amnon shabo (shvo), phd co-chair & facilitator, clinical genomics work group co-editor, cda r2...

Amnon Shabo (Shvo), PhD

Co-Chair & Facilitator, Clinical Genomics Work Group

Co-Editor, CDA R2 & CCD

Co-Editor, HL7 Pedigree (Family History) Standard

IBM Research Lab in Haifa

Kevin S. Hughes, MD., FACS

Surgical Director,Breast Screening

Co-Director, Avon Comprehensive Breast Evaluation Center

Massachusetts General Hospital , Partners Healthcare

Co-Editor, HL7 Clinical Genomics Pedigree Specification

W. Gregory Feero, MD, PhD

Chief, Genomic Healthcare Branch

National Human Genome Research Institute

National Institutes of Health

HL7 Clinical GenomicsFamily History (Pedigree)

From PHR to CDS through EHR

Haifa Research Lab

Family History: PHR-EHR-GEN Convergence

EHR PHR

Genomics

Enable

Decision Support

e.g., risk analysis

algorithms

Status of the HL7 Pedigree Specification

HL7 v3 ANSI Normative (2007)

Selected by HITSP to exchange FH between EHR and Clinical Decision Support (CDS) Applications

CCD provides the medical history of the patient whose pedigree is exchanged

EHR

CDS

PHR

HL7 CCD

HL7 v3

Pedigree

HL7 v3

Pedigree

PersonclassCode*: <= PSNdeterminerCode*: <= INSTANCEid: II [0..1]name: BAG<EN> [0..*]telecom: BAG<TEL> [0..*]administrativeGenderCode: CE CWE [0..1] <= AdministrativeGenderbirthTime: TS [0..1]deceasedInd: BL [0..1] "false"deceasedTime: TS [0..1]raceCode: SET<CE> CWE [0..*] <= RaceethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity

1..1 patientPerson

0..1 providerOrganization

PatientclassCode*: <= PATid: II [0..1]

0..1 relationshipHolder

Relative 0..* relative

classCode*: <= PRScode*: CE CWE [1..1] <= FamilyMember

Note:Person holds details that are not specific the family role played by Person.Person is also the scoper of the relative roles (for more details see theV3 RoleCode vocabulary, domain = PersonalRelationshipRoleType).Linking back from Relative to Person allows placing personal details of the relative.It also enables a recursive representation of any higher degree of relations,e.g., grandfather, through the same association nesting in Person, for both‘pure’ hierarchical representation as well as specifying father and mother ids.

Note:This is the GeneticLocus CMET),the main artifact of the HL7Clinical Genomics SIG,dealing with all types ofgenomic data.

ClinicalObservationclassCode*: <= OBSmoodCode*: <= EVNid: SET<II> [0..*]code*: CD CWE [1..1]negationInd: BL [0..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime: IVL<TS> [0..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityuncertaintyCode: CE CNE [0..1] <= ActUncertaintyvalue: ANY [0..1]methodCode: SET<CE> CWE [0..*]

ClinicalGenomicChoice

Note:Shadow of the Clinical Genomicschoice similar to the choiceassociated with the Patient role(the entry point of this model).

DataEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode*: CD CWE [1..1]value: IVL<REAL> [0..1]

0..1 dataEstimatedAge

typeCode*: <= SUBJsubject

Note:Holds the estimated age of the subject(i.e., the patient or one of the relatives)when the observation was made.

DeceasedEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode*: CD CWE [1..1]value: IVL<REAL> [0..1]

Note:Estimated age (current or deceased)of the patient / relative in cases wherehis/her birth date is unknown.

SubjectEstimatedAge

LivingEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode*: CD CWE [1..1]value: IVL<REAL> [0..1]

Note:Shadow of theestimated agechoice for currentor deceased age.

Note:A generic placeholder to hold common clinical data(e.g., problems, diagnoses, reactions to drugs, allergies, etc.).

