Copyright © 2009
Proprietary & Confidential
Copyright © 2013 - Proprietary & Confidential
DO YOU SPEAK BIOBANK?
Biosamples...
Copyright © 2013 - Proprietary & Confidential
Do you speak biobank?
sprechen Sie Biobank? hablas biobanco
你说生物资料库
parlez-v...
Copyright © 2013 - Proprietary & Confidential
….babel as a confusion of languages?
Copyright © 2013 - Proprietary & Confidential
Biosamples & Babel [Fish]*
*Hitchhiker’s guide to the galaxy
Universal Langu...
Copyright © 2013 - Proprietary & Confidential
Why do we care?
Copyright © 2013 - Proprietary & Confidential
SAMPLE
POWER
I could
help cure
cancer
I could help
cure
Parkinsons
I could
h...
Copyright © 2013 - Proprietary & Confidential
HIGH QUALITY
HIGHLY ANNOTATED
CONSENTED
PATIENT LINKED
SAMPLE
Copyright © 2013 - Proprietary & Confidential
Patients Samples Biomarkers New drugs
New targeted therapies
Copyright © 2013 - Proprietary & Confidential
The vision of personalized medicine..
Personalized
medicine
Externalization
...
Copyright © 2013 - Proprietary & Confidential
“… that have access to millions
of highly annotated
biospecimens with clear
...
Copyright © 2013 - Proprietary & Confidential
Access to more and more samples &
data
Thousands of trials
Thousands of pati...
Copyright © 2013 - Proprietary & Confidential
And more…
Disease specific biobanks
Patient registries
Hospital/Institute bi...
Copyright © 2013 - Proprietary & Confidential
Operating environment in flux
Limiting the potential for use of samples and ...
Copyright © 2013 - Proprietary & Confidential
Internet of things
Copyright © 2013 - Proprietary & Confidential
Biobank of things
Copyright © 2013 - Proprietary & Confidential
NO
UNIVERSAL
LANGUAGE
Ich helfen
könnte
Krebs heilen
Je pourrais
aider à gué...
Copyright © 2013 - Proprietary & Confidential
Why do we need a universal language?
Copyright © 2013 - Proprietary & Confidential
We want to ask questions!
Patient Profile
DCIS
T size>1cm, ER+, HER2/neu+, N...
Copyright © 2013 - Proprietary & Confidential
Questions are in depth
Copyright © 2013 - Proprietary & Confidential
Questions span domains
Multiple data
sources
Domain expertise
More data
sour...
Copyright © 2013 - Proprietary & Confidential
General Barriers to the Biobank of
Things
Future
Biomedical
Research
Multipl...
Copyright © 2013 - Proprietary & Confidential
How do we get there?
Copyright © 2013 - Proprietary & Confidential
Today, focus in on the data
Future
Biomedical
Research
Multiple
disparate, d...
Copyright © 2013 - Proprietary & Confidential
Harmonization
Meaning
Copyright © 2013 - Proprietary & Confidential
Multiple, disparate data sources
SEP
22
Sample tracking and sample storage d...
Copyright © 2013 - Proprietary & Confidential
Sometimes feels like this…
Copyright © 2013 - Proprietary & Confidential
Harmonization of disparate data
A hub of harmonized
information linking pati...
Copyright © 2013 - Proprietary & Confidential
Variety of standards/best practices
Biobanking best practices
Biobanking IT ...
Copyright © 2013 - Proprietary & Confidential
Variety of biobanking standards/best
practices
ISBER, NCI, OECD, BBMRI, CAP
...
Copyright © 2013 - Proprietary & Confidential
Copyright © 2013 - Proprietary & Confidential
Copyright © 2013 - Proprietary & Confidential
Copyright © 2013 - Proprietary & Confidential
Standards & ontologies identify data
elements
Copyright © 2013 - Proprietary & Confidential
Map sample tracking workflow
Subject presents
(demographics, diagnoses, etc)...
Copyright © 2013 - Proprietary & Confidential
Sample Tracking & Storage Elements
• Collection date
• Volume
• Sample Quali...
