High-quality biobanking for personalized precision medicine: BioSpecimen Sciences at the helm

MINI-SYMPOSIUM: QUALITY ASSURANCE IN SURGICAL PATHOLOGY AND BIOBANKING

High-quality biobanking forpersonalized precisionmedicine: BioSpecimenSciences at the helmDianne Chadwick

Michael HA Roehrl

AbstractOptimal procurement and deep molecular (“omic”) characterization of

human biospecimens are the key elements of success for developing

truly personalized precision medicine of the future. We review key ele-

ments of developing and implementing a high-quality, cutting-edge Bio-

Specimen Sciences Program. Using our recently established academic

programme as a specific example, we focus on quality of biospecimen

practice covering topics including research consent of patients, logistics

of ultra-rapid biobanking, computational and database aspects, quality

control measures, proficiency testing, and optimal pathophysiome-

preservation for data-rich omic interrogation of biospecimens. We empha-

size that Pathology as the central medical speciality of personalized pre-

cision medicine will be the key driver for high-quality BioSpecimen

Sciences in the modern healthcare setting.

Keywords BioSpecimen Sciences; human samples; pathology; person-

alized diagnostics; precision medicine

Introduction

Carefully collected high-quality biospecimens linked to accurate

clinical and pathologic data are crucial for advancing personal-

ized medicine using next generation “omic” technologies such as

deep genomic and transcriptomic sequencing, proteomics, or

metabolomics.1,2 A biobank or biorepository is the infrastructure

within which biospecimens are identified, collected, annotated,

stored, and retrieved for use in current and future basic, trans-

lational, and clinical trial research. Biospecimens are biological

materials and their molecular derivatives originating from the

human body. They may be obtained as part of a patient’s routine

clinical care, but are typically considered excess or additional

and not directly required for diagnosis.3 Biospecimens include

but are not limited to: solid tissues, blood, body fluids, hair, nail

clippings, or infectious disease specimens as well as laboratory-

Dianne Chadwick PhD Program in BioSpecimen Sciences, University

Health Network and University of Toronto, Toronto, Ontario, Canada.

Conflicts of interest: none declared.

Michael HA Roehrl MD PhD Director, Program in BioSpecimen Sciences,

University Health Network and University of Toronto, Toronto, Ontario,

Canada. Conflicts of interest: none declared.

DIAGNOSTIC HISTOPATHOLOGY 19:12 447

derived products such as cell lines, plasma, serum, paraffin

blocks, DNA, RNA, proteins, or metabolites. Patient data that can

be integrated with biospecimens may include medical and family

history, lifestyle information, and specimen-derived research

data such as genomic mutation profiles.

Carefully procured and preserved biospecimens that are

linked to accurate and complete clinical and pathologic annota-

tions are key to the success of any scientific project utilizing

human samples. Similar to routine diagnostic samples, quality

research biospecimens are typically collected, annotated, and

stored using standard protocols, and quality biorepositories

should follow standard operating procedures (SOPs) and adhere

to best laboratory practices.4 Without high-quality biospecimens

that faithfully represent the specific pathophysiology of the in-

dividual patient, erroneous research data will result, misleading

not only the investigator but potentially the entire research

community (“garbage in, garbage out”). Accurate and complete

clinical annotation is required to ensure that all applicable study-

specific inclusion and exclusion criteria for the use of specific

biospecimens are met. In this review, we describe best practices

and quality assurance methodologies established by the UHN

BioSpecimen Sciences Program (BSP) designed to ensure the

availability of highest-quality biospecimens that satisfy and

typically exceed the scientific requirements of current cutting-

edge genomics, transcriptomics, and proteomics. Furthermore,

we will discuss our approach to “future-proofing” biospecimen

collections to be in an optimal position for future research in

functional kinomics, dynamic metabolomics, and other emerging

technologies.

The University Health Network Program in BioSpecimen Sciences

as a model for Quality Assurance in Biobanking

University Heath Network (UHN) is a large multi-campus qua-

ternary care academic institution comprised of four research

hospitals (Toronto General Hospital, Toronto Western Hospital,

Toronto Rehabilitation Hospital, and Princess Margaret Cancer

Centre). Affiliated with the University of Toronto, the scope of

research and complexity of cases at UHN have made it a national

and international leader in medical discovery, education, and

patient care. Its large hospital-based research programme is

recognized internationally in oncology, genomic medicine, car-

diology, transplantation, neuroscience, surgical innovation, in-

fectious disease, and rehabilitation medicine. While research

biospecimen collection has been an activity of many individual

investigators at UHN for decades, fully integrated large-scale and

coordinated institutional biobanking started in 2001 when it

became clear that there will be a rapidly growing demand for

human tissue for research purposes. Initially designed as a solid

tumour bank, there is now a full-scale multidisciplinary research

programme (i.e., the UHN Program in Biospecimen Sciences) that

is staffed with dedicated Clinical Research Coordinators, Pa-

thology Assistants, Research Technicians, Postdoctoral Fellows,

Research Students, a Manager, and a Director. The Programme

actively interacts with subspeciality pathologists, scientists, and

clinicians from all clinical programmes and research institutes

within UHN and maintains extensive national and international

research activities.

