How a Hospital Biobank Supports Patient Care and Research Programs

National Cancer Center HospitalTokyo, Japan

October 25, 2012

Mark E. Sobel, MD, PhDExecutive Officer,

American Society for Investigative Pathologymesobel@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

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Giovanni Battista Morgagni(1682—1771)

Images from: Encyclopaedia Britannica, adapted from Dr. Bruce McManus, University of British Columbia

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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”

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

Why all the fuss?

• 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

Biobanks and Clinical Research

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Health Policy Research

Health Outcomes Research

Population and Public Health

Translational Research

Clinical Trials of Drugs

Clinical Trials of Devices

Clinical Trials ofDiagnostics

Clinical Trials ofModels of Care

Research Involving Patients

Reduce Costs Improve Health

The Translational Research Cycle The Biobank is Essential to Provide Solutions

Adapted from Dr. Bruce McManus, UBC

Translational Research

Cycle

Investigative ModelsPatients as Partners

Models of Human Disease

BiobankTissues, Cells, Fluids, & Products and Dry Data

Pathophysiological and Sociobiological

Processes

Identification of Novel Markers and Targets

Biomarker or Target Validation

Multi-population Assessment, High-

throughput ScreeningClinical Trials

Technology Transfer

ToolsGenetics, Genomics, Proteomics, Imaging, Physiology, Biophysics, Biochemistry, Nanotechnology,

Informatics, Sociology, Epidemiology, Statistics

Research Questions

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 tumorAscertain which patients are most likely to benefit from a given therapy

Patients with same diagnosis

Adapted, Courtesy Slide from Howard L. McLeodInstitute for Pharmacogenomics and Individualized TherapyUNC – 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 2 D 6 *1Supergene family

Family

Subfamily

Isoenzyme

Allelic variant

CYP Nomenclature

*1 is usually wild-type

Tamoxifen

Approved by the US FDA for the treatment and prevention of breast cancerAnti-estrogen

SERM: selective estrogen receptor modulator

Tamoxifen: A Prodrug Requiring Extensive Metabolism

Adapted from Goetz, M. P. et al. J Clin Oncol; 23:9312-9318 2005

Tamoxifen

N-desmethylTAM

CYP3A4/5

CYP2D64-hydroxyTAM

CYP2D6Endoxifen

CYP3A4/5

MAJOR METABOLITE-SAME POTENCY

MINOR METABOLITE -100X POTENCY

MODERATE METABOLITE-100X POTENCY

Genetic variants of CYP2D6 and drugs that modulate this enzyme significantly affect outcome in tamoxifen-treated patients

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 flashesEndometrial cancerThromoembolic 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.

Coming to a clinic near you…

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

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Basic Ethical PrinciplesIdeal of respect for persons

•Public beneficence

•Responsible stewardship

•Intellectual freedom and responsibility

•Democratic deliberation

•Justice and fairness

Presidential Commissionfor the Study of Bioethical Issues

Washington, DCOctober 2012

http://www.bioethics.gov

International Society for Biological and Environmental Repositories

A Division of American Society for Investigative Pathology

Communication among Repositories across the Globewww.isber.org

ISBER’s Mission ISBER creates opportunities for sharing ideas internationally and

harmonizing approaches to evolving challenges in

biobanking and repository operation.