Copyright © 2013 - Proprietary & Confidential
Mapping common data elements
+
Map data elements into a common data model
Sa...
Copyright © 2013 - Proprietary & Confidential
Common Data Elements for sample tracking/sample storage
Copyright © 2013 - Proprietary & Confidential
Common Data Elements for sample tracking/sample storage
Copyright © 2013 - Proprietary & Confidential
Mapping common data elements
+
Map data elements into a canonical data model...
Copyright © 2013 - Proprietary & Confidential
Canonical Data Mapping – data elements vary by study, data model accomodates...
Copyright © 2013 - Proprietary & Confidential
Canonical Data Mapping – data elements vary by study, data model accomodates...
Copyright © 2013 - Proprietary & Confidential
Mapping common data elements
Federated view –pulls common data elements
Samp...
Copyright © 2013 - Proprietary & Confidential
Harmonization of disparate data
A hub of harmonized
information linking
pati...
Copyright © 2013 - Proprietary & Confidential
Standards & Ontologies
Plenty of choice!
Can vs. should
Copyright © 2013 - Proprietary & Confidential
Foolproof nomenclature = Simple
Copyright © 2013 - Proprietary & Confidential
Universal Language = enough to be
understood
Enough for data interchange
Wor...
Copyright © 2013 - Proprietary & Confidential
Minimum Information Standards, e.g. MIAME
Copyright © 2013 - Proprietary & Confidential
Minimum Information About Biobank
data Sharing
MIABIS
A Minimum Data Set for...
Copyright © 2013 - Proprietary & Confidential
MIABIS
• 52 attributes across biobank data to enable data
exchange about the...
Copyright © 2013 - Proprietary & Confidential
Minimum Information About a Biobank
Sample
MIABS
Need this standard or MIABI...
Copyright © 2013 - Proprietary & Confidential
Meaning
Semantics critical to asking questions
Copyright © 2013 - Proprietary & Confidential
Controlled vocabularies aid meaning
NCI CBM Vocab and meaning
Copyright © 2013 - Proprietary & Confidential
Controlled vocabularies aid meaning
Copyright © 2013 - Proprietary & Confidential
Controlled vocabularies
• Sample Quality
– Not assigned
– Acceptable
– Poor ...
Copyright © 2013 - Proprietary & Confidential
Sample tracking/storage vocabulary
Controlled vocabularies for sample quality
Copyright © 2013 - Proprietary & Confidential
Biosamples & Babel [Fish]*
*Hitchhiker’s guide to the galaxy
Copyright © 2013 - Proprietary & Confidential
SEP
22
Sample tracking, sample
storage etc, data
Universal language for
aski...
Copyright © 2013 - Proprietary & Confidential
SEP
22
Ontologies
Standards
Minimum Information
Standards
Common Data Models...
Copyright © 2013 - Proprietary & Confidential
SEP
22
MIABE
Ontology Lookup services
Linked to biobank
informatics systems
...
Copyright © 2013 - Proprietary & Confidential
Summary
• Biobank as a knowledgebase for biomarker
research
• Standard & foo...
Copyright © 2013 - Proprietary & Confidential
Thanks – Questions?
Biobanking & data management software for
the personaliz...
Copyright © 2013 - Proprietary & Confidential
Resources
• http://www.oecd.org/sti/biotech/guidelinesforhumanbiobanksandgen...
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Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample storage nomenclature

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Do you speak biobank? presentation given at the IIR Biorepositories meeting, Boston, MA. September 25-27, 2013.
We discuss the need for biobank data exchange standards, the importance of ontologies and semantics and why this is so critical to biomarker research and the vision of personalized medicine

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  • Do you speak biobank – or perhaps more importatly do oyur samples
  • Why do we care that samples and sample related data can be universally understood no matter where, when and how collected and for what ever use
  • Widely held belief that samples and their data can play a vital role in future biomedical research
  • Not just any samples though….