0..* clinicalGenomicChoicetypeCode*: <= SBJsubjectOf2

0..* subjectEstimatedAgetypeCode*: <= SBJsubjectOf1

FamilyHistoryclassCode*: <= OBSmoodCode*: <= EVNid: SET<II> [0..*]code*: CD CWE [1..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime: TS [0..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityuncertaintyCode: CE CNE [0..1] <= ActUncertaintylanguageCode: CE CWE [0..1] <= HumanLanguagemethodCode: SET<CE> CWE [0..*]

0..1 patient

typeCode*: <= SBJsubject

0..*

subjectOf1

0..*

subjectOf2

0..* pedigreeAnalysisResults

typeCode*: <= RISK

risk

PedigreeAnalysisResultsclassCode*: <= OBSmoodCode*: <= RSKid: SET<II> [0..*]code: CD CWE [0..1]negationInd: BL [0..1]derivationExpr: ST [0..1]text: ED [0..1]effectiveTime: IVL<TS> [0..1]methodCode: SET<CE> CWE [0..*]

AnalysisResultclassCode*: <= OBSmoodCode*: <= RSKcode*: CD CWE [1..1]value: ANY [0..1]

AgeclassCode*: <= OBSmoodCode*: <= RSKcode*: CD CWE [1..1]value: IVL<REAL> [0..1]

ProbabilityclassCode*: <= OBSmoodCode*: <= RSKcode*: CD CWE [1..1]value: REAL [0..1]

Choice

0..* choice

typeCode*: <= COMP

component

1..1 probability

typeCode*: <= PERTpertinentInformation

Note:This class is a catcher for any analysisthat cannot be represented through theother classes in this choice box, suchas the age-probability pairs or the riskclasses.

PercentageRiskclassCode*: <= OBSmoodCode*: <= RSKcode*: CD CWE [1..1]value: REAL [0..1]

RelativeRiskclassCode*: <= OBSmoodCode*: <= RSKcode*: CD CWE [1..1]value: REAL [0..1]

InputParametersclassCode*: <= OBSmoodCode*: <= EVN.CRTcode: CD CWE [0..1]text: ED [0..1]value: ANY [0..1]

0..* inputParameters

typeCode*: <= CTRLVlocalVariableName: ST [0..1]

controlVariable

Note:The probability of having the disease ormutation identified in the ‘code’ attributeof the source act.

0..* clinicalGenomicChoice

typeCode*: <= COMPcomponent

Note:Use this association to represent a problem known in the familythat cannot be attributed to a specific family member.

sourceOf

0..* clinicalObservation

typeCode*: <= ActRelationshipType

Probability

Note:Multiple loci, utilizing the Genetic Locus CMET for each locus.

0..* relatedParty

typeCode*: <= INFinformant

CMET: (ORG) E_Organization

[universal](COCT_MT150000UV)

CMET: (ROL) R_RelatedParty


0..1 scopedRoleName

The code attribute shall hold a code representingFamily History data in general, for example: the LOINCcode 10157-6, HISTORY OF FAMILY MEMBER DISEASESor any other code that carries similar semantics.

Constraint: FamilyHistory.code

Family History(POCG_RM000040UV)

The entry point of the family history modelis the FamilyHistory class which has a subject patient.

The code attribute shall hold a code representingage of subject at the effective time when thesource observation was made for that subject.

Constraint: DataEstimatedAge.code

The code shall represent semantics similarto the LOINC code 39016-1 (AGE AT DEATH).

Constraint: DeceasedEstimatedAge.code

The the code shall represent semantics similarto the LOINC code "21611-9" that represents theconcept of an estimated age (as opposed to precise age).

Constraint: LivingEstimatedAge.code

CMET: (LOC) A_GeneticLoci


CMET: (LOC) A_GeneticLocus


Note:The Relative class represents a patient's relative and is scopedby the Person entity. The basis of this part of the model is in theRIM definition of family member relationships which are based onthe relationship between a scoping entity and a role. For example,the code CHILD is defined as "The player of the role is a child of thescoping entity", and the same goes for any type of family relationship.Note that this is valid not only to the relationship between the patientand a relative directly associated with the patient, rather this is truefor any relationship between family members on this pedigree, forexample, between the patient's mother (the scoper) and her father(the role).

Note:This class represents the results of analysis done to thedata captured in the family history pedigree.

Note:The controlVariable association links PedigreeAnalysisResults toinput parameters used in the analysis like sensitivity and specificityin the BRCAPRO algorithm. For example, if the code attributeholds "sensitivity" then the value attribute holds the sensitivity itself.

Note:The age at which there is a probability ofhaving the disease or mutation identifiedin the ‘code’ attribute of the source act.The probablity is represnetre in thetarget act.

Note:The probability (expressed in percentages)of having the disease or mutation identifiedin the ‘code’ attribute of the source class.

