Abstract
Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at-80°C or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of tim-in-storage was observed in samples stored over a period of 13-17 years. Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.
| Original language | English |
|---|---|
| Pages (from-to) | 480-487 |
| Number of pages | 8 |
| Journal | Environmental Health Perspectives |
| Volume | 121 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - Apr 2013 |
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Keywords
- Biomarkers
- Epigenomics
- Metabolomics
- Metabonomics
- Molecular epidemiology
- Proteomics
- Transcriptomics
ASJC Scopus subject areas
- Health, Toxicology and Mutagenesis
- Public Health, Environmental and Occupational Health
Cite this
Performance in omics analyses of blood samples in long-term storage : Opportunities for the exploitation of existing biobanks in environmental health research. / Hebels, Dennie G A J; Georgiadis, Panagiotis; Keun, Hector C.; Athersuch, Toby J.; Vineis, Paolo; Vermeulen, Roel; Portengen, Ützen; Bergdahl, Ingvar A.; Hallmans, Göran; Palli, Domenico; Bendinelli, Benedetta; Krogh, Vittorio; Tumino, Rosario; Sacerdote, Carlotta; Panico, Salvatore; Kleinjans, Jos C S; de Kok, Theo M C M; Smith, Martyn T.; Kyrtopoulos, Soterios A.
In: Environmental Health Perspectives, Vol. 121, No. 4, 04.2013, p. 480-487.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Performance in omics analyses of blood samples in long-term storage
T2 - Opportunities for the exploitation of existing biobanks in environmental health research
AU - Hebels, Dennie G A J
AU - Georgiadis, Panagiotis
AU - Keun, Hector C.
AU - Athersuch, Toby J.
AU - Vineis, Paolo
AU - Vermeulen, Roel
AU - Portengen, Ützen
AU - Bergdahl, Ingvar A.
AU - Hallmans, Göran
AU - Palli, Domenico
AU - Bendinelli, Benedetta
AU - Krogh, Vittorio
AU - Tumino, Rosario
AU - Sacerdote, Carlotta
AU - Panico, Salvatore
AU - Kleinjans, Jos C S
AU - de Kok, Theo M C M
AU - Smith, Martyn T.
AU - Kyrtopoulos, Soterios A.
PY - 2013/4
Y1 - 2013/4
N2 - Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at-80°C or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of tim-in-storage was observed in samples stored over a period of 13-17 years. Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.
AB - Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at-80°C or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of tim-in-storage was observed in samples stored over a period of 13-17 years. Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.
KW - Biomarkers
KW - Epigenomics
KW - Metabolomics
KW - Metabonomics
KW - Molecular epidemiology
KW - Proteomics
KW - Transcriptomics
UR - http://www.scopus.com/inward/record.url?scp=84875900573&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84875900573&partnerID=8YFLogxK
U2 - 10.1289/ehp.1205657
DO - 10.1289/ehp.1205657
M3 - Article
VL - 121
SP - 480
EP - 487
JO - Environmental Health Perspectives
JF - Environmental Health Perspectives
SN - 0091-6765
IS - 4
ER -