How a Hospital Biobank Supports
Patient Care and Research Programs
National Cancer Center Hospital
Tokyo, Japan
October 25, 2012
Mark E. Sobel, MD, PhD
Executive Officer,
American Society for Investigative Pathology mesobel@asip.org
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

To investigate the causes of death, to examine carefully the condition of organs, after such changes have gone on in them as to render existence impossible and to apply such knowledge to the prevention and treatment of disease, is one of the highest objects of the physician.
—Sir William Osler (1849–1919)
Extracted from his Graduation thesis “Pathologic Anatomy”
4

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.

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

• Known abuses of populations and patients
• Naxi experiments
• Radiation experiments (U.S.)
• Tuskegee Syphilis Study
• Taking advantage of prisoners and mentally handicapped

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

Health Policy
Research
Biobanks and Clinical Research
Health Outcomes
Research
Population and
Public Health
Translational
Research
Research Involving Patients
Reduce Costs Improve Health
Clinical Trials of Drugs
Clinical Trials of Devices
Clinical Trials of
Diagnostics
Clinical Trials of
Models of Care
20

The Translational Research Cycle
The Biobank is Essential to Provide Solutions
Investigative Models
Patients as Partners
Models of Human Disease
Research
Questions
Technology Transfer
Biobank
Tissues, Cells, Fluids, &
Products and Dry Data
Tools
Genetics, Genomics, Proteomics,
Imaging, Physiology, Biophysics,
Biochemistry, Nanotechnology,
Informatics, Sociology, Epidemiology,
Statistics
Pathophysiological and
Sociobiological
Processes
Translational
Research
Cycle
Identification of Novel
Markers and Targets
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?

Goals of Personalized Medicine
 50% of first treatments do not work
 Optimize treatment for individual patients
 Minimize adverse drug events
 Maximize drug efficacy
 Develop more targeted drugs
 The right drug at the right dose

Application to Oncology


Determine the preferred therapeutic agent for each tumor
Ascertain which patients are most likely to benefit from a given therapy

Patients with same diagnosis
Adapted, Courtesy Slide from Howard L. McLeod
Institute for Pharmacogenomics and Individualized Therapy
UNC – Chapel Hill, NC

All patients with same diagnosis
Toxic Responder: Lower dose or alternate drug

All patients with same diagnosis
Non-Responder: higher dose or alternate drug

Pharmacogenetics: The Study of Variations in Genes that Affect Responses to Drugs
• Genetic changes specifically within malignant tumor cells
• Inherited genetic variability in a targeted gene or group of functionally-related genes affecting response to drugs

Pharmacogenetics: The Study of Variations in Genes that Affect Responses to Drugs
• Genetic changes specifically within malignant tumor cells
• Estrogen Receptor Status
• Treatment with SERMs- selective ER modulators
• Tamoxifen
• Raloxifene
• Multigene analysis:
• OncoType DX assay (21 genes)
• MammaPrint assay (70 genes)
• Epidermal growth factor receptor (EGFR) Status
• HER2/neu (Herceptin therapy)

Pharmacogenetics: The Study of Variations in Genes that Affect Responses to Drugs
• Genetic changes specifically within malignant tumor cells
• Inherited genetic variability in a targeted gene or group of functionally-related genes affecting response to drugs

Pharmacokinetics: What the Body Does to the Drug
• Absorption – substance enters the body
• Distribution – drug disperses to fluids and tissues
• Metabolism – transform parent compound into daughter compounds
• Excretion – elimination of parent drug and daughter compounds from the body

Pharmacokinetic Metabolism: transform parent compound into daughter metabolites
• Parent compounds are converted to metabolites that are more water soluble so they can be more easily excreted
• Bioactivation: Prodrugs are converted into therapeutically active compounds

Cytochrome P450 Enzymes
•Supergene family
•Active in the liver and small intestine
•Named for the characteristic absorption spectra of the protein products (450 nm)
•Human genome: 57 CYP genes
•15 genes involved in metabolism of xenobiotics
•75% of total metabolism of drugs
•14 genes involved in metabolism of sterols
•4 genes oxidize fat-soluble vitamins
•9 involved in metabolism of fatty acids and eicosanoids
•15 unknown function

CYP Nomenclature
Supergene family
Family
CYP 2 D 6 *1
Subfamily
Isoenzyme
Allelic variant
*1 is usually wild-type

Tamoxifen


Approved by the US FDA for the treatment and prevention of breast cancer
Anti-estrogen
 SERM: selective estrogen receptor modulator

Tamoxifen:
A Prodrug Requiring Extensive Metabolism
Tamoxifen
CYP2D6
4-hydroxyTAM
MINOR METABOLITE -
100X POTENCY
CYP3A4/5
CYP3A4/5
CYP2D6
N-desmethylTAM Endoxifen
MAJOR METABOLITEMODERATE METABOLITE-
100X POTENCY
SAME POTENCY
Genetic variants of CYP2D6 and drugs that modulate this enzyme significantly affect outcome in tamoxifen-treated patients
Adapted from Goetz, M. P. et al. J Clin Oncol; 23:9312-9318 2005

CYP2D6 and Tamoxifen
•At least 70 CYP2D6 allelic variants
•Reduced activity of CYP2D6
→ reduced metabolism of tamoxifen
→ poor response to tamoxifen
•Classification of alleles
•Poor metabolizers
•Intermediate metabolizers
•Extensive metabolizers
•Ultrarapid metabolizers
•Ethnic variation –
•CYP2D6*4 – poor metabolizer
•12% - 21% Northern Europeans
•1% - 2% Asians and Black Africans
•CYP2D6*10 – intermediate metabolizer
•Most common allele in Asians

Tamoxifen Side Effects
 Hot flashes
 Endometrial cancer
 Thromoembolic events

Side effects of Tamoxifen and
Treatment with Antidepressants
•Hot flashes most common side effect
•Treated with antidepressants:
•SSRIs (selective serotonin reuptake inhibitors)
•Inhibit CYP2D6 activity
•Potent inhibitors (paroxetene, fluoxetine) reduce endoxifen levels
•Less potent inhibitors (venlafaxine) have little effect
•Patients with decreased metabolism:
•Shorter time to recurrence
•Worse relapse-free survival
•Potent CYP2D6 inhibitors such as certain SSRIs are contraindicated in tamoxifen-treated patients

CYP2D6 Poor Metabolizers
• Patients diagnosed with breast cancer should be treated with alternatives to tamoxifen (e.g. aromatase inhibitors)
• For breast cancer prevention, raloxifene is a viable alternative to tamoxifen
Recommended reading:
Snozek CLH, O’Kane DJ, and Algeciras-Schimnich A.:
Pharmacogenetics of Solid Tumors: Directed Therapy in reat, Lung, and Colorectal Cancer. J Mol Diagn 2009,
11:381-389, DOI: 10.2353/jmoldx.2009.090003

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.

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.

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)

The Potential of Tissue Based Analysis
46

Basic Ethical Principles
Ideal of respect for persons
• Public beneficence
• Responsible stewardship
• Intellectual freedom and responsibility
• Democratic deliberation
• Justice and fairness

Presidential Commission
for the Study of Bioethical Issues
Washington, DC
October 2012 http://www.bioethics.gov

Communication among
Repositories across the Globe www.isber.org
A Division of American Society for Investigative Pathology