Is the Anonymized Sample in Research an Endangered Species?

Mark E. Sobel MD, PhDExecutive Officer

American Society for Investigative Pathologymesobel@asip.orgASIP Digital Library

Stowell Symposium: Trends in Experimental Pathology: The Role of Biospecimens in Precision Medicine

ASIP 2014 Annual Meeting at Experimental BiologySaturday, April 26, 2014

Disclosures

I have no relevant financial disclosures

Some content of this presentation represents my personal views, which have been influenced by my conversations with members of the ASIP

Public Affairs Working Group, but they have not been officially endorsed by the ASIP PAWG

or ASIP Council.

Outline

Precision Medicine in Context: A Transformative Event

A Primer on Ethical Issues of Human Biospecimens Impact of New Molecular Technologies on

Research Utilizing Human Biospecimens Next Generation Sequencing (NGS)

How Can We Safeguard the Use of Anonymized Samples in Research?

Advance Knowledge and Improve Global Health Respect the Rights of Human Subjects (donors of

samples)

Every Era Has Transformative Events

4

Giovanni Battista Morgagni(1682—1771)

The Father of Modern Pathology –Study of the Patient (via Autopsy)

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

The Era of Precision Medicine:A transformation of the practice of medicine

Public’s expectations for improved health Public’s fears:

Loss of privacy Loss of employment Loss of insurance Social stigmatization

The Era of Precision Medicine

•Convergence of:•Molecular techniques

•Human Genome Project•Information technology

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 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.

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…

http://en.wikipedia.org/wiki/File:TOSopeninglogo.png

http://www.hd-report.com/2009/02/21/star-trek-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 know 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 running 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.”

A Primer on Ethical Considerations

1974 – National Research Act

• Created the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research

• Impetus: a series of scandals involving abuse of human subjects• Nazi experiments• Radiation experiments (US)• Tuskegee Syphilis Study (US)• Taking advantage of vulnerable populations

A Primer on Ethical Considerations

The Belmont Report (1979)http://

www.hhs.gov/ohrp/humansubjects/guidance/belmont.html

Respect for persons (autonomy) Beneficence

Justice

The Common Rule

"Code of Federal Regulations - Title 45 Public Welfare CFR 46

".

A baseline standard of ethics by which any government-funded research in the United States is held, and nearly all academic institutions hold their researchers to these statements of rights

regardless of funding.

The Common Rule

A rule of ethics regarding biomedical and behavioral research involving human subjects in the US.

Regulations governing Institutional Review Boards (IRBs) for oversight of human research came.

Went into effect in 1981 following the 1975 revision of the Declaration of Helsinki and the Belmont Report of 1979.

Revised in 1991. Notification of advanced rule making in 2011.

The Common Rule

Rights in addition to autonomy, beneficence, and justice Privacy Right to withdraw Informed consent

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)

Identification of Specimens

• Any human biospecimen that can be identified by any one person, anywhere, is an identifiable sample

• If a sample is coded, and any investigator keeps a key to the code, the sample is identifiable.

• Exception (Office of Human Protections): If the recipient of the human biospecimen signs an agreement that there is no intent to identify the sample, the sample may be considered unidentifiable.

Definition of a Human Subject Does NOT Include:

• Deceased persons (autopsy specimens)• Publicly available information• Unidentifiable samples

The Common Rule

An IRB may grant a waiver of informed consent under the Common Rule if four criteria are met: Minimal risk Respect for autonomy and the rights of the

individual Impracticable Notification

The Common Rule

Waivers are rarely granted for identified samples

Waivers are usually granted for collecting anonymous samples

Waivers are usually granted for suing anonymous or anonymized samples

Waivers are occasionally granted for coded (linked) samples

And then 11 years ago, along came HIPAA

Health Insurance Portability Authorization Act – April 2003

http:www.hhs.gov/ocr/hipaa There are inconsistencies (lack of

harmonization) between HIPAA and the Common Rule

Privacy of information extends to the family and survives beyond the death of the donor (50 years).