� 2013 Published by Elsevier Ltd.

http://dx.doi.org/10.1016/j.mpdhp.2013.11.009


The UHN Biospecimen Sciences Program (UHN BSP) compre-

hensively harvests and stores biospecimens from patients with

cancer and non-malignant diseases. Biobanking within the Pro-

gramme has resulted in a diverse collection of solid tissues, blood

samples, and body fluids (such as ascites) from large numbers of

individuals. The number of solid tissue samples and their distri-

bution by disease site are illustrated in Figure 1a. Many of the

16000

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Total: >92000

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Year of collection

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Cumulative acquisition of frozen tissue samples by UHN BSP

Figure 1


biospecimens represent tumour and matched normal tissue from

the same patient. A large number of cancer surgeries are per-

formed at UHN resulting in ready availability of excess research

tissue beyondwhat is needed for pathological diagnosis, and there

is significant intramural demand for cancerous tissue for basic and

translational clinical research including clinical trials. In a given

year, approximately 10e15% of samples collected by UHN BSP

estin

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2011 2012 2013




are immediately used in an intramural research project. Examples

of non-cancerous diseased tissues that are routinely banked

include thyroid goitres, hepatic cirrhosis, pulmonary emphysema,

ulcerative colitis, uterine leiomyomas, polycystic kidney disease,

benign prostatic hypertrophy, cardiac and vascular disease, and

numerous other conditions. The annual rate of solid tissue sample

accrual (i.e., excluding blood and other liquid samples) is shown

in Figure 1b. Note that the number of solid tissue samples per year

has increased from about 3000 in the first year of banking when

biospecimens were banked at one hospital only to our current rate

of more than 12000 samples per year from three hospital

campuses.

Quality assurance is a key element of the Programme and

elements are built in throughout the UHN BSP workflow. Gov-

erning principles, policies, and standard operating procedures

have been established as approved written documents and are

adhered to in order to preserve the quality of the collection and to

protect the privacy of patients who generously donate their

biospecimens to the Programme for biomedical research. This is

possible because of a unique BSP workflow that interfaces with

but is separate and distinct from clinical care, the collaborative

spirit of pathologists, physicians, surgeons, interventional radi-

ologists, and researchers, and financial support from UHN

research foundations and grants from government organizations.

The high quality of the Biospecimen Sciences Program at UHN

has led to very successful local and international research

collaborations with The Cancer Genome Atlas (TCGA),5,6 with

the International Cancer Genome Consortium (ICGC),7 with the

COEUR ovarian cancer repository,8 in cancer stem cell

research,9,10 in immunologic biomarker research,11 in personal-

ized medicine initiatives,12 in drug development,13,14 and in

specimen-centred molecularly-driven clinical trials.15,16

Defined governing principles formalize biobanking at UHN as an

institutional resource

The Biospecimen Sciences Program at UHN bases its foundation

on an institutional policy document entitled “UHN BioBank

Guiding Principles and Governance”. The document states that

the Director will be a physician and certified pathologist with

expert knowledge in the science of research biobanking. The

document stipulates that research banking of all types of human

biospecimens should be done in a safe and appropriate manner.

Research access to biospecimens should be equitable, fair, and

timely so that meaningful research is facilitated and maximized

for all UHN researchers. Small individual “Investigator Bio-

banks” that also exist at UHN are held to the same standards as

the UHN Program in Biospecimen Sciences. The need for

informed patient consent for research, disease site approval, and

institutional (including Research Ethics Board) authorization for

all studies using UHN biospecimens are stipulated. The docu-

ment also establishes an institutional Biobank Executive Com-

mittee that is jointly chaired by the Vice Presidents of Research

and Medical Affairs and is comprised of medical directors from

all nine UHN clinical programmes (pathology, oncology, surgery,

medicine, orthopedics/arthritis, medical imaging, neurosciences,

transplant medicine, and cardiology). Key roles of the Biobank

Executive Committee include dispute resolution and approval of

policies recommended by the UHN Biospecimen Working Group.


