BioSHaRE conference July 28th, 2015, Milan - Latest tools and services for data sharing Stream 3: Study application and results Contact info: Dr. Gabriele Anton Helmholtz Zentrum München, Germany gabriele.anton@helmholtz-muenchen.de Keywords: biobank, bioshare, cohort, standardisation sample handling

1. Biosample quality for OMICs downstream
analysis
Gabriele Anton
Milan, 2015

2. Standardization of Sample Handling
 Literature review
 Best practices of
participating cohorts
and experts
within the consortium
 Scientific research

3. Life cycle of a biospecimen
Végvári A, Welinder C, Lindberg H, Fehniger TE, Marko-Varga G - (2011)

4. The patient
 Fasting vs. non-fasting

5. The patient – fasting status
Variation in metabolites
during fasting and subsequent
SLD (standard liquid diet)
+ interindividual variation
Krug et al. 2012

6. The patient
 Fasting vs. non-fasting
 Sex, age, BMI
 Lifestyle (long-term, short-term prior to sampling,
e.g heavy physical activity, alcohol consumption)

7. The patient – alcohol consumption
Same metabolites affected
in atherosclerosis,
inflammatory diseases
or ischaemia → correction
necessary
Jaremek et al. 2013

8. 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!!!

9. Sampling
 Decision on matrix (e.g. plasma vs. serum)

10. Sampling
Yu et al, 2011
Concentration differences
in metabolites
between plasma and serum
samples of the same probands

11. 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

12. Sampling - disinfection
Van der Sar et al, 2015
Variable
Ethanol signal
in CSF samples
measured by
H-NMR
metabolomics

13. 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)

14. Sampling – device
Breier et al, 2014
Difference in Methionine
Sulfoxide between serum
tubes with clotting
activator and gel-barrier tubes

15. 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!!!

16. 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

17. Sample processing – Time/Temperature
Breier et al, 2014
Changes in plasma
metabolites due to
handling time
and temperature

18. Sample processing – Time/Temperature
Ratio of total
lysophosphatidylcholines to
total phosphatidylcholines
in serum samples stored at
different temperatures
Anton et al, 2015

19. Sample processing – Time/Temperature
Anton et al, 2015
Marker for prolonged
room temperature
exposure

20. 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!!!

21. 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

22. Sample Transport
Time
Temperature
Use loggers to document conditions
Documentation!!!

23. 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

24. 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)

25. 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

26. Questions?
Gabriele Anton
Research Unit of Molecular Epidemiology (AME)
Institute of Epidemiology II
German Research Center for Environmental Health
gabriele.anton@helmholtz-muenchen.de
http://www.helmholtz-muenchen.de/ame