Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.
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.
International Agency for Research on Cancer, Lyon, France.
Elodie
E
Caboux
Christophe
C
Lallemand
Gilles
G
Ferro
Bertrand
B
Hémon
Maimuna
M
Mendy
Carine
C
Biessy
Matt
M
Sims
Nick
N
Wareham
Abigail
A
Britten
Anne
A
Boland
Amy
A
Hutchinson
Afshan
A
Siddiq
Paolo
P
Vineis
Elio
E
Riboli
Isabelle
I
Romieu
Sabina
S
Rinaldi
Marc J
MJ
Gunter
Petra H M
PH
Peeters
Yvonne T
YT
van der Schouw
Ruth
R
Travis
H Bas
HB
Bueno-de-Mesquita
Federico
F
Canzian
Maria-José
MJ
Sánchez
Guri
G
Skeie
Karina Standahl
KS
Olsen
Eiliv
E
Lund
Roberto
R
Bilbao
Núria
N
Sala
Aurelio
A
Barricarte
Domenico
D
Palli
Carmen
C
Navarro
Salvatore
S
Panico
Maria Luisa
ML
Redondo
Silvia
S
Polidoro
Laure
L
Dossus
Marie Christine
MC
Boutron-Ruault
Françoise
F
Clavel-Chapelon
Antonia
A
Trichopoulou
Dimitrios
D
Trichopoulos
Pagona
P
Lagiou
Heiner
H
Boeing
Eva
E
Fisher
Rosario
R
Tumino
Claudia
C
Agnoli
Pierre
P
Hainaut
D000328:Adult; D000367:Age Factors; D000368:Aged; D015992:Body Mass Index; D016022:Case-Control Studies; D004247:DNA / Q000097:blood / Q000302:isolation & purification*; D004912:Erythrocytes / Q000737:chemistry; D005260:Female; D060005:Genotyping Techniques; D006461:Hemolysis; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000737:chemistry*; D008297:Male; D008875:Middle Aged; D015588:Observer Variation; D011446:Prospective Studies; D015203:Reproducibility of Results; D012737:Sex Factors; D012907:Smoking; D013048:Specimen Handling / Q000592:standards*
D004247:DNA