Note:The probability of having the disease ormutation identified in the ‘code’ attributeof the source class. Relative risk is a ratioof the probability of the event occurringin the exposed group versus the control(non-exposed) group

Note:A recursive association that addresses morecomplex data sets, and in consistent with theClinical Statement model.

Note:Informant represents the source of informationfrom which this family history was collected.

Note: The healthcare provider scoping the patientwhile the family history was collected.

Note:The subject of this family hsitory.

The Family History Model (ANSI 2007)

Genomics Models

Patient

RelativeHL7 Vocabulary=

“FAMMEMB”

Recursive

Relation

Clinical

Data

Family History

Risk Assessment

ResultsEstimated

age of subject

Estimated age of

subject at diagnosis

Relative Mother &

Father IDs

Genotype – Phenotype Associations

From PHR to CDS

PHR:Dr. Greg FeeroHHS Surgeon General FH tool

• Patient enters data• Data exported as HL7 Pedigree instance

CDS:Dr. Kevin HughesHughesRiskApps

• Patient data from Surgeon General tool is imported• Pedigree is constructed• Risk assessment algorithms run

We call EHR vendors to integrate FH communication through the EHR!

Greg Feero, MD, PhD, Chief, Genomic Healthcare Branch, National Human Genome Research Institute

Uses of family history

• Organizing knowledge of family relationships and structure

• Learning of patient’s concerns

• Informing differential diagnosis

• Case-finding

• Risk Assessment

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As a tool for risk assessment, family health history is:• Comparatively inexpensive and accessible• Predictive of substantially increased risk of

common disease especially if more than one close relative is affected Butterworth A. Public Health Genomics Unit, 2007

• Generally quite accurate when obtained from patients, especially for close relatives AHRQ/McMaster University EPC, 2007

• Part of many guidelines for care

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Risk Assessment Tool

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First Edition

• Launched in 2004

• More than half a million downloads

• Internet-based

Ideally electronic family health tools would-

• Collect structured data for CDs

• Utilize interoperable data structures

• Aid with interpretation

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Next-Generation

• Standardized data• XML-based• Share-able

• Downloadable

• Customizable

Key considerations for consumers

• HHS supplies a secure portal• Individual’s health information stays with the

patient (NOT resident on government servers)• Consumers can send (electronically) or carry the

information to other family members • Consumers visit the site, complete the data and

maintain information control and security

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Sponsoring Federal Agencies

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• Indian Health Service

• National Human Genome Research Institute

• National Cancer Institute

• Agency for Healthcare Research and Quality

• National Institute of Diabetes and Digestive and Kidney Disorders

• Office of Rare Diseases, National Institutesof Health

• Substance Abuse and Mental Health Services Administration

• National Office of Public Health Genomics,

• Centers for Disease Control and Prevention

• Office of the National Coordinator for Health Information Technology

• Office of Minority Health

• Office of the Surgeon General

• Office of the Assistant Secretary for Planning and Evaluation

• Federal Health Architecture (Veterans Health Administration and Department of Defense)

Arriving at standards for Family Health History• Achieved in 2008 by a public/private task

force convened by the AHIC Personalized Health Care workgroup

• Defined the minimum FHH data elements that every EHR and PHR should be able to capture

• HITSP approved interoperability Dec. 2008

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New Standards and Enhanced Utility for Family Health History Information in the Electronic Health Record: An Update from the American Health Information Community's Family Health History Multi-Stakeholder WorkgroupW. Gregory Feero, Mary Beth Bigley, Kristin M. Brinner The Family Health History Multi-Stakeholder Workgroup of the American Health Information Community J Am Med Inform Assoc 2008; 15: 723-728.

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Standards-based• HL7 family history model

• LOINC

• SNOMED-CT

• HL7 Vocabulary

• Minimum core data set

Family Health History Portal

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Create History

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Family health history tool download features

• We encourage organizations wanting to augment consumer use to:• Develop links to the site AND/OR• Download and adapt the program to meet your needs

• Customize displays• Connect with risk assessment tools• Link to other consumer e-information

• New HIPAA FAQs on Family Health History:

http://www.hhs.gov/ocr/hipaa/

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Where should you go to download the tool?• GForge site: http://gforge.nci.nih.gov/projects/fhh• Site has automated capabilities for downloading• Related information available on the site

