in the Era of Precision Medicine JSCO 50 th Annual Meeting Yokohama Japan October 27 2012 Mark E Sobel MD PhD Executive Officer American Society for Investigative Pathology mesobelasiporg ID: 1045604
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1. Best Practices for Biobanking in the Era of Precision MedicineJSCO 50th Annual MeetingYokohama, JapanOctober 27, 2012Mark E. Sobel MD, PhDExecutive OfficerAmerican Society for Investigative Pathologymesobel@asip.orghttp://www.asip.org/about/executive_officer.cfm
2. The Era of Molecular MedicineA transformation of the practice of medicine AND the public’s fears and expectations Molecular techniquesHuman Genome ProjectInformation technology
3. Every Era Has Transformative Events3Giovanni Battista Morgagni(1682—1771)Images from: Encyclopaedia Britannica, adapted from Dr. Bruce McManus, University of British Columbia
4. Clinical Diagnostic Genome SequencingThe introduction of high-throughput, next-generation sequencing (NGS) in 2005 heralded a critical and transformative step in the history of DNA sequencing.
5. http://en.wikipedia.org/wiki/File:TOSopeninglogo.pnghttp://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
6. NEXT-GENERATION SEQUENCING FROM THE POINT OF VIEW OFSTAR 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.”
7. NEXT-GENERATION SEQUENCING FROM THE POINT OF VIEW OFSTAR 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.”
8. DefinitionsHuman genome- the “whole genome” of a human consists of 3 gigabytes of information3 billion base pairs of DNA46 chromosomes (diploid genome)Approximately 98% is “intergenic”“between genes”Junk DNA?Does not encode proteinsHuman exome2% of the genome 22,000 pairs of genesOn average, there are 8 exons (protein-encoding segments) per gene = 176,000 exonsHuman transcriptome (DNA> RNA> protein)The expressed RNA transcripts of genesWhat a cell is doing at a particular point in time
9. DefinitionsGenotype – what the cell is capable of doingGenome analysisPhenotype- what the cell is doingProteomic analysis (proteins)Germline or somatic?Germline- InheritabilityImplications for immediate and extended familyImplications for ethnic group“Normal” tissuesSomatic-Acquired mutationsUse of “diseased” tissuesNo heritable implications for family
10. Clinical Diagnostic Genome SequencingWGS: Whole genome sequencingWGA: Whole genome analysisBiospecimens are required!
11. Repository or Biobank?A repository is an organized collection of samplesA biobank is a repository of biological samples
12. Biospecimens in a Human BiobankTissue samplesBiopsyResection of tissue (surgery)Dissection of tissue (autopsy)Blood, sputum, urine, bone marrowAssociated dataClinical historyEnvironmental historyFamily historyDemographics (gender, age)How the sample was collected
13. Biospecimens in a Human BiobankFreshly obtainedFrozenFixed Formalin-fixed paraffin-embedded (FFPE)Alcohol-fixedOther fixatives
14. Types of BiobanksFreezer banks or Cold storage roomsGlass slide collectionsTissue blocks (FFPE)Liquid specimens (blood, urine…)Buccal (cheek) swabsExtracted analytes (DNA, RNA, protein, etc)
15. Who is Involved?Donor PatientFamilyEthnic groupPhysicianNurseAdministrative assistantsLaboratory techniciansEthical oversight
16. Requirements of BiobanksRecord keeping Associated dataInformed consentWhat permissions or restrictions are associated with the use of the specimen?TemperatureHumidityLight/darkControlled access – only authorized individuals can retrieve specimens
17. Confidentiality and PrivacyConfidentiality- 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 partyPrivacy - culturally specific concept defining the extent, timing, and circumstances of sharing oneselfPhysicalBehavioralMedical
18. Identification of Specimens Anonymous- the sample was collected without the identity of the donorAnonymized – the sample was collected with the known identity, but the identification was removedCoded (Linked) – the sample is given a unique identifier that cannot be easily decipheredIdentified – the sample has a common identifier (name, hospital number)
19. Personalized (Precision) Molecular MedicinePublic’s expectationsImproved health carePersonalized medicinePublic’s fearsLoss of privacyLoss of employment Loss of insuranceSocial stigmatization
20. Biomedical Research and Biobanks:Translational Research involves interactions between the laboratory bench and patient’s bedIncrease knowledgeUnderstand biological processesImprove public health New diagnostic testsNew prognostic testsNew or improved therapy
21. Biobanks and Clinical Research21Health Policy ResearchHealth Outcomes ResearchPopulation and Public HealthTranslational ResearchClinical Trials of DrugsClinical Trials of DevicesClinical Trials ofDiagnosticsClinical Trials ofModels of CareResearch Involving PatientsReduce CostsImprove Health
22. The Translational Research Cycle The Biobank is Essential to Provide SolutionsAdapted from Dr. Bruce McManus, UBCTranslational Research CycleInvestigative ModelsPatients as PartnersModels of Human DiseaseBiobankTissues, Cells, Fluids, & Products and Dry DataPathophysiological and Sociobiological ProcessesIdentification of Novel Markers and TargetsBiomarker or Target ValidationMulti-population Assessment, High-throughput ScreeningClinical TrialsTechnology TransferToolsGenetics, Genomics, Proteomics, Imaging, Physiology, Biophysics, Biochemistry, Nanotechnology, Informatics, Sociology, Epidemiology, Statistics Research Questions
23. The Path to Clinical Implementation from Translational ResearchAnalytical 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?
