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

2.50
Hdl Handle:
http://hdl.handle.net/10146/296982
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
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.
Citation:
PLoS ONE 2012, 7 (7):e39821
Journal:
PloS one
Issue Date:
2012
URI:
http://hdl.handle.net/10146/296982
DOI:
10.1371/journal.pone.0039821
PubMed ID:
22808065
Additional Links:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039821; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396633/
Type:
Article
Language:
en
ISSN:
1932-6203
Sponsors:
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).
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorCaboux, Elodieen_GB
dc.contributor.authorLallemand, Christopheen_GB
dc.contributor.authorFerro, Gillesen_GB
dc.contributor.authorHémon, Bertranden_GB
dc.contributor.authorMendy, Maimunaen_GB
dc.contributor.authorBiessy, Carineen_GB
dc.contributor.authorSims, Matten_GB
dc.contributor.authorWareham, Nicken_GB
dc.contributor.authorBritten, Abigailen_GB
dc.contributor.authorBoland, Anneen_GB
dc.contributor.authorHutchinson, Amyen_GB
dc.contributor.authorSiddiq, Afshanen_GB
dc.contributor.authorVineis, Paoloen_GB
dc.contributor.authorRiboli, Elioen_GB
dc.contributor.authorRomieu, Isabelleen_GB
dc.contributor.authorRinaldi, Sabinaen_GB
dc.contributor.authorGunter, Marc J.en_GB
dc.contributor.authorPeeters, Petra H. M.en_GB
dc.contributor.authorvan der Schouw, Yvonne T.en_GB
dc.contributor.authorTravis, Ruthen_GB
dc.contributor.authorBueno-de-Mesquita, H Basen_GB
dc.contributor.authorCanzian, Federicoen_GB
dc.contributor.authorSánchez, Maria-Joséen_GB
dc.contributor.authorSkeie, Gurien_GB
dc.contributor.authorOlsen, Karina Standahlen_GB
dc.contributor.authorLund, Eiliven_GB
dc.contributor.authorBilbao, Robertoen_GB
dc.contributor.authorSala, Núriaen_GB
dc.contributor.authorBarricarte, Aurelioen_GB
dc.contributor.authorPalli, Domenicoen_GB
dc.contributor.authorNavarro, Carmenen_GB
dc.contributor.authorPanico, Salvatoreen_GB
dc.contributor.authorRedondo, Maria Luisaen_GB
dc.contributor.authorPolidoro, Silviaen_GB
dc.contributor.authorDossus, Laureen_GB
dc.contributor.authorBoutron-Ruault, Marie Christineen_GB
dc.contributor.authorClavel-Chapelon, Françoiseen_GB
dc.contributor.authorTrichopoulou, Antoniaen_GB
dc.contributor.authorTrichopoulos, Dimitriosen_GB
dc.contributor.authorLagiou, Pagonaen_GB
dc.contributor.authorBoeing, Heineren_GB
dc.contributor.authorFisher, Evaen_GB
dc.contributor.authorTumino, Rosarioen_GB
dc.contributor.authorAgnoli, Claudiaen_GB
dc.contributor.authorHainaut, Pierreen_GB
dc.date.accessioned2013-07-24T10:18:41Z-
dc.date.available2013-07-24T10:18:41Z-
dc.date.issued2012-
dc.identifier.citationPLoS ONE 2012, 7 (7):e39821en_GB
dc.identifier.issn1932-6203-
dc.identifier.pmid22808065-
dc.identifier.doi10.1371/journal.pone.0039821-
dc.identifier.urihttp://hdl.handle.net/10146/296982-
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.en_GB
dc.description.sponsorshipThe 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).en_GB
dc.language.isoenen
dc.relation.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039821en_GB
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396633/en_GB
dc.rightsArchived with thanks to PloS oneen_GB
dc.subjectCancer risken_GB
dc.subjectNutrition Surveysen_GB
dc.subjectDNAen_GB
dc.subjectGenotypingen_GB
dc.subjectLeukocytes, Mononuclearen_GB
dc.subjectHumansen_GB
dc.subjectCase-Control Studiesen_GB
dc.subjectProspective Studiesen_GB
dc.subject.meshAdult-
dc.subject.meshAge Factors-
dc.subject.meshAged-
dc.subject.meshBody Mass Index-
dc.subject.meshCase-Control Studies-
dc.subject.meshDNA-
dc.subject.meshErythrocytes-
dc.subject.meshFemale-
dc.subject.meshGenotyping Techniques-
dc.subject.meshHemolysis-
dc.subject.meshHumans-
dc.subject.meshLeukocytes, Mononuclear-
dc.subject.meshMale-
dc.subject.meshMiddle Aged-
dc.subject.meshObserver Variation-
dc.subject.meshProspective Studies-
dc.subject.meshReproducibility of Results-
dc.subject.meshSex Factors-
dc.subject.meshSmoking-
dc.subject.meshSpecimen Handling-
dc.titleSources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.en
dc.typeArticleen
dc.identifier.journalPloS oneen_GB

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