The UHN Biospecimen Working Group, chaired by the Di-

rector of the Biospecimen Sciences Program and composed of

members are from all nine clinical programmes and the five

research institutes at UHN, engages in strategic planning,

development of operational improvements, as well as formula-

tion of standards for annotation, storage, and use of research

biospecimens. The working group adopts terms of reference,

oversees common areas of development such as new Information

Technology for biospecimen management, and addresses con-

cerns such as equitable access to biospecimens. Clinician-

scientists from diverse disciplines offer a wide range of exper-

tise and viewpoints ensuring deep understanding of quality is-

sues related to biobanking.

Policies and standard operating procedures ensure quality and

consistency in biobanking

A major challenge of banking, storing, distributing, and anno-

tating biospecimens is ensuring and documenting quality. When

biospecimens are cut off from the body’s blood supply during

surgery or biopsy and exposed to abrupt changes in temperature

following removal from the body, they undergo stress. The

length of time the sample stays at room temperature before it is

frozen, the time and type of fixative, the rate at which it is frozen,

and the size and shape of aliquots will all affect sample quality.

Differences in any of these variables may result in numerous

changes such as fluctuation of gene expression or changes in

protein phosphorylation.1 Furthermore, these preanalytical in-

fluences affect biological target molecules differentially. For

example, while genomic DNA may be relatively stable, other

entities such as mRNA, miRNA, proteins, lipids, metabolites, etc.

will all be affected to varying degrees and at varying rates.

To address this problem, we believe that “time and thermo-

dynamics are your friends”. To this end, hospital biorepositories

need to work closely with surgical teams so that the time from

excision to snap freezing in liquid nitrogen is as short as possible

(at least less than 30 minutes). For gene expression studies and

proteomics, 10e15 minutes or even shorter may be necessary.2

For particularly sensitive research studies (such as measuring

posttranslational modifications of signalling proteins or metab-

olomics), the UHN Program has developed “ultra-rapid bio-

banking” (<5 minutes transit time) or even intra-OR freezing

adjacent to the patient (Figure 2). Speed is also important for

tissues collected post mortem. Tissue samples collected at the

time of autopsy need to be collected and fixed or frozen within a

few (ideally 1e3) hours of death (“rapid autopsy”’) to be suitable

for next generation sequencing.17

Except perhaps for genomic DNA, most biomolecules are best

preserved as rapidly as possible after removal from the patient.

While genomics research is possible on formalin-fixed paraffin-

embedded tissue, DNA and RNA extracted from fixed blocks vary

in quality and analysis can be difficult. Delayed or unknown

freeze times and additives such as OCT and RNAlater� to fresh

samples may unnecessarily limit their use for future research.2

Consequently, research biospecimens are best snap frozen in

liquid nitrogen and stored in vapour phase liquid nitrogen as

soon as possible after collection (“time and thermodynamics are

your friends”). We refer to this practice as “future-proofing” of

the biobank because the avoidance of additives to samples will



<5 min

0 min

1 min

5 min

10 min

Consultation Ultra-Rapid BioBanking

<5

Consultation Ultra-Rapid BioBanki

Figure 2 UHN BSP’s “ultra-rapid biobanking” programme makes use of the existing intraoperative “frozen section” consultation process.


not impose a limit on any future technique or procedure that we

may use in the future to analyze the particular sample. Thawing

and refreezing samples is to be avoided, and freezer tempera-

tures are continuously monitored electronically and also manu-

ally at least daily by measuring the depth of liquid nitrogen in the

vapour phase storage tanks. Preanalytical variables that describe

how each sample was collected and stored need to be carefully

documented in the specimen management IT system.1,2,4

Patient cliPatient charts

screened for consentby UHN BSP

Research Coordinators

Patient charts screened for consent

by UHN BSPPathology Assistants

Patientadmissio

Surgery ware

Patient s

Post-opepatie

Multi-layered research consent process

Figure 3 Multi-layered approach to obtaining and ve


Policies, Standard Operating Procedures, and Best Practices

for collection, storage, retrieval, and distribution of biological

materials for research can be adopted from published resources

including the Canadian Tumour Repository Network (CTRnet)

(www.ctrnet.ca), the National Cancer Institutes (NCI) Best

Practices (www.biospecimens.cancer.gov/bestpractices/), and

the International Society of Biological and Environmental Re-

positories (ISBER) Best Practices.18 The CTRnet Policies and

nic visit

Patients approachedfor consentby UHN BSP

Research Coordinators

pre-n visit

aiting a

urgery

rativents

at UHN BSP

rifying patient consent for research banking.


http://www.ctrnet.ca

http://www.biospecimens.cancer.gov/bestpractices/



Standard Operating Procedures are available online as Word files

that may be easily adapted to local practice. CTRnet also has a

Certification Programme that focuses on education to commu-

nicate best practices and address quality assurance and gover-

nance issues.19 ISBER has recently launched a Proficiency

Testing Program for biorepositories (www.isber.org) to assess

the accuracy of quality control focussing on 4 test areas: DNA

quantification, RNA integrity, cell viability, and tissue histology.

