BioSHaRE: Biosample quality for omics downstream analysis - Gabriele Anton - HMGU
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Transcript of BioSHaRE: Biosample quality for omics downstream analysis - Gabriele Anton - HMGU
Biosample quality for OMICs downstreamanalysis
Gabriele AntonMilan, 2015
Standardization of Sample Handling
Literature review
Best practices of
participating cohorts
and experts
within the consortium
Scientific research
Life cycle of a biospecimen
Végvári A, Welinder C, Lindberg H, Fehniger TE, Marko-Varga G - (2011)
The patient
Fasting vs. non-fasting
The patient – fasting status
Variation in metabolites
during fasting and subsequent
SLD (standard liquid diet)
+ interindividual variation
Krug et al. 2012
The patient
Fasting vs. non-fasting
Sex, age, BMI
Lifestyle (long-term, short-term prior to sampling,
e.g heavy physical activity, alcohol consumption)
The patient – alcohol consumption
Same metabolites affected
in atherosclerosis,
inflammatory diseases
or ischaemia → correction
necessary
Jaremek et al. 2013
The patient
Fasting vs. non-fasting
Sex, age, BMI
Lifestyle (long-term, short-term prior to sampling,
e.g heavy physical activity, alcohol consumption)
Pregnancy
Menstrual cycle
Medication (e.g. surgery patients)
Documentation!!!
Sampling
Decision on matrix (e.g. plasma vs. serum)
Sampling
Yu et al, 2011
Concentration differences
in metabolites
between plasma and serum
samples of the same probands
Sampling
Decision on matrix (e.g. plasma vs. serum)
Position of the proband, resting time before sampling,
Clamping, manipulations (warmth, pumping) (blood)
Location for sampling (tissue specificity of e.g. epigenetic marks)
Disinfection of sampling site
Sampling - disinfection
Van der Sar et al, 2015
Variable
Ethanol signal
in CSF samples
measured by
H-NMR
metabolomics
Sampling
Position of the proband, resting time before sampling,
Clamping, manipulations (warmth, pumping) (blood)
Location for sampling (tissue specificity of e.g. epigenetic marks)
Disinfection of sampling site
Collection devices, additives, order of tubes (tubes with additives last)
Sampling – device
Breier et al, 2014
Difference in Methionine
Sulfoxide between serum
tubes with clotting
activator and gel-barrier tubes
Sampling
Position of the proband, resting time before sampling,
Clamping, manipulations (warmth, pumping) (blood)
Location for sampling (tissue specificity of e.g. epigenetic marks)
Disinfection of sampling site
Collection devices, additives, order of tubes (tubes with additives last)
Standardization and Documentation!!!
Sample processing
Time:
Blood, urine: until centrifugation cells still in contact with liquid, artefacts
by cell rupture; avoid harsh treatment like shaking, low temperatures)
Processing after centrifugation: cooling, fast sample handling
Sample processing – Time/Temperature
Breier et al, 2014
Changes in plasma
metabolites due to
handling time
and temperature
Sample processing – Time/Temperature
Ratio of total
lysophosphatidylcholines to
total phosphatidylcholines
in serum samples stored at
different temperatures
Anton et al, 2015
Sample processing – Time/Temperature
Anton et al, 2015
Marker for prolonged
room temperature
exposure
Sample processing
Time:
Blood, urine: until centrifugation cells still in contact with liquid, artefacts
by cell rupture; avoid harsh treatment like shaking, low temperatures)
Processing after centrifugation: cooling, fast sample handling
Tissue: warm and cold ischemia time, type of conservation
Standardization and Documentation!!!
Sample processing
Processing requirements depend on desired downstream analysis:
DNA quite stable (but: epigenetics?),
proteins and metabolites very variable stability
RNA rather instable
For biobanked samples markers can help to take decisions on
possible downstream applications
Sample Transport
TimeTemperatureUse loggers to document conditions
Documentation!!!
Sample Storage
Liquid samples: small aliquots to avoid freeze-thaw
Temperature: liquid nitrogen vs. -80°C ?
New solutions for room temperature storage of e.g DNA
Summary
Use standardization as far as possible, especially
for multi-center studies
Good documentation of all steps of biosample generation
very important (SPREC)
For biobanked samples, markers for desired downstream
analysis necessary (quality control)
Acknowledgements
The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 261433 (Biobank Standardisation and Harmonisation for Research Excellence in the European Union - BioSHaRE-EU)
Participating biobanks, especially: Life Lines - UMGC, HUNT, KORA, German National Cohort and their staff
BioSHaRE collaborators
Questions?
Gabriele Anton
Research Unit of Molecular Epidemiology (AME)Institute of Epidemiology IIGerman Research Center for Environmental Health
[email protected]://www.helmholtz-muenchen.de/ame