Best Practices for Biobanking in the Era of Precision

Report
Best Practices for Biobanking in
the Era of Precision Medicine
JSCO 50th Annual Meeting
Yokohama, Japan
October 27, 2012
Mark E. Sobel MD, PhD
Executive Officer
American Society for Investigative Pathology
[email protected]
http://www.asip.org/about/executive_officer.cfm
The Era of Molecular Medicine
A transformation of the practice of
medicine AND the public’s fears and
expectations
•Molecular techniques
•Human Genome Project
•Information technology
Every Era Has Transformative Events
Giovanni Battista Morgagni
(1682—1771)
Images from: Encyclopaedia Britannica, adapted from Dr. Bruce McManus, University of British Columbia
3
Clinical Diagnostic Genome Sequencing
The introduction of high-throughput,
next-generation sequencing (NGS) in 2005
heralded a critical and transformative step
in the history of DNA sequencing.
http://en.wikipedia.org/wiki/File:
TOSopeninglogo.png
http://www.hd-report.com/2009/02/21/startrek-the-original-series-coming-to-blu-ray/
Acknowledgement: Dr. Daniel Farkas,
Sequenom Center for Molecular Medicine
NEXT-GENERATION SEQUENCING
FROM THE POINT OF VIEW OF
STAR TREK’S DOCTOR McCOY (“BONES”)
Dr. McCoy scanned the patient while Captain Kirk waited impatiently for a diagnosis.
“Damn it, Jim. I’m a simple country doctor– this is gonna take a few seconds,”
McCoy shouted.
“Doctor, I need to now if this Aleuvian Ambassador is going to live or not,” Kirk
demanded.
“OK, OK, it’s coming together. My tricorder’s on board DNA sequence scanner is
detecting foreign DNA sequences in this patient’s genome. Jim, this man has Vulcan
Encephalopathy Viral Fever. It’s fatal in Aleuvians.”
“Dammit Bones. This man has to live or these negotiations will break down.”
NEXT-GENERATION SEQUENCING
FROM THE POINT OF VIEW OF
STAR TREK’S DOCTOR McCOY (“BONES”)
“Hold on. I’m running the sequence through the Medical Database. It’ll compare
the viral sequences with the proviral therapeutics in the Pharmacy. Scotty’s still
runing that damned Engineering diagnostic so it’s going to take a few minutes.
Great ship, Jim, but I’ve been after you for months now to upgrade my computers to
keep up with all this data. I may as well be working with catgut and floppy disc
drives.”
“OK, it’s coming through now. There’s one drug that can help him but I don’t dare
give it to him. I don’t dare, Jim!- without getting his consent. There are some
strange sequences in his DNA. I just don’t know the significance of this adenine
track and can’t predict the outcome--- this nucleotide therapy will cure him or kill
him. This patient is going to have to decide.”
“Dammit Bones, you’re risking interstellar war here.”
“Captain, I am a doctor and I’ve taken an oath to do no harm. I will not proceed
without talking to this patient or at least doing some more genomic investigation.”
Definitions
•Human genome- the “whole genome” of a human
consists of 3 gigabytes of information
•3 billion base pairs of DNA
•46 chromosomes (diploid genome)
•Approximately 98% is “intergenic”
•“between genes”
•Junk DNA?
•Does not encode proteins
•Human exome
•2% of the genome
•22,000 pairs of genes
•On average, there are 8 exons (protein-encoding
segments) per gene = 176,000 exons
•Human transcriptome (DNA> RNA> protein)
•The expressed RNA transcripts of genes
•What a cell is doing at a particular point in time
Definitions
•Genotype – what the cell is capable of doing
•Genome analysis
•Phenotype- what the cell is doing
•Proteomic analysis (proteins)
•Germline or somatic?
•Germline•Inheritability
•Implications for immediate and extended family
•Implications for ethnic group
•“Normal” tissues
•Somatic•Acquired mutations
•Use of “diseased” tissues
•No heritable implications for family
Clinical Diagnostic Genome Sequencing
WGS: Whole genome sequencing
WGA: Whole genome analysis
Biospecimens are required!