The College of American Pathologists (CAP) has also developed

an accreditation programme for biorepositories (www.cap.org/

apps/docs/laboratory_accreditation/build/pdf/bap_standards.

pdf). Similar to CAP accreditation of clinical laboratories, there is

a checklist of required practices such as whether there is tracking

of samples that have been thawed and refrozen and whether

freezer alarms have been installed. When facilities meet the re-

quirements, they can apply for accreditation and schedule an on-

site inspection.

Biobanking workflow that interfaces with but is separate and

distinct from clinical care

The UHN Biospecimen Sciences Program has been granted

Research Ethics Board (REB) approval for Program staff to

review patient clinic lists and medical charts and to approach

patients to obtain consent for research biobanking. A scheme of

our current multi-layered consent workflow is shown in Figure 3.

Potential donors are identified on patient clinic lists by Program

Clinical Research Coordinators (CRCs). CRCs approach selected

patients for consent at their preadmission visit and order

research blood. On the day of the procedure (surgery or other

intervention), the Electronic Patient Record (EPR) is reviewed for

diagnosis and consent for research biobanking is verified. Bio-

specimens are collected by BSP Pathology Assistants (BSP PAs)

in surgical pathology (solid tissue) or relevant clinics (body

fluids) or by BSP Research Technicians from the clinical labo-

ratory (research blood samples). Research biospecimens are

processed, deidentified, stored, and annotated with relevant

clinical data.

To optimize research biobanking, a number of modifications

have been made in the clinical workflow:

A universal research banking consent is part of the surgical

preadmission package

According to the International Conference on Harmonisation e

Good Clinical Practice (http://www.ich.org/fileadmin/Public_

Web_Site/ICH_Products/Guidelines/Efficacy/E6_R1/Step4/

E6_R1__Guideline.pdf) and the Canadian Tri-Council Policy

Statement: Ethical Conduct for Research Involving Humans

(Canadian Institutes for Health Research, 2010), documentation

of informed consent is a requirement before human tissue can be

released for research. Only in certain limited cases, a waiver of

consent may be obtained from the institution’s Research Ethics

Board (REB) or Institutional Review Board (IRB). To facilitate

patient consenting, a universal UHN research banking consent

form entitled “Consent for Use of Tissue, Blood, and Body Fluids

for Future Research” is included in every surgical preadmission

package. In addition, a brochure entitled “Medical Research at

UHN e Information about Providing Your Tissue for Medical

Research” is also presented to each patient. According to hospital


policy, surgeons are responsible for ensuring that their patients

are provided with the Medical Research brochure and given an

opportunity to ask questions. In most cases, informed consent is

obtained prior to the procedure, but on occasion the patient is

approached after surgery.

The research consent form allows for the banking of excess

(i.e., deemed not required for making the pathologic diagnosis)

tissue, blood, and body fluids removed during the course of a

procedure as well as the collection of additional blood, urine,

and/or saliva samples collected specifically for research

biobanking.

We have recently monitored the effectiveness of our bio-

banking consent process studying over 4000 patients in a 12-

month period (unpublished data). The overwhelming majority

of our patients (>90%), when approached for consent, support

banking of their tissues for future research. The surgical pread-

mission package can be an effective mechanism for providing

patients with an opportunity to donate their biospecimens, but

there is variability between clinical site groups in response rates

due to physician and staff buy-in, variable consent logistics

during preadmission, and competing specialized research con-

sents limited to a particular site group or study. In addition, we

found that CRCs are highly effective in optimizing consent rates

for biobanking, with a >95% rate of acceptance. Direct personal

involvement of BSP research staff, including personal patient

encounters for explaining the importance of biomedical research

and the rationale for banking human biospecimens for research,

is key for achieving optimal research consent rates.