  • By obtaining samples
  • Tracing our way back, start with the end in mind and work our way back as to how to get there
  • There are 2 issues at stake – what I’ll call harmonization, i..e how data about samples is linked, described, what data elements are needed and so on – this is a wider problem than just sample tracking and sample storage nomenclature, but we’ll focus in on that to illustrate the issues
  • Once we have solved the harmonization problem about what data elements we’re collecting, now we need to address what data is recorded and it’s meaning
  • Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample storage nomenclature

    1. 1. Copyright © 2009 Proprietary & Confidential Copyright © 2013 - Proprietary & Confidential DO YOU SPEAK BIOBANK? Biosamples and Babel: Constructing foolproof sample tracking and storage nomenclature Mark A. Collins Ph.D IIR Biorepositories Meeting September 25th, 2013
    2. 2. Copyright © 2013 - Proprietary & Confidential Do you speak biobank? sprechen Sie Biobank? hablas biobanco 你说生物资料库 parlez-vous biobanque あなたは、バイオバンクを話します ydych chi'n siarad Biobank μιλάτε βιοτράπεζα talar du biobank parli biobanca Вы говорите биобанке Eğer biobank konuşuyorsunuz Disclaimer: Google translate was used for this slide – any harm to any language is unintentional
    3. 3. Copyright © 2013 - Proprietary & Confidential ….babel as a confusion of languages?
    4. 4. Copyright © 2013 - Proprietary & Confidential Biosamples & Babel [Fish]* *Hitchhiker’s guide to the galaxy Universal Language
    5. 5. Copyright © 2013 - Proprietary & Confidential Why do we care?
    6. 6. Copyright © 2013 - Proprietary & Confidential SAMPLE POWER I could help cure cancer I could help cure Parkinsons I could help cure Alzheimers
    7. 7. Copyright © 2013 - Proprietary & Confidential HIGH QUALITY HIGHLY ANNOTATED CONSENTED PATIENT LINKED SAMPLE
    8. 8. Copyright © 2013 - Proprietary & Confidential Patients Samples Biomarkers New drugs New targeted therapies
    9. 9. Copyright © 2013 - Proprietary & Confidential The vision of personalized medicine.. Personalized medicine Externalization Big Data Targeted Therapy & Companion DiagnosticsTargeted Trials Translational Research / Biomarkers / Patient Segmentation Clinical data Clinical samples Biobanks
    10. 10. Copyright © 2013 - Proprietary & Confidential “… that have access to millions of highly annotated biospecimens with clear consent, traceability and tools to rapidly mine for desired profiles will have an edge in biomarker- based discovery, segmenting patients for clinical trials and developing companion diagnostic /theranostic applications”
    11. 11. Copyright © 2013 - Proprietary & Confidential Access to more and more samples & data Thousands of trials Thousands of patients Millions of samples Billions of data points (and growing) Offer a Huge POTENTIAL for Future Biomedical Research (FBR)
    12. 12. Copyright © 2013 - Proprietary & Confidential And more… Disease specific biobanks Patient registries Hospital/Institute biobanks National biobanks
    13. 13. Copyright © 2013 - Proprietary & Confidential Operating environment in flux Limiting the potential for use of samples and their data for FBR Increasing externalization Global trials Complex consent landscape Large amounts of complex data
    14. 14. Copyright © 2013 - Proprietary & Confidential Internet of things
    15. 15. Copyright © 2013 - Proprietary & Confidential Biobank of things
    16. 16. Copyright © 2013 - Proprietary & Confidential NO UNIVERSAL LANGUAGE Ich helfen könnte Krebs heilen Je pourrais aider à guérir la maladie de Parkinson I could help cure Alzheimers
    17. 17. Copyright © 2013 - Proprietary & Confidential Why do we need a universal language?
    18. 18. Copyright © 2013 - Proprietary & Confidential We want to ask questions! Patient Profile DCIS T size>1cm, ER+, HER2/neu+, Node negative Radiation therapy BRCA1 mutation 185delAG HOXB7 gene overexpression Tissue banked for immunohistochemistry? What is the incidence of breast cancer recurrence in patients with the following profile? Type of Data Clinical Genotype Gene Expression Sample Management
    19. 19. Copyright © 2013 - Proprietary & Confidential Questions are in depth
    20. 20. Copyright © 2013 - Proprietary & Confidential Questions span domains Multiple data sources Domain expertise More data sources More data sources Requires considerable IT resources
    21. 21. Copyright © 2013 - Proprietary & Confidential General Barriers to the Biobank of Things Future Biomedical Research Multiple disparate, dispersed data sources Lack of a universal language Increased regulatory scrutiny Information bottlenecks Increased resource usage “Operating environment” negatively impacts future FBR potential
    22. 22. Copyright © 2013 - Proprietary & Confidential How do we get there?