Repository or Biobank?
•A repository is an organized collection of samples
•A biobank is a repository of biological samples
Biospecimens in a Human Biobank
•Tissue samples
•Biopsy
•Resection of tissue (surgery)
•Dissection of tissue (autopsy)
•Blood, sputum, urine, bone marrow
•Associated data
•Clinical history
•Environmental history
•Family history
•Demographics (gender, age)
•How the sample was collected
Biospecimens in a Human Biobank
•Freshly obtained
•Frozen
•Fixed
•Formalin-fixed paraffin-embedded (FFPE)
•Alcohol-fixed
•Other fixatives
Types of Biobanks
•Freezer banks or Cold storage rooms
•Glass slide collections
•Tissue blocks (FFPE)
•Liquid specimens (blood, urine…)
•Buccal (cheek) swabs
•Extracted analytes (DNA, RNA, protein, etc)
Who is Involved?
•Donor
•Patient
•Family
•Ethnic group
•Physician
•Nurse
•Administrative assistants
•Laboratory technicians
•Ethical oversight
Requirements of Biobanks
•Record keeping
•Associated data
•Informed consent
•What permissions or restrictions are associated
with the use of the specimen?
•Temperature
•Humidity
•Light/dark
•Controlled access – only authorized
individuals can retrieve specimens
Confidentiality and Privacy
•Confidentiality- the principle in medical ethics that the
information a patient reveals to a health care provider is
private and has limits on how and when it can be
disclosed to a third party
•Privacy - culturally specific concept defining the extent,
timing, and circumstances of sharing oneself
•Physical
•Behavioral
•Medical
Identification of Specimens
• Anonymous- the sample was collected without the
identity of the donor
• Anonymized – the sample was collected with the
known identity, but the identification was
removed
• Coded (Linked) – the sample is given a unique
identifier that cannot be easily deciphered
• Identified – the sample has a common identifier
(name, hospital number)
Personalized (Precision) Molecular Medicine
• Public’s expectations
– Improved health care
– Personalized medicine
• Public’s fears
– Loss of privacy
– Loss of employment
– Loss of insurance
– Social stigmatization
Biomedical Research and Biobanks:
Translational Research involves interactions
between the laboratory bench and patient’s bed
•Increase knowledge
•Understand biological processes
•Improve public health
•New diagnostic tests
•New prognostic tests
•New or improved therapy
Biobanks and Clinical Research
Health Policy
Research
Health Outcomes
Research
Population and
Translational
Public Health
Research
Research Involving Patients
Reduce Costs
Improve Health
Clinical Trials
Clinical Trials
Clinical Trials of
Clinical Trials of
of Drugs
of Devices
Diagnostics
Models of Care
21
The Translational Research Cycle
The Biobank is Essential to Provide Solutions
Biobank
Tissues, Cells, Fluids, &
Products and Dry Data
Tools
Genetics, Genomics, Proteomics,
Imaging, Physiology, Biophysics,
Biochemistry, Nanotechnology,
Informatics, Sociology, Epidemiology,
Statistics
Investigative Models
Patients as Partners
Models of Human Disease
Research
Questions
Translational
Research
Cycle
Pathophysiological and
Sociobiological
Processes
Identification of Novel
Markers and Targets
Technology Transfer
Biomarker or Target
Validation
Multi-population
Assessment, Highthroughput Screening
Clinical Trials
Adapted from Dr. Bruce McManus, UBC
The Path to Clinical Implementation
from Translational Research
•Analytical validity - Technical feasibility and optimization
– does the test measure what we say?
•Clinical validity – Diagnostic accuracy - does the test
measure a value associated with a clinical condition?
•Sensitivity (false negatives)
•Specificity (false positives)
•Clinical utility
•will the test improve making a healthcare decision?
•Will the test be cost effective?
