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Title: Sources of Pre-Analytical Variations in Yield of DNA Extracted from Blood Samples: Analysis of 50,000 DNA Samples in EPIC
Author: Caboux, Elodie
Lallemand, Christophe
Ferro, Gilles
Hémon, Bertrand
Mendy, Maimuna
Biessy, Carine
Sims, Matt
Wareham, Nicholas J.
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, María José
Skeie, Guri
Standahl Olsen, Karina
Lund, Eiliv
Bilbao, Roberto
Sala Serra, 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
Keywords: ADN
Issue Date: 13-Jul-2012
Publisher: Public Library of Science (PLoS)
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.
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It is part of: PLoS One, 2012, vol. 7, num. 7, p. e39821
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Appears in Collections:Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))

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