BSP staff have access to clinic lists, the Electronic Patient

Record (EPR) System, and the Clinical Laboratory

Management System (CoPath)

The UHN BSP staff receives daily patient schedules for the Pre-

admission Clinic, Operating Rooms (ORs), and chemotherapy

units. To verify consent for biobanking, CRCs use the Pread-

mission Clinic lists to select patient charts to be reviewed for

consent status and to identify patients who they will approach in

person to obtain consent for specific studies. The OR list is used

to flag patients from whom surgical tissue is likely to be suitable

for banking. EPR and CoPath are used by the BSP PAs and CRCs

to collect patient demographic and clinical information such as

pathologic diagnosis, family history, comorbidities, treatment

history, surgical procedures and dates, and disease status

(recurrence/progression) to determine suitability for fresh tissue

distribution to specific research studies and clinical trials. The

chemotherapy units’ lists are screened by CRCs to identify pa-

tients who are scheduled for paracentesis and thoracocentesis

procedures and from whom body fluids may be banked and

distributed fresh under certain research protocols.

The Electronic Patient Record (EPR) System has a “research”

module for documenting consent and ordering dedicated

research blood samples for banking

The universal banking consent at UHN contains language that

allows for the banking of “additional” blood, urine, and/or saliva

samples for future research. Once consent is obtained and

documented electronically in EPR, CRCs and hospital staff may

place an order for research blood samples under a dedicated

“research” tab in the Laboratory Medicine Program (LMP) order


http://www.isber.org

http://www.cap.org/apps/docs/laboratory_accreditation/build/pdf/bap_standards.pdf



http://www.ich.org/fileadmin/Public_Web_Site/ICH_Products/Guidelines/Efficacy/E6_R1/Step4/E6_R1__Guideline.pdf





set. The order is tied to a scheduled hospital visit, such as the

preadmission clinic, so that the blood samples may be obtained

by LMP core lab phlebotomists at the same time as bloods or-

dered for clinical purposes. The research blood tube labels

generated by the EPR are clearly marked as “research” and

“Biospecimen Sciences Progam” to avoid confusion with routine

diagnostic samples.

BSP closely coordinates with the work flow of diagnostic

surgical pathology

Surgical specimens from the ORs are immediately transported

fresh (without formalin) to surgical pathology where they are

accessioned into CoPath (the Clinical Laboratory Management

System) and brought to the research biobank bench. BSP PAs

process the surgical specimens following disease and tissue site

specific clinical protocols and obtain and bank excess tissue, live

cells, and/or fluids for research. BSP PAs confirm identity of the

sample, evaluate the tissue, take measurements, ink margins,

and make serial sections to visualize and assess lesions and

corresponding normal tissue for banking. Once banking is com-

plete, the surgical specimens are fixed in formalin for subsequent

diagnostic grossing by the clinical PAs.

The biobanking specimen IT management system interfaces

with EPR and CoPath

We have adapted and highly customized caTissue Suite, an open-

source, web-based biospecimen management system (www.

cabig.cancer.gov/solutions/applications/catissue/). One of our

Site(e.g., colon)

Global site-derivative model

Patient event #1(e.g., colectomy)

Pathology full textreport for event #1

Sample si(e.g., tum

Sample si(e.g., adjacent

Sample si(e.g., ulcerative

…

Sample si(e.g., norma

Global “site-derivative” data model for caTissue Suite devel

Figure 4 Global “site-derivative” data model for caTissue Suite that can handle

linkage to molecular derivatives of primary samples (the example of a colect


development requirements included direct interfaces with the

EPR and CoPath. Using a Medical Record Number, all patient

demographics such as name, date of birth, and gender are

automatically imported into caTissue Suite from UHN’s EPR.

This minimizes specimen mix-ups and transcription errors. A

novel HL7 interface with CoPath has also been established such

that all relevant corresponding pathology reports are automati-

cally imported into caTissue Suite.

The following were some of the other requirements for

developing our state-of-the art biobanking information technol-

ogy (IT) system for documenting, tracking, and annotating a

large diverse collection of high-quality biospecimens and their

molecular derivatives for use in research studies:

� The system must be flexible enough to allow entry of any

research biospecimen (solid tissue, bloods, body fluids,

and derivatives) from any patient (internal or external to

UHN) and from any procedure (surgical resection, biopsy,

venipuncture, paracentesis, autopsy, etc.). To this end, we

implemented a “global site-derivative” data model for

caTissue Suite (Figure 4).

� The system should handle all daily workflow in a single

database, including registering patients for upcoming

outpatient clinic appointments and inpatient procedures,

documenting research consent, documenting clinical in-

formation (pretreatment status, frozen section diagnosis),

and documenting specific information such as whether a

sample is “on hold” for a particular clinical trial or other

research study.