24. Clinical Diagnostic Genome SequencingThe introduction of high-throughput, next-generation sequencing (NGS) in 2005 heralded a critical and transformative step in the history of DNA sequencing.
25. 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)
26. Coming to a clinic near you…
27. The Potential of Tissue Based Analysis27
28. NGS PlatformsAlthough 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.
29. NGS TechnologyAll 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.
30. Advantages of NGS TechnologyIndividual sequencing assays based on capillary electrophoresis tend to be:ExpensiveLaboriousLess comprehensive, necessitating serial gene-by-gene testing to identify causative mutation(s)
31. Informed Consent and Ethical ConsiderationsThe 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.
32. Bioinformatics Requirements Major computations performed with NGS data:Data assembly with base calling at the level of individual readsAlignment of the assembled sequence to a reference sequenceVariant calling
33. Variant CallingDifferent computational analyses devoted to SNPs, small indels, structural variants or large indels, copy number variantsGeneration of an unprecedented amount of medical data that result in special informatics needs and require tools for data management, storage, analysis, and archivingManage the large data set without error and to ensure proper quality and documentation.
34. Electronic Health RecordReporting of NGS test results raises several issues:Ordering of the testReceiving a document that summarizes the clinical interpretationStorage of the interpretation
35. Incidental FindingsAn 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!
36. Presidential Commissionfor the Study of Bioethical IssuesWashington, DCOctober 2012http://www.bioethics.gov
37. Challenges Facing Biobanks:Shortage of Quality BiospecimensLack of standard and uniform operating procedures for:CollectionProcessingAnnotationStorageTransport
38. International Society for Biological and Environmental RepositoriesA Division of American Society for Investigative Pathology Communication among Repositories across the Globewww.isber.org
39. Biospecimen ScienceWhat 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 storageWhy 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
40. Biospecimen ScienceQuality of human biospecimens is multifactorial and is determined by:Type of specimen: Normal tissue, tumor tissue, serum, plasmaPhysical state of the specimenAmount and type of specimen characterization dataAmount and type of quality control exercisedAmount and type of clinical dataPermitted use of the specimenThe analysis to be performed and the biomolecules targeted by the analysisThe goal of the research (application of the data)40
41. International Society for Biological and Environmental RepositoriesSecond Edition: Cell Preservation Technology, Volume 6, Number 1, 2008Third Edition: Biopreservation and BiobankingVolume 10, Number 2, 201241Best Practices for Repositories:Collection, Storage, Retrieval and Distribution of Biological Materials for Research
42. Quality Control - definitionNestler W. Effect of Quality Control programs on the organizational structure of the hospitals. Bull. NY Acad. Med. 1976;52:157-163Glenn GC, Hathaway TK. Effects of specimen evaporation on quality control. Am. J. Clin. Pathol. 1976;66:645-652Calam RR. Reviewing the importance of specimen collection. J. Am. Med. Tech. 1977;39:297-302« the operational techniques and activities that are used to satisfy quality requirements », ISO9000:2000« confirmation through provision of objective evidence that requirements for a specific intended use or application are fulfilled », ISO9000:200042
43. Integrated Quality Control Systems43Sample Processing MethodQuality Control AssayBiobankBiobank or Research LabQC / ValidationMethod Validation / Proficiency Testing
44. in vivo Preanalytical Variables Position- Fasting- Smoking- Stress- Circadian rhythms- Menstrual cycle- Pregnancy- Physical excercise Caffeine : - phosphodiesterase cAMP degradation - adrenalin secretion - triglycleride lipase lipid acids linked to albumin # of albumin-available sites44
45. in vitro Preanalytical Variables Collection tubes shedding of components from the tubesilicones, 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 48hfreeze-thaw cycles, controversy (peptide aggregation, precipitation and adsorption)45
46. SPREC-01Biospecimen preanalytical codeStandard Preanalytical Coding for BiospecimensCancer Epidemiology Biomarkers and Prevention 2010;19:1004-1146
47. Ideal QC Biomarkers Ubiquitous Measurable by widely accessible methods On/Off responseStability :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 conditionsISBER BS WG, Cancer Epidemiol Biomarkers Prevention 2009;18:1017-2547
48. Why validate QC methods ?give full confidence in sample qualityuse samples after a long timeprovide « reference materials »ensure validity of research results 48
49. How Can We Improve?Proficiency TestingAccreditation 49
50. ISBER Proficiency Testing Program:Interlaboratory comparisons to identify problems in laboratories and interlaboratory differences50Launched in 2011DNA QuantificationRNA Integrity and QuantificationAdded in 2012 Cell ViabilityTissue HistologyTissue Antigenicity
51. cap.orgCAP Innovates Accreditation for Biorepositories
52. Summary The Era of Precision Medicine Transformative events - NGS Translational research needs quality biospecimens Biospecimen Science and Best Practices Proficiency Testing and Biobank Accreditation