Clinical Diagnostic Genome Sequencing
The introduction of high-throughput,
next-generation sequencing (NGS) in 2005
heralded a critical and transformative step
in the history of DNA sequencing.
This report of the Whole Genome Analysis group of the Association for Molecular Pathology
illuminates the opportunities and challenges associated with clinical diagnostic genome
sequencing. With the reality of clinical application of next-generation sequencing, technical aspects
of molecular testing can be accomplished at greater speed and with higher volume, while much
information is obtained. Although this testing is a next logical step for molecular pathology
laboratories, the potential impact on the diagnostic process and clinical correlations is
extraordinary and clinical interpretation will be challenging. We review the rapidly evolving
technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent;
and address the analytic, postanalytic, and professional implications. (J Mol Diagn 2012,
14:525540; http://dx.doi.org/10.1016/j.jmoldx.2012.04.006)
Coming to a clinic near you…
The Potential of Tissue Based Analysis
27
NGS Platforms
Although the NGS platforms differ in design
and specific chemistries, they are
fundamentally related by a paradigm in which
sequencing of spatially separated, clonally
amplified DNA templates or single DNA
molecules is performed in a massively parallel
manner.
NGS Technology
All NGS technologies offer the ability to
simultaneously sequence thousands to
millions of relatively short nucleic acid
sequences in parallel. They can provide
orders of magnitude more information, at
competitive costs, when large regions of
the genome are sequenced.
Advantages of NGS Technology
Individual sequencing assays based on
capillary electrophoresis tend to be:
•Expensive
•Laborious
•Less comprehensive, necessitating serial geneby-gene testing to identify causative
mutation(s)
Informed Consent and Ethical Considerations
The capacity to perform large-scale sequencing on the human
genome presents unique challenges regarding the provision of
informed consent, particularly in deciding on the level of detail that
needs to be shared.
No specific guidance exists, and each institution offering such
testing is deriving its own policies.
With genome testing by NGS, the perceived and real potential risks
are magnified compared with genetic tests that target only one
gene at a time.
Bioinformatics Requirements
Major computations performed with NGS data:
•Data assembly with base calling at the level of
individual reads
•Alignment of the assembled sequence to a
reference sequence
•Variant calling
Variant Calling
•Different computational analyses devoted to
SNPs, small indels, structural variants or large
indels, copy number variants
•Generation of an unprecedented amount of
medical data that result in special informatics
needs and require tools for data management,
storage, analysis, and archiving
•Manage the large data set without error and
to ensure proper quality and documentation.
Electronic Health Record
Reporting of NGS test results raises several
issues:
•Ordering of the test
•Receiving a document that summarizes the
clinical interpretation
•Storage of the interpretation
Incidental Findings
An incidental finding is a finding concerning an individual
in the course of conducting research that has potential
health or reproductive importance and is discovered in
the course of conducting research, but is beyond the aims
of the study and is not anticipated in the research
protocol.
Susan M. Wolf, et al. (2012). Genetics in Medicine, 12: 361-384.
What about incidental findings that occur in the
course of clinical testing? Especially WGS!
Presidential Commission
for the Study of Bioethical Issues
Washington, DC
October 2012
http://www.bioethics.gov
Challenges Facing Biobanks:
Shortage of Quality Biospecimens
Lack of standard and uniform operating
procedures for:
•Collection
•Processing
•Annotation
•Storage
•Transport
International
Society for
Biological and
Environmental
Repositories
Communication among
Repositories across the Globe
www.isber.org
A Division of American Society for Investigative Pathology
Biospecimen Science
What is biospecimen science?
Biospecimen Science is the multidisciplinary field of study
responsible for establishing tested and proven biospecimen
resource-related procedures based on experimentation in the areas
of specimen collection, processing, shipping, and storage
Why is it needed?
Biospecimens are composed of active and reactive living cells or
cell products, making them highly complex.
The collection, handling, and storage process can profoundly alter
the molecular profile and quality of biospecimens.
Such alterations, though artificial, can be misinterpreted as disease
related or disease specific.