Individualpathological header

diagnoses

Sample #1 (LN frozen)Sample #2 (paraffin)

Sample #N

Derivative #1 (DNA)Derivative #2 (RNA)

Derivative #1 (HE slide)Derivative #2 (IHC slide)

te #1or)

te #2adenoma)

te #3colitis/IBD)

te #Nl colon)

oped at UHN BSP

any specimen type in any combination and allows logical and hierarchical

omy specimen is shown).


http://www.cabig.cancer.gov/solutions/applications/catissue/

http://www.cabig.cancer.gov/solutions/applications/catissue/



� Patient events (procedures) should be listed in temporal

order, and the system should have prepopulated drop-

down menus to facilitate sample annotation and

searches. Documentation should include type of proce-

dure, organ site, tissue site, gross pathological status, lat-

erality, as well as preanalytical variables such as

collection, receipt, and freezing times and preservatives

used (if any).

� De-identified biospecimen numbers and storage locations

should be generated automatically. Scanner and human-

readable alphanumeric and 2-dimensional barcode labels

should be generated by the system and printed onto cas-

settes, vial labels, and slide labels.

� Legacy data from previous research biobank database

should be imported ensuring the integrity of the collection.

� The system should be electronically federated with all of

UHN’s site- and disease-specific clinical databases.

Figure 5 depicts the IT model in which caTissue Suite is

federated with other UHN clinical research databases

including eCare, DADOS, MosaiQ, and Caisis databases via

SAP technology.

Subspeciality pathologists work closely with a multidisciplinary

team of internists, surgeons, oncologists, cardiologists,

interventional radiologists, and researchers to ensure highest-

quality biobanking

The Laboratory Medicine Program (LMP) at UHN is one of the

largest diagnostic academic pathology laboratories in North

America. With more than 50 subspeciality pathologists on staff,

LMP is recognized as a world leader in pathology research and

education and the adoption of new technologies such as tele-

pathology and digital image analysis. The subspeciality pathol-

ogists have established specific banking protocols for each organ

CaisisClinical

annotations

CoPathUHN pathologysynoptic reports

UHN advancedclinical

documentation

UHNPatient demo

Clinicaltrials Data f

and r

Recom

SAP-based data federation between mu

Figure 5 SAP-based database federation between different research database


site. BSP PAs are trained in biobanking and grossing protocols

established by staff subspeciality pathologists. When surgical

specimens are received by BSP PAs, initial handling for research

banking is performed simultaneously with preparation of the

sample for fixation and clinical-diagnostic workup. Lesional and

matched normal tissues are sampled and snap frozen in liquid

nitrogen from as many specimens and sites as possible without

negatively affecting the diagnostic pathological interpretation of

the specimen. The amount of tissue banked is kept in proportion

to the size of the lesion. In general, lesions <1 cm in maximum

dimension are not banked without direct oversight by the

responsible pathologist. Three or more vials of tumour are taken

from larger tumours. Lesional tissue is sampled away from

grossly visible necrosis and haemorrhage. Great care is taken to

leave all margins intact which are inked prior to sectioning and

sampling and must not be compromised. Photographic docu-

mentation of the specimen is routinely used. Assessment of sizes

of both specimen and lesion(s) must also not be compromised,

and specimens that need to be submitted in toto for accurate

characterization of a lesion are not banked. A notation “tissue

taken frozen” is made in the gross clinical description whenever

tissue is banked. A piece of tissue adjacent to each site of banked

fresh frozen tissue is fixed in formalin and banked for research in

a “mirror image” research paraffin block. In addition, fresh live

tissue from larger tumours may be distributed under specific

protocols to researchers for cell sorting, xenografting into

immune-deficient mice, establishment of cell lines, or for isola-

tion of viable tumour infiltrating lymphocytes. Snap frozen

biospecimens are stored in 2 ml cryovials for rapid uniform

freezing and storage efficiency. If surgical specimens are

received late and/or are placed in formalin before banking, only

fixed research paraffin blocks are banked. In the following, ex-

amples of how UHN BSP handles various specimen types are

given.

UHNBioBank

EPRgraphic info

caTissue SuiteSpecimen

management

eCare DADOS MosaiQ

Clinical annotation

SAPederationeporting

searchmunity

ltiple UHN research databases

systems in operation at UHN.




