Abstract
Background
Population-based biorepositories are important resources, but sample handling can affect data quality.
Objective
Identify metabolites of value for clinical investigations despite extended postcollection freezing delays, using protocols representing a California mid-term pregnancy biobank.
Methods
Blood collected from non-pregnant healthy female volunteers (n = 20) underwent three handling protocols after 30 min clotting at room temperature: (1) ideal—samples frozen (− 80 °C) within 2 h of collection; (2) delayed freezing—samples held at room temperature for 3 days, then 4 °C for 9 days, the median times for biobank samples, and then frozen; (3) delayed freezing with freeze–thaw—the delayed freezing protocol with a freeze–thaw cycle simulating retrieved sample sub-aliquoting. Mass spectrometry-based untargeted metabolomic analyses of primary metabolism and complex lipids and targeted profiling of oxylipins, endocannabinoids, ceramides/sphingoid-bases, and bile acids were performed. Metabolite concentrations and intraclass correlation coefficients (ICC) were compared, with the ideal protocol as the reference.
Results
Sixty-two percent of 428 identified compounds had good to excellent ICCs, a metric of concordance between measurements of samples handled with the different protocols. Sphingomyelins, phosphatidylcholines, cholesteryl esters, triacylglycerols, bile acids and fatty acid diols were the least affected by non-ideal handling, while sugars, organic acids, amino acids, monoacylglycerols, lysophospholipids, N-acylethanolamides, polyunsaturated fatty acids, and numerous oxylipins were altered by delayed freezing. Freeze–thaw effects were assay-specific with lipids being most stable.
Conclusions
Despite extended post-collection freezing delays characteristic of some biobanks of opportunistically collected clinical samples, numerous metabolomic compounds had both stable levels and good concordance.
Abbreviations
- CBP:
-
California Biobank Program
- PM:
-
Primary metabolism
- CL:
-
Complex lipids
- TA:
-
Targeted assays
- IP:
-
Ideal protocol
- DFP:
-
Delayed freezing protocol
- DFFTP:
-
Delayed freezing with freeze–thaw protocol
- CE:
-
Cholesteryl esters
- PC:
-
Phosphatidylcholines
- PE:
-
Phosphotidylethanolamines
- LPC:
-
Lysophosphotidylcholines
- LPE:
-
Lysophosphotidylethanolamines
- Cers:
-
Ceramides
- SM:
-
Sphingomyelins
- TAG:
-
Triacylglycerides
- DAG:
-
Diacylglycerols
- MAG:
-
Monoacylglycerols
- ICC:
-
Intraclass correlation coefficients
- AA:
-
Amino acids
- NEFA:
-
Non-esterified fatty acids
- NAE:
-
N-Acylethanolamides
- PUFA:
-
Polyunsaturated fatty acids
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Acknowledgements
This research was supported by: the March of Dimes Foundation Prematurity Research Center at Stanford University School of Medicine (22-FY18-808; GMS, DKS); the Lucile Packard Foundation for Children’s Health; the Stanford Child Health Research Institute, the National Institutes of Health (UL1-TR001085, [SLC, CM, MH, GMS, DKS]; U24-DK097154, [OF, JWN]) and the USDA (2032-51530-022-00D, JWN). The USDA is an equal opportunity employer and provider.
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Project design—SLC, TLP, GMS, DKS, JWN. Performed research—MRL, TS, MH, RW, TLP, OF, JWN. Analyzed data—MRL, CM, KB, JWN. Wrote paper—MRL, SLC, LR, JWN. Reviewed manuscript—all authors.
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This study was approved by Stanford University IRB and conducted in accordance with the ethical standards set forth by the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards.
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La Frano, M.R., Carmichael, S.L., Ma, C. et al. Impact of post-collection freezing delay on the reliability of serum metabolomics in samples reflecting the California mid-term pregnancy biobank. Metabolomics 14, 151 (2018). https://doi.org/10.1007/s11306-018-1450-9
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DOI: https://doi.org/10.1007/s11306-018-1450-9