TY - JOUR
T1 - Sources of pre-analytical variations in yield of DNA extracted from blood samples
T2 - Analysis of 50,000 DNA samples in EPIC
AU - Caboux, Elodie
AU - Lallemand, Christophe
AU - Ferro, Gilles
AU - Hémon, Bertrand
AU - Mendy, Maimuna
AU - Biessy, Carine
AU - Sims, Matt
AU - Wareham, Nick
AU - Britten, Abigail
AU - Boland, Anne
AU - Hutchinson, Amy
AU - Siddiq, Afshan
AU - Vineis, Paolo
AU - Riboli, Elio
AU - Romieu, Isabelle
AU - Rinaldi, Sabina
AU - Gunter, Marc J.
AU - Peeters, Petra H M
AU - van der Schouw, Yvonne T.
AU - Travis, Ruth
AU - Bueno-de-Mesquita, H. Bas
AU - Canzian, Federico
AU - Sánchez, Maria José
AU - Skeie, Guri
AU - Olsen, Karina Standahl
AU - Lund, Eiliv
AU - Bilbao, Roberto
AU - Sala, Núria
AU - Barricarte, Aurelio
AU - Palli, Domenico
AU - Navarro, Carmen
AU - Panico, Salvatore
AU - Redondo, Maria Luisa
AU - Polidoro, Silvia
AU - Dossus, Laure
AU - Boutron-Ruault, Marie Christine
AU - Clavel-Chapelon, Françoise
AU - Trichopoulou, Antonia
AU - Trichopoulos, Dimitrios
AU - Lagiou, Pagona
AU - Boeing, Heiner
AU - Fisher, Eva
AU - Tumino, Rosario
AU - Agnoli, Claudia
AU - Hainaut, Pierre
PY - 2012/7/13
Y1 - 2012/7/13
N2 - 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.
AB - 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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U2 - 10.1371/journal.pone.0039821
DO - 10.1371/journal.pone.0039821
M3 - Article
C2 - 22808065
AN - SCOPUS:84863764712
VL - 7
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 7
M1 - e39821
ER -