Breast tumour banking

Breast tumours may be banked from grossly visible invasive le-

sions that are at least 1 cm in size. Non-lesional tissue is takenwell

away from the tumour and from more fibrous areas of breast pa-

renchyma. In an attempt to bankmore cases of breast cancer, UHN

BSP has developed a new workflow in which additional research

blocks are taken up to 24 hours after fixation under the direction of

a breast pathologists. The research blocks and slides are processed

and reviewed with the clinical case and only repurposed into the

clinical domain if necessary. Over a 12-month period, this

approach has significantly increased the number of fixed tissue

blocks banked for research. Approximately half of the more than

250 cases banked under the new protocol would have been

considered too small for traditional banking. Only very few (<5%)

research blocks collected under the new protocol had to be

repurposed back into the clinical archives (unpublished data).

Gynaecological tissue banking

Tissue is banked frozen with corresponding fixed blocks from

each ovary and Fallopian tube, endometrium, myometrium, and

any visible tumour. If the patient is known to carry a BRACA

germline mutation, the ovaries and tubes are submitted to

diagnostic pathology in toto. Benign and malignant ovarian tu-

mours are banked according to general protocols as well as from

metastatic sites such as omentum.

Research biopsies and fine needle aspirates

Increasingly, researchbiopsies arebeingperformed for insights into

disease progression, particularly to interrogate the molecular evo-

lution of cancer.2,15 BSP staff play an integral role in study design,

processing, storing, and annotating research core needle biopsies

and fine needle aspirates. The challenge is to ensure that the sam-

ples are representative, viable, andadequate for omic profiling such

as targeted next generation exome sequencing or transcriptome

sequencing. Preanalytical variables need to be carefully controlled,

and histological evaluation by a pathologist is essential in order to

determine tumour adequacy and confirm the diagnosis.

Blood sample banking

Blood samples can be banked as whole blood, serum (serum

separator tube), plasma, or buffy coat (EDTA or ACD tube).

Serum and plasma banked for biomarker research is separated

from cellular components by centrifugation and snap frozen as

quickly as possible after the blood draw. Tentative disease status

as well as preanalytical variables such as date and time of blood

draw, receipt by the lab, and freeze time are documented. The

buffy coat is frequently be used as a source of germline DNA, and

thus great care needs to be taken to harvest sufficient quantities.

Banking of body fluids

Excess body fluids are collected and processed most commonly

from patients with breast and ovarian cancer. A small aliquot is

processed into a cytospin slide, fixed, and stained for pathology

review to evaluate the presence and purity of tumour cells.

Another aliquot is processed by centrifugation to separate the

cellular and liquid components for snap freezing. Body fluids are

also frequently distributed fresh to researchers in 500-ml aliquots

for cancer stem cell work, tumour infiltrating lymphocytes, and

other studies requiring fresh, viable cells.


Cardiovascular tissue banking

Tissue is banked from cases of cardiomyopathy, atrial tumours,

and heart transplants. Typical biospecimens include cardiac tu-

mours, myocardium, valves, and aorta. Careful and precise

documentation of the anatomic sites from which cardiovascular

biospecimens originate is required to ensure the quality of future

cardiovascular research. Transcriptome sequencing studies of

diseased heart tissue requires very rapid processing after surgical

excision (<10 minutes).

All research studies involving BSP biospecimens have a

designated UHN study pathologist

UHN biospecimens are used in more than 50 ongoing

institutionally-approved research projects, including specimen-

centred molecularly-driven oncology clinical trials. A designated

study pathologist is involved in project design, performs an

expert review of tissue sections to confirm diagnoses, and en-

sures adequate quality and quantity of lesional and control tissue

for downstream analysis. In the case of body fluids, the study

pathologist evaluates an H&E stained cytospin slide for the

presence of tumour cells and lymphocytes. Many of our research

projects are multi-institutional and international genomics ini-

tiatives including the International Cancer Genome Consortium

(pancreas and prostate) and The Cancer Genome Atlas (thyroid,

adrenal and paraganglioma, endometrial, head and neck,

gastroesophageal, lung). The UHN Cancer Stem Cell Program has

successfully established human tumour xenograft models of

ovarian, breast, colon, pancreatic, and other solid tumours in

immune-deficient mice towards enhancing our understanding of

cancer stem cells, the tumour microenviroment, and as patient-

derived drug treatment models.9,10,14 Other researchers use

fresh solid tumours from surgical resection and body fluid

specimens to isolate and study tumour infiltrating lympho-

cytes.20 Tissues from BSP’s fixed blocks are frequently used in

clinical trials. One of the largest trials at UHN involves molecular

profiling of fixed tumours from patients with advanced cancers.15

Highest-quality research biospecimens are particularly important

when used for such trials.

