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.
Highlights
In recent years, the use of automated methods for DNA extraction from venous blood samples has generated large amounts of material for the mapping of genetic variations that underlie susceptibility to common human diseases [1,2]
We have assessed the yield of DNA extracted from approximately 50,000 individual samples collected from individuals in the European Prospective Investigation into Cancer over a period of 5 years, and we have examined the impact of a range of pre-analytical variables on the amount of DNA generated using an automated DNA extraction system
Study Design This study has used data on DNA extraction processed at International Agency for Research on Cancer (IARC)
Summary
The use of automated methods for DNA extraction from venous blood samples has generated large amounts of material for the mapping of genetic variations that underlie susceptibility to common human diseases [1,2]. The European Prospective Investigation into Cancer (EPIC) is a long-term, multi-centric prospective cohort study with a focus on nutrition, investigating the etiology of cancers at various sites as well as other forms of chronic diseases in relation to diet and lifestyle [5]. The study started in 1992 with 17 research centers in seven core EPIC countries (France, Germany, Greece, Italy, The Netherlands, Spain and the UK). The most recent follow-up period for cancer incidence was performed between 2004 and 2010, and has identified 50,336 subjects who developed cancer after cohort enrollment (incident cases). These cancers cover a very wide range of anatomic sites and morphologies
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