Affects clinical treatment and research

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 but may encode non-coding RNA molecules and regulatory signals

•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!

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 /community group

•Members of the healthcare team•Physician•Nurse

•Researcher•Administrative assistants•Laboratory technicians•Ethical oversight

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

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

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?

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

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

• Security: maintaining confidentiality

Presidential Commissionfor the Study of Bioethical Issues

Washington, DCOctober 2012

http://www.bioethics.gov

The Question

Does the ability to inexpensively and rapidly sequence the genome of an individual from a single cell of a biospecimen nullify the concept of an anonymous or anonymized sample?

Is the anonymized sample an endangered species?

How Can We Safeguard Archived Pathology Resources?

Data confidentiality, integrity, security, and controlled access to information should be ensured.

The level of security should coincide with the sensitivity of the information.

Researchers, Institutional Review Boards (IRBs), and institutions providing support for research endeavors should oversee the consent requirement, maintenance, access, and use of archived pathology resources.

How Can We Safeguard Archived Pathology Resources?

Investigative pathologists are well-positioned to assume a leadership role in addressing the concerns involved with archived pathology specimens, providing stewardship and ensuring that these specimens remain a vital resource.

How Can We Safeguard Archived Pathology Resources?

Unless specific donor consent is granted, all individuals working with archived pathology samples should not attempt to identify previously unidentified (or anonymized) samples. Do not use advanced technologies to identify a

donor Do not access a research database for purposes of

identification

How Can We Safeguard Archived Pathology Resources?

All individuals working with archived pathology samples should receive training in the applicable regulations. Health Information Technology for Economic and

Clinical Health Act (HITECH) Health Insurance Portability and Accountability Act

(HIPAA) Common Rule

What is the Threshold?

Is there a difference between research involving no or a limited amount of genetic information versus research that specifies a significant portion or all of the genome?

Where there is a question of whether a sample contains sufficient information to render it identifiable, researchers are encouraged to adopt a model of “preventive consent” in which consent is obtained in the face of uncertainty.

The Research Paper That Broke the Anonymized Sample’s Back

Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y: Identifying personal genomes by surname inference. Science 2013, 339:321

Research using anonymous or anonymized samples in which a significant portion of the genome is sequenced may result in the specimen being considered identifiable and thus worthy of appropriate protections under human subjects research regulations.

What is the Threshold?

Identifiability is generally not a risk where research is conducted on: Anonymous or anonymized specimens; AND No genetic information is being studied OR

Only a targeted area of the genome is used OR The research is examining only diseased

(somatic) tissue where the specimen contains substantive mutations and poses no risk of donor identification

Protected Health Information

Archived pathology samples collected outside of the healthcare setting should not default to being considered Protected Health Information (PHI). Specimens collected during the provision of

healthcare are subject to the HIPAA standards of PHI.

The Common Rule regulates research on specimens collected outside of the healthcare setting.

Data Confidentiality and Security

Pathology research can be safely conducted using broad donor consent IF: Data confidentiality Data security Controlled access to information

Obligations of the Researcher

Researchers have an obligation to respect individual privacy.

Policies on public access of data should balance the shared goals of: Advancing research Ensuring donor trust through ethical behavior of

the researcher

Publication of Data

Researchers should release genetic sequences to journals or other sources when EITHER: The sequence is focused on a target gene sequence

or extremely limited number of gene pairs, insufficient to allow for re-identification through either a reference sample or in combination with metadata OR

The donor’s consent specifically acknowledges that data, as part of the scientific publication process, will be released that might potentially be used for re-identification.

Publication of Data

Publishers and genetic information databases should develop guidelines that balance the need to: Respect individual privacy Broadly share research data to allow for

collaboration and replication Guidelines should ensure consistency between donor

consent and potential uses of data.

How Can We Safeguard Archived Pathology Resources?

Ethically conducted research is good research and helps build public confidence to support participation in research and consent for

biospecimens to be studied.