Performance in omics analyses of blood samples in long-term storage: Opportunities for the exploitation of existing biobanks in environmental health research

Environmental Health Perspectives

Volumn 121, Issue 4, 2013, Pages 480-487

  Hebels, Dennie G A J ^a   Georgiadis, Panagiotis ^b   Keun, Hector C ^c   Athersuch, Toby J ^c   Vineis, Paolo ^c   Vermeulen, Roel ^d   Portengen, Ützen ^d   Bergdahl, Ingvar A ^e   Hallmans, Göran ^e   Palli, Domenico ^f   Bendinelli, Benedetta ^f   Krogh, Vittorio ^g   Tumino, Rosario ^h   Sacerdote, Carlotta ^i,j   Panico, Salvatore ^k   Kleinjans, Jos C S ^a   de Kok, Theo M C M ^a   Smith, Martyn T ^l   Kyrtopoulos, Soterios A ^b  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b INSTITUTE OF BIOLOGY   (Greece)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d UTRECHT UNIVERSITY   (Netherlands)

^e UMEÅ UNIVERSITY   (Sweden)

^f Cancer Prevention and Research Institute   (Italy)

^g NATIONAL CANCER INSTITUTE   (Italy)

^h CIVILE M P AREZZO HOSPITAL   (Italy)

ⁱ Center for Cancer Prevention CPO Piemonte   (Italy)

^j Human Genetics Foundation   (Italy)

^k UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^l UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

Biomarkers; Epigenomics; Metabolomics; Metabonomics; Molecular epidemiology; Proteomics; Transcriptomics

Indexed keywords

BETA 2 MICROGLOBULIN; CITRIC ACID; CXCL1 CHEMOKINE; EDETIC ACID; GELATINASE B; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HEME OXYGENASE 1; HEPARIN; INTERLEUKIN 1BETA; INTERLEUKIN 2; INTERLEUKIN 6; INTERLEUKIN 8; LIQUID NITROGEN; PHOSPHOPROTEIN PHOSPHATASE 1; TAMSULOSIN; TRANSCRIPTOME;

ARTICLE; BLOOD SAMPLING; DNA ISOLATION; EPIGENETICS; GENE EXPRESSION; HUMAN; LONG TERM EXPOSURE; MASS SPECTROMETRY; MEDICAL RESEARCH; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; SPECTROPHOTOMETRY; STORAGE TEMPERATURE; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY;

ANTICOAGULANTS; BIOLOGICAL MARKERS; BIOLOGICAL SPECIMEN BANKS; ENVIRONMENTAL HEALTH; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; METABOLOMICS; RNA; SPECIMEN HANDLING; TIME FACTORS;

EID: 84875900573     PISSN: 00916765     EISSN: 15529924     Source Type: Journal    
DOI: 10.1289/ehp.1205657     Document Type: Article

References (19)

1. 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study. Int J Epidemiol 37(suppl 1):i31-i40.
2. Beekman JM, Reischl J, Henderson D, Bauer D, Ternes R, Peña C, et al. 2009. Recovery of microarray-quality RNA from frozen EDTA blood samples. J Pharmacol Toxicol Methods 59:44-49.
3. Bingham S, Riboli E. 2004. Diet and cancer-the European Prospective Investigation into Cancer and Nutrition. Nat Rev Cancer 4:206-215.
4. Chatziioannou A, Moulos P, Kolisis FN. 2009. Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB. BMC Bioinformatics 10: 354; doi:10.1186/1471-2105-10-354 [Online 27 October 2009].
5. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM. 2010. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11:587; doi:10.1186/1471-2105-11-587 [Online 30 November 2010].
6. Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N, et al. 2011. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatog raphy and liquid chromatography coupled to mass spectrometry. Nat Protoc 6:1060-1083.
7. Dunn WB, Broadhurst D, Ellis DI, Brown M, Halsall A, O'Hagan S, et al. 2008. A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols. Int J Epidemiol 37(suppl 1):i23-i30.
8. Ellinger-Ziegelbauer H, Aubrecht J, Kleinjans JC, Ahr HJ. 2009. Application of toxicogenomics to study mechanisms of genotoxicity and carcinogenicity. Toxicol Lett 186:36-44.
9. Ernst J, Bar-Joseph Z. 2006. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7:191; doi:10.1186/1471-2105-7-191 [Online 5 April 2006].
10. Hallmans G, Agren A, Johansson G, Johansson A, Stegmayr B, Jansson JH, et al. 2003. Cardiovascular disease and diabetes in the Northern Sweden Health and Disease Study Cohort-evaluation of risk factors and their interactions. Scand J Public Health Suppl 61:18-24.
11. Karlovich C, Duchateau-Nguyen G, Johnson A, McLoughlin P, Navarro M, Fleurbaey C, et al. 2009. A longitudinal study of gene expression in healthy individuals. BMC Med Genomics 2:33; doi:10.1186/1755-8794-2-33 [Online 7 June 2009].
12. Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA. 2006. The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med 147:126-132.
13. Lubin JH, Colt JS, Camann D, Davis S, Cerhan JR, Severson RK, et al. 2004. Epidemiologic evaluation of measurement data in the presence of detection limits. Environ Health Perspect 112:1691-1696.
14. Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G. 2011. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. BMC Res Notes 4:546; doi:10.1186/1756-0500-4-546 [19 December 2011].
15. McHale CM, Zhang L, Hubbard AE, Smith MT. 2010. Toxico genomic profiling of chemically exposed humans in risk assessment. Mutat Res 705:172-183
16. Rappaport SM, Smith MT. 2010. Environment and disease risks. Science 330:460-461.
17. Saberi-Hosnijeh F, Krop EJ, Scoccianti C, Krogh V, Palli D, Panico S, et al. 2010. Plasma cytokines and future risk of non-Hodgkin lymphoma (NHL): a case-control study nested in the Italian European Prospective Investigation into Cancer and Nutrition. Cancer Epidemiol Biomarkers Prev 19:1577-1584.
18. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, et al. 2006. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7:3; doi:10.1186/1471-2199-7-3 [Online 31 January 2006].
19. Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, et al. 2009. Development of a robust and repeatable UPLC-MS method for the long-term metabo lomic study of human serum. Anal Chem 81:1357-1364.