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

Elodie Caboux, Christophe Lallemand, Gilles Ferro, Bertrand Hémon, Maimuna Mendy, Carine Biessy, Matt Sims, Nick Wareham, Abigail Britten, Anne Boland, Amy Hutchinson, Afshan Siddiq, Paolo Vineis, Elio Riboli, Isabelle Romieu, Sabina Rinaldi, Marc J. Gunter, Petra H M Peeters, Yvonne T. van der Schouw, Ruth TravisH. Bas Bueno-de-Mesquita, Federico Canzian, Maria José Sánchez, Guri Skeie, Karina Standahl Olsen, Eiliv Lund, Roberto Bilbao, Núria Sala, Aurelio Barricarte, Domenico Palli, Carmen Navarro, Salvatore Panico, Maria Luisa Redondo, Silvia Polidoro, Laure Dossus, Marie Christine Boutron-Ruault, Françoise Clavel-Chapelon, Antonia Trichopoulou, Dimitrios Trichopoulos, Pagona Lagiou, Heiner Boeing, Eva Fisher, Rosario Tumino, Claudia Agnoli, Pierre Hainaut

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article numbere39821
JournalPLoS One
Volume7
Issue number7
DOIs
Publication statusPublished - Jul 13 2012

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Fingerprint

Dive into the research topics of 'Sources of pre-analytical variations in yield of DNA extracted from blood samples: Analysis of 50,000 DNA samples in EPIC'. Together they form a unique fingerprint.

Cite this