Funding and infrastructure of a Biospecimen Sciences Program

In order to establish a quality biobanking programme, infra-

structure and operational funding are required. Infrastructure

includes offices and computers for the CRCs, workspace, com-

puters, printers, and short term liquid nitrogen storage in surgical

pathology for the BSP PAs, a core lab with computers, printers,

centrifuges, and biosafety cabinets for blood and body fluid

processing, a secure long-term cryogenic storage facility with

vapour phase freezers and monitoring equipment, a temperature-

controlled slide and block storage facility, and a molecular

biology lab for biospecimen analysis, quality control, and

research. A quality biorepository should have processing capa-

bility for extraction and analysis of nucleic acids and proteins, an

analysis lab with arrayers for building tissue microarrays, a

digital slide scanner with automated immunohistochemical

analysis software, and a laser capture microscope. Close prox-

imity to diagnostic pathology fosters collaboration with sub-

speciality pathologists and ensures optimal logistics. Long-term




institutional operational funding ensures appropriate staffing for

day-to-day operations of banking, distribution, annotation, and

quality control of biospecimens.

Next-generation biobanking

Research biobanking of well annotated, carefully preserved bio-

specimens is crucial for the molecular interrogation of complex

disease processes and the discovery and development of new

diagnostic tools and treatment options.1 Advances in our un-

derstanding of disease at the molecular level are prerequisites for

truly personalized precision medicine, i.e., “finding the right

treatment for the right patient at the right time”.

Next-generation biobanking differs from traditional bio-

banking in a number of ways: a more multidisciplinary team

approach is needed for sample collection including interventional

radiologists to perform dedicated research biopsies and cytopa-

thologists for fine needle aspirations. Biospecimens will become

increasingly smaller (biopsies) and more frequently obtained

(serial sampling of lesions at various time points during treat-

ment and as disease progresses) rather than from a single time

point surgical resection. Ultra-rapid procurement of fresh tissue

and long-term storage at �185 C is essential for faithfully pre-

serving the pathophysiome of samples and to future-proof for the

next generation of high-throughput technologies.

Expert pathology oversight will be crucial to ensure that

biospecimens are representative, viable, and adequate for next-

generation “omic” technologies in the study of cancer, cardiac,

autoimmune, neurologic, and other diseases. Research is

already shifting from genomics towards transcriptomics, prote-

omics, lipidomics/glycomics, and metabolomics, and biobanks

must be prepared to meet this need by ensuring very rapid (<10

minutes) procurement of biospecimens, including both solid

tissues and blood samples. This will require significant infra-

structural investments because it goes significantly above and

beyond current standards for surgical pathology or laboratory

medicine.

Quality assurance in biobanking requires robust institutional

oversight and governing principles to ensure appropriate acqui-

sition and use of biospecimens, standard operating procedures

overseen by qualified pathologists so that biospecimens are

carefully processed, stored, and annotated, close multidisci-

plinary collaboration between researchers and clinicians, and

long-term investment in information technology, specialized

equipment, and infrastructure to preserve the integrity of the

collection for future research. As more innovative and targeted

approaches are developed towards improving the diagnosis,

monitoring, and treatment disease, next-generation bio-

specimens from quality biobanks will play a decisive role in

advancing personalized precision medicine. A

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FURTHER READING

Canadian Institutes of Health Research, Natural Sciences and Engineering

Research Council of Canada, Social Sciences and Humanities Research


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http://dx.doi.org/10.1002/path.4287

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Council of Canada. Tri-council policy statement: ethical conduct for

research involving humans December, 2010.

Canadian Tumour Repository Network (CTRnet). http://www.ctrnet.ca/.

CAP Accreditation for Biobanks. http://www.cap.org/apps/docs/

laboratory_accreditation/build/pdf/bap_standards.pdf.

caTissueSuite. http://cabig.cancer.gov/solutions/applications/catissue/.

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registration of pharmaceuticals for human use. http://www.ich.org/

fileadmin/Public_Web_Site/ICH_Products/Guidelines/Efficacy/E6_R1/

Step4/E6_R1__Guideline.pdf.


International Society of biological and Environmental Repositories. www.

isber.org.

NCI Best Practices. http://biospecimens.cancer.gov/bestpractices/.

Acknowledgements

We would like to thank the members of the UHN Program in

BioSpecimen Sciences and the UHN Laboratory Medicine Program

for their dedication to world-class biospecimen research.




http://www.ctrnet.ca/



http://cabig.cancer.gov/solutions/applications/catissue/






http://biospecimens.cancer.gov/bestpractices/


High-quality biobanking for personalized precision medicine: BioSpecimen Sciences at the helm

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