Research & Innovation DG project BBMRI (Biobanking and Biomolecular Resources Research Infrastructure,http://www.bbmri.eu), project number 212111 and by the Regular Budget of International Agency for Research on Cancer (IARC). DNA extraction data used in the study were generated as part of molecular epidemiological studies approved by the Steering Committee of the European Prospective Investigation into Cancer and Nutrition (EPIC, http://epic.iarc.fr). Detailed information about the funding of EPIC is available at http://epic.iarc.fr/funding.php. The funding agencies and organizations which provided funds for DNA extraction in specific EPIC studies were Imperial College London (ICL, BRCD study); Medical Research Council UK (MRC UK, EPHD study); European Community INTERACT project (through MRC Cambridge, UK, INT study, http://www.inter-act.eu); International Agency for Research on Cancer (IARC) and Imperial College London (ICL) (LUND study), EU FP6 Network of Excellence Environmental Cancer Risk, Nutrition and Individual Susceptibility (ECNIS, http:// www.ecnis.org); and Cancer Research UK (CRCUK) (LYMD study).
dc.date.accessioned2013-10-11T11:08:54Z
dc.date.available2013-10-11T11:08:54Z
dc.date.issued2012-07-13
dc.descriptionJournal Article; Multicenter Study; Research Support, Non-U.S. Gov't;es
dc.description.abstractThe 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.es
dc.description.versionYeses
dc.identifier.citationCaboux 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):e39821es
dc.identifier.doi10.1371/journal.pone.0039821
dc.identifier.essn1932-6203
dc.identifier.pmcPMC3396633
dc.identifier.pmid22808065
dc.identifier.urihttp://hdl.handle.net/10668/1328
dc.journal.titlePloS one
dc.language.isoen
dc.publisherPublic Library of Sciencees
dc.relation.publisherversionhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039821es
dc.rights.accessRightsopen access
dc.subjectFactores de Edades
dc.subjectAncianoes
dc.subjectÍndice de Masa Corporales
dc.subjectADNes
dc.subject.meshMedical Subject Headings::Health Care::Health Care Quality, Access, and Evaluation::Quality of Health Care::Epidemiologic Factors::Age Factorses
dc.subject.meshMedical Subject Headings::Named Groups::Persons::Age Groups::Adult::Agedes
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Physical Examination::Body Constitution::Body Weights and Measures::Body Mass Indexes
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Case-Control Studieses
dc.subject.meshMedical Subject Headings::Chemicals and Drugs::Nucleic Acids, Nucleotides, and Nucleosides::Nucleic Acids::DNAes
dc.subject.meshMedical Subject Headings::Anatomy::Cells::Blood Cells::Erythrocyteses
dc.subject.meshMedical Subject Headings::Check Tags::Femalees
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Genotyping Techniqueses
dc.subject.meshMedical Subject Headings::Diseases::Pathological Conditions, Signs and Symptoms::Pathologic Processes::Hemolysises
dc.subject.meshMedical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humanses
dc.subject.meshMedical Subject Headings::Anatomy::Cells::Blood Cells::Leukocytes::Leukocytes, Mononucleares
dc.subject.meshMedical Subject Headings::Check Tags::Malees
dc.subject.meshMedical Subject Headings::Named Groups::Persons::Age Groups::Adult::Middle Agedes
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Errors::Observer Variationes
dc.subject.meshMedical 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 Studieses
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Research Design::Reproducibility of Resultses
dc.subject.meshMedical Subject Headings::Health Care::Health Care Quality, Access, and Evaluation::Quality of Health Care::Epidemiologic Factors::Sex Factorses
dc.subject.meshMedical Subject Headings::Psychiatry and Psychology::Behavior and Behavior Mechanisms::Behavior::Habits::Smokinges
dc.subject.meshMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Diagnosis::Diagnostic Techniques and Procedures::Clinical Laboratory Techniques::Specimen Handlinges
dc.subject.meshMedical Subject Headings::Named Groups::Persons::Age Groups::Adultes
dc.titleSources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.es
dc.typeresearch article
dc.type.hasVersionVoR
dspace.entity.typePublication

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