High degrees of sensitivity and specificity in new molecular
techniques raise the bar for analyte (specimen) data and quality.
39
Biospecimen Science
Quality of human biospecimens is multifactorial and is determined by:
•
•
•
•
•
•
•
Type of specimen: Normal tissue, tumor tissue, serum, plasma
Physical state of the specimen
Amount and type of specimen characterization data
Amount and type of quality control exercised
Amount and type of clinical data
Permitted use of the specimen
The analysis to be performed and the biomolecules targeted by the
analysis
• The goal of the research (application of the data)
40
International Society for Biological and
Environmental Repositories
Best Practices for Repositories:
Collection, Storage, Retrieval and Distribution of
Biological Materials for Research
Second Edition: Cell Preservation Technology,
Volume 6, Number 1, 2008
Third Edition: Biopreservation and Biobanking
Volume 10, Number 2, 2012
41
Quality Control - definition
« the operational techniques and activities that are
used to satisfy quality requirements », ISO9000:2000
Nestler W. Effect of Quality Control programs on the organizational structure
of the hospitals. Bull. NY Acad. Med. 1976;52:157-163
Glenn GC, Hathaway TK. Effects of specimen evaporation on quality control.
Am. J. Clin. Pathol. 1976;66:645-652
Calam RR. Reviewing the importance of specimen collection.
J. Am. Med. Tech. 1977;39:297-302
« confirmation through provision of objective evidence
that requirements for a specific intended use or
application are fulfilled », ISO9000:2000
42
Integrated Quality Control Systems
QC / Validation
Biobank
Sample Processing Method
Biobank or Research Lab
Quality Control Assay
Method Validation / Proficiency Testing
43
in vivo Preanalytical Variables
- Position
- Fasting
- Caffeine :
- phosphodiesterase
 cAMP degradation
- Smoking
- adrenalin secretion 
- Stress
- triglycleride lipase
 lipid acids linked to albumin
- Circadian rhythms
 # of albumin-available sites
- Menstrual cycle
- Pregnancy
- Physical excercise
44
in vitro Preanalytical Variables
• Collection tubes
• shedding of components from the tube
• silicones, polymeric surfactants, clot inhibitors or activators, rubber
stoppers and plastics
• adsorption of serum proteins, RNA, DNA to the tube
• Anticoagulants
• citrate (dilution)
• heparin (binding)
• EDTA (platelet clumping)
• Clotting
time and time of incubation before centrifugation
• Storage conditions
• RT, changes after 8h (m/z<3000)
• 4°C, changes after 48h
• freeze-thaw cycles, controversy (peptide aggregation,
precipitation and adsorption)
45
SPREC-01
Biospecimen preanalytical code
Standard Preanalytical Coding for Biospecimens
Cancer Epidemiology Biomarkers and Prevention 2010;19:1004-11
46
Ideal QC Biomarkers

Ubiquitous

Measurable by widely accessible methods

On/Off response
Stability :
capability of a sample material to retain the initial
value of a measured quantity for a defined period of
time within specific limits when stored under defined
conditions
ISBER BS WG, Cancer Epidemiol Biomarkers Prevention 2009;18:1017-25
47
Why validate QC methods ?
•
give full confidence in sample quality
• use samples after a long time
• provide « reference materials »
• ensure validity of research results
48
How Can We Improve?
•
•
Proficiency Testing
Accreditation
49
ISBER Proficiency Testing Program:
Interlaboratory comparisons to identify problems in
laboratories and interlaboratory differences
Launched in 2011
•DNA Quantification
•RNA Integrity and Quantification
Added in 2012
•Cell Viability
•Tissue Histology
•Tissue Antigenicity
50
CAP Innovates Accreditation for Biorepositories
cap.org
Summary
 The Era of Precision Medicine
 Transformative events - NGS
 Translational research needs quality biospecimens
 Biospecimen Science and Best Practices
 Proficiency Testing and Biobank Accreditation

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