Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample...

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Copyright © 2013 - Proprietary & Confidential

DO YOU SPEAK BIOBANK?Biosamples and Babel: Constructing foolproof sample tracking and storage nomenclature

Mark A. Collins Ph.DIIR Biorepositories Meeting September 25th, 2013


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


….babel as a confusion of languages?


Biosamples & Babel [Fish]**Hitchhiker’s guide to the galaxy

Universal Language


Why do we care?


SAMPLEPOWER

I could help cure

cancer

I could help cure

Parkinsons

I could help cure

Alzheimers


HIGH QUALITYHIGHLY ANNOTATED

CONSENTEDPATIENT LINKED

SAMPLE


Patients Samples Biomarkers New drugs

New targeted therapies


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


“… 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”


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)


And more…

Disease specific biobanks

Patient registries

Hospital/Institute biobanks

National biobanks


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


Internet of things


Biobank of things


NO UNIVERSAL LANGUAGE

Ich helfen könnte

Krebs heilen

Je pourrais aider à guérir la maladie de

Parkinson

I could help cure

Alzheimers


Why do we need a universal language?


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


Questions are in depth


Questions span domainsMultiple data

sources

Domain expertiseMore data sources

More data sources

Requires considerable IT resources


General Barriers to the Biobank of Things

Future Biomedical Research

Multiple disparate, dispersed

data sources

Lack of a universal language

Increased regulatory

scrutinyInformation bottlenecks

Increased resource

usage

“Operating environment” negatively impacts future FBR potential


How do we get there?


Today, focus in on the data

Future Biomedical Research

Multiple disparate, dispersed

data sources

Lack of a universal language

Increased regulatory

scrutinyInformation bottlenecks

Increased resource

usage


Harmonization

Meaning


Multiple, disparate data sources

SEP

22

Sample tracking and sample storage data is one piece of a very complex picture


Sometimes feels like this…


Harmonization of disparate data

A hub of harmonized information linking patient,

specimen, consent, clinical and molecular data

SEP

22

Turn disparate, complex, distributed sample and

sample related data

SEP

22


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


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


Standards & ontologies identify data elements


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, #thaws , CoC)

Sample request & processing

(aliquots, derivatives etc, CoC)

Determine standard data elements for data collection & harmonization, using ontologies/standards


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…


Mapping common data elements

+

Map data elements into a common data model

Sample Data #2Sample Data #1 Biobank Database common model


Common Data Elements for sample tracking/sample storage



+

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


Canonical Data Mapping – data elements vary by study, data model accomodates all



Federated view –pulls common data elements

Sample Data #2

Sample Data #1

Biobank Database Federated View


Harmonization of disparate data

A hub of harmonized information linking patient,

specimen, consent, clinical and molecular data

SEP

22

Turn disparate, complex, distributed sample and

sample related data

SEP

22

Powered by


Standards & Ontologies

Plenty of choice!

Can vs. should


Foolproof nomenclature = Simple


Universal Language = enough to be understood

Enough for data interchange

World is full of overly complex standards and ontologies


Minimum Information Standards, e.g. MIAME


Minimum Information About Biobank data Sharing

MIABISA Minimum Data Set for Sharing Biobank Samples, Information, and Data:

MIABIS

Norlin et al (2012)BIOPRESERVATION AND BIOBANKING Volume 10, Number 4, 2012


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


Minimum Information About a Biobank Sample

MIABS

Need this standard or MIABIS to be extended to include much more detail on sample nomenclature


Meaning

Semantics critical to asking questions


Controlled vocabularies aid meaning

NCI CBM Vocab and meaning


Controlled vocabularies aid meaning


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


Sample tracking/storage vocabulary

Controlled vocabularies for sample quality


Biosamples & Babel [Fish]*

*Hitchhiker’s guide to the galaxy


SEP

22

Sample tracking, sample storage etc, data

Universal language for asking questions

Science Fiction?


SEP

22

OntologiesStandards

Minimum Information Standards

Common Data ModelsSample tracking, sample storage etc, data

Universal understanding to ask questions

Science Fiction?


SEP

22

MIABEOntology Lookup services

Linked to biobank informatics systems

Sample tracking, sample storage etc, data

Universal understanding to ask questions

Scientific reality


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


Thanks – Questions?

Biobanking & data management software for the personalized medicine era


Resources

• http://www.oecd.org/sti/biotech/guidelinesforhumanbiobanksandgeneticresearchdatabaseshbgrds.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

http://www.oecd.org/sti/biotech/guidelinesforhumanbiobanksandgeneticresearchdatabaseshbgrds.htm

http://www.oecd.org/sti/biotech/guidelinesforhumanbiobanksandgeneticresearchdatabaseshbgrds.htm

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500833/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500833/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633318/%23ref15

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633318/%23ref15

http://training.seer.cancer.gov/coding/structure/

http://training.seer.cancer.gov/coding/structure/

http://www.ihtsdo.org/snomed-ct/

http://www.ihtsdo.org/snomed-ct/

http://www.obofoundry.org/

http://www.obofoundry.org/



Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample...

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Transcript of Do you speak biobank? Biospecimens and Babel: Constructing foolproof sample tracking and sample...