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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? 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. ...

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 Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample storage nomenclature Presentation Transcript

  • 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
  • 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
  • Copyright © 2013 - Proprietary & Confidential ….babel as a confusion of languages?
  • Copyright © 2013 - Proprietary & Confidential Biosamples & Babel [Fish]* *Hitchhiker’s guide to the galaxy Universal Language
  • 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 help cure Alzheimers
  • 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 Big Data Targeted Therapy & Companion DiagnosticsTargeted Trials Translational Research / Biomarkers / Patient Segmentation Clinical data Clinical samples Biobanks
  • 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”
  • 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)
  • Copyright © 2013 - Proprietary & Confidential And more… Disease specific biobanks Patient registries Hospital/Institute biobanks National biobanks
  • 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
  • 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 guérir la maladie de Parkinson I could help cure Alzheimers
  • 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+, 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
  • Copyright © 2013 - Proprietary & Confidential Questions are in depth
  • Copyright © 2013 - Proprietary & Confidential Questions span domains Multiple data sources Domain expertise More data sources More data sources Requires considerable IT resources
  • 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
  • Copyright © 2013 - Proprietary & Confidential How do we get there?
  • 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
  • Copyright © 2013 - Proprietary & Confidential Harmonization Meaning
  • Copyright © 2013 - Proprietary & Confidential Multiple, disparate data sources SEP 22 Sample tracking and sample storage data is one piece of a very complex picture
  • Copyright © 2013 - Proprietary & Confidential Sometimes feels like this…
  • 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
  • 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
  • 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
  • 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) 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
  • 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…
  • 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
  • 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 (aggregates all data elements whether common or not) Sample Data #2Sample Data #1 Biobank Database common model
  • Copyright © 2013 - Proprietary & Confidential Canonical Data Mapping – data elements vary by study, data model accomodates all
  • Copyright © 2013 - Proprietary & Confidential Canonical Data Mapping – data elements vary by study, data model accomodates all
  • Copyright © 2013 - Proprietary & Confidential Mapping common data elements Federated view –pulls common data elements Sample Data #2 Sample Data #1 Biobank Database Federated View
  • 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
  • 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 World is full of overly complex standards and ontologies
  • 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 Sharing Biobank Samples, Information, and Data: MIABIS Norlin et al (2012) BIOPRESERVATION AND BIOBANKING Volume 10, Number 4, 2012
  • 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
  • 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
  • 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 quality – Comments… • Sample Status – Reserved – In inventory – stored – In inventory – Lost – In transfer – Checked-out will return – Exhaustd – Destroyed
  • 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 asking questions Science Fiction?
  • 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?
  • 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
  • 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
  • Copyright © 2013 - Proprietary & Confidential Thanks – Questions? Biobanking & data management software for the personalized medicine era
  • 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