    23. 23. Copyright © 2013 - Proprietary & Confidential Today, focus in on the data Future Biomedical Research Multiple disparate, dispersed data sources Lack of a universal language Increased regulatory scrutiny Information bottlenecks Increased resource usage
    24. 24. Copyright © 2013 - Proprietary & Confidential Harmonization Meaning
    25. 25. Copyright © 2013 - Proprietary & Confidential Multiple, disparate data sources SEP 22 Sample tracking and sample storage data is one piece of a very complex picture
    26. 26. Copyright © 2013 - Proprietary & Confidential Sometimes feels like this…
    27. 27. Copyright © 2013 - Proprietary & Confidential Harmonization of disparate data A hub of harmonized information linking patient, specimen, consent, clinical and molecular data SEP 22 Turn disparate, complex, distrib uted sample and sample related data SEP 22
    28. 28. Copyright © 2013 - Proprietary & Confidential Variety of standards/best practices Biobanking best practices Biobanking IT best practices Ontologies for clinical data Ontologies for biospecimens Software standards Ontologies for genomic/assay data
    29. 29. Copyright © 2013 - Proprietary & Confidential Variety of biobanking standards/best practices ISBER, NCI, OECD, BBMRI, CAP ISBER, NCI, BBMRI (poorly covered) SNOMED, CDISC, ICD-0 caBIG/OBBR/Common Biorepository Model Webservices, HTML, databases etc SNOMED, OBO, MIAME standards
    30. 30. Copyright © 2013 - Proprietary & Confidential
    31. 31. Copyright © 2013 - Proprietary & Confidential
    32. 32. Copyright © 2013 - Proprietary & Confidential
    33. 33. Copyright © 2013 - Proprietary & Confidential Standards & ontologies identify data elements
    34. 34. Copyright © 2013 - Proprietary & Confidential Map sample tracking workflow Subject presents (demographics, diagnoses, etc) Sample collected (sample type, quantity, sample quality, CoC etc) Sample Temp Storage (location, CoC etc) Sample shipment/transfer (shipping container, time, CoC)) Receive at Biobank (time, sample quality etc) Sample QC (quality, discrepancies etc) Temporary Storage (location , time, CoC) Storage in biobank (location, environmental, #thaw s , CoC) Sample request & processing (aliquots, derivatives etc, CoC) Determine standard data elements for data collection & harmonization, using ontologies/standards
    35. 35. Copyright © 2013 - Proprietary & Confidential Sample Tracking & Storage Elements • Collection date • Volume • Sample Quality • Sample Type • Barcode • Unique ID • Source • Preservation Type • Time to preservation • Storage location • Environmental conditions • Facility • #thaws • CoC • More…
    36. 36. Copyright © 2013 - Proprietary & Confidential Mapping common data elements + Map data elements into a common data model Sample Data #2Sample Data #1 Biobank Database common model
    37. 37. Copyright © 2013 - Proprietary & Confidential Common Data Elements for sample tracking/sample storage
    38. 38. Copyright © 2013 - Proprietary & Confidential Common Data Elements for sample tracking/sample storage
    39. 39. Copyright © 2013 - Proprietary & Confidential Mapping common data elements + Map data elements into a canonical data model (aggregates all data elements whether common or not) Sample Data #2Sample Data #1 Biobank Database common model
    40. 40. Copyright © 2013 - Proprietary & Confidential Canonical Data Mapping – data elements vary by study, data model accomodates all
    41. 41. Copyright © 2013 - Proprietary & Confidential Canonical Data Mapping – data elements vary by study, data model accomodates all
    42. 42. Copyright © 2013 - Proprietary & Confidential Mapping common data elements Federated view –pulls common data elements Sample Data #2 Sample Data #1 Biobank Database Federated View
    43. 43. Copyright © 2013 - Proprietary & Confidential Harmonization of disparate data A hub of harmonized information linking patient, specimen, consen t, clinical and molecular data SEP 22 Turn disparate, complex, distrib uted sample and sample related data SEP 22 Powered by
    44. 44. Copyright © 2013 - Proprietary & Confidential Standards & Ontologies Plenty of choice! Can vs. should
    45. 45. Copyright © 2013 - Proprietary & Confidential Foolproof nomenclature = Simple
    46. 46. Copyright © 2013 - Proprietary & Confidential Universal Language = enough to be understood Enough for data interchange World is full of overly complex standards and ontologies
    47. 47. Copyright © 2013 - Proprietary & Confidential Minimum Information Standards, e.g. MIAME
    48. 48. Copyright © 2013 - Proprietary & Confidential Minimum Information About Biobank data Sharing MIABIS A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS Norlin et al (2012) BIOPRESERVATION AND BIOBANKING Volume 10, Number 4, 2012
    49. 49. Copyright © 2013 - Proprietary & Confidential MIABIS • 52 attributes across biobank data to enable data exchange about the biobank • Not detailed enough for samples /sample tracking • Good to compare biobanks and their contents for search purposes – What samples does a biobank have? – What patient/medical conditions does the bank have samples from
    50. 50. Copyright © 2013 - Proprietary & Confidential Minimum Information About a Biobank Sample MIABS Need this standard or MIABIS to be extended to include much more detail on sample nomenclature
    51. 51. Copyright © 2013 - Proprietary & Confidential Meaning Semantics critical to asking questions
    52. 52. Copyright © 2013 - Proprietary & Confidential Controlled vocabularies aid meaning NCI CBM Vocab and meaning
    53. 53. Copyright © 2013 - Proprietary & Confidential Controlled vocabularies aid meaning
    54. 54. Copyright © 2013 - Proprietary & Confidential Controlled vocabularies • Sample Quality – Not assigned – Acceptable – Poor quality – Comments… • Sample Status – Reserved – In inventory – stored – In inventory – Lost – In transfer – Checked-out will return – Exhaustd – Destroyed
    55. 55. Copyright © 2013 - Proprietary & Confidential Sample tracking/storage vocabulary Controlled vocabularies for sample quality
    56. 56. Copyright © 2013 - Proprietary & Confidential Biosamples & Babel [Fish]* *Hitchhiker’s guide to the galaxy
    57. 57. Copyright © 2013 - Proprietary & Confidential SEP 22 Sample tracking, sample storage etc, data Universal language for asking questions Science Fiction?
    58. 58. Copyright © 2013 - Proprietary & Confidential SEP 22 Ontologies Standards Minimum Information Standards Common Data ModelsSample tracking, sample storage etc, data Universal understanding to ask questions Science Fiction?
    59. 59. Copyright © 2013 - Proprietary & Confidential SEP 22 MIABE Ontology Lookup services Linked to biobank informatics systems Sample tracking, sample storage etc, data Universal understanding to ask questions Scientific reality
    60. 60. Copyright © 2013 - Proprietary & Confidential Summary • Biobank as a knowledgebase for biomarker research • Standard & foolproof nomenclatures needed • Beyond the sample • Specific ontologies, standards, vocabularies needed • Drive to MIABS – ISBER? • BioFortis offers biobanking/translational research informatics platforms that implement these standards
    61. 61. Copyright © 2013 - Proprietary & Confidential Thanks – Questions? Biobanking & data management software for the personalized medicine era
    62. 62. Copyright © 2013 - Proprietary & Confidential Resources • http://www.oecd.org/sti/biotech/guidelinesforhumanbiobanksandgeneticrese archdatabaseshbgrds.htm • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500833/ • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633318/#ref15 • http://training.seer.cancer.gov/coding/structure/ -ICD-0 • http://www.ihtsdo.org/snomed-ct/ • http://www.obofoundry.org/ • An Online Tool for Improving Biospecimen Data Element Reporting- http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0033

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