• Click through End-User Agreement• Architecture Review Committee documents• Systems Architecture Document• Interoperability Document (sample implementation

applications)• Frequently Asked Questions

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Help Desk Support

• Technical help is available from:• CBITT Application Support• Email: [email protected]• Local: 301-451-4384• Toll-Free: 888-478-4423• Monday – Friday 8 a.m. to 8 p.m. ET• http://ncicb.nci.nih.gov/support

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Bottom-line• Consumer convenience and control

• Standards-driven

• Portability, share-ability

• EHR- and PHR-ready

• Downloadable and customizable

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Visithttps://familyhistory.hhs.gov/

Questions:[email protected]

Evaluating risk of hereditary syndromes

QualitativePedigree

Patterns of disease in the family

QuantitativeRisk algorithms determine•Risk of carrying a disease causing mutation•Risk of developing disease over time

27Surgeon General's My Family Health Portrait

From PHR to CDS

PHR:Dr. Greg FeeroHHS Surgeon General FH tool

• Patient enters data• Data exported as HL7 Pedigree instance

CDS:Dr. Kevin HughesHughesRiskApps

• Patient data from Surgeon General tool is imported• Pedigree is constructed• Risk assessment algorithms run

We call EHR vendors to integrate FH communication through the EHR!

Evaluating risk of hereditary syndromes

QualitativePedigree

Patterns of disease in the family

QuantitativeRisk algorithms determine•Risk of carrying a disease causing mutation•Risk of developing disease over time


The standard data structure of My Family Health Portrait allows interoperabilty with other software

Value• My Family Health Portrait data can be imported into clinical systems that draw pedigrees and run risk analyses

Example:• We will pull data into HughesRiskApps

– Developed at Mass General Hospital/Newton Wellesley Hospital

• Import data• Edit data• Risk analyses


DEMO


Bottom left side of the screen, BRCAPRO has been run for each relevant family member, with the risk of mutation shown for each

Top left side of the screen, Genetic Testing recommendations are made

Top right side of the screen, Myriad and BRCAPRO results are shown with the ability to use the slider to set the clinician’s decision as to the risk of mutation

Right bottom side of the screen, family members are listed in order of likelihood of mutation. The willingness of each to be tested can be recorded.

Lifetime risk of breast cancer and the management suggestions are shown for multiple scenarios: without testing (Current synthesis), as if the patient tested positive, as if the patient tested negative and the population risk

Lifetime risk of ovarian cancer and the management suggestions are shown for multiple scenarios: without testing (Current synthesis), as if the patient tested positive, as if the patient tested negative and the population risk

Lifetime risk of ovarian cancer

Gail model results are displayed

Claus model results are displayed

Myriad model results are displayed

Colorectal Models in prototype

References

Scheuner 2004 AmJMedGenSeminars Contribution Of Mendelian Disorders To Common Chronic Disease Hughes KS, Roche CA, Campbell CT, Siegel N, Salisbury L, Chekos A, Katz MS, Edell E. Prevalence of Family History of Breast and Ovarian Cancer in a Single

Primary Care Practice Using a Self-Administered Questionnaire. The Breast Journal 9: 19-25. Jones JL, Hughes KS, Howard-McNatt M, Kopans DB, Moore RH, Hughes SS, Lee NY, Roche CA, Siegel N, Gadd MA, Smith BL, Michaelson JS. Evaluation of

Hereditary Risk in a Screening Mammography Population. Clinical Breast Cancer 6(1): 38-44. Shabo A and Hughes, KS. Family History Information Exchange Services Using HL7 Clinical Genomics Standard Specifications. Int'l Journal on Semantic Web &

Information Systems 1(4): 42-65 Dominguez FJ, Jones JL, Zabicki K, Smith BL, Gadd MA, Specht MC, Kopans DB, Moore RH, Michaelson JS, Hughes KS. Prevalence of Hereditary Breast/Ovarian

Cancer Risk in Patients with a Personal History of Breast or Ovarian Cancer in a Mammography Population Cancer 2005; 104: 1849-53.

Dominguez FJ, Lawrence C, Halpern EF, Drohan B, Grinstein G, Black DM, Smith BL, Gadd MA, Specht MC, Kopans DB, Moore RH, Hughes SS, Roche CA, Hughes

KS. Accuracy of Self-Reported Personal History of Cancer in an Outpatient Breast Center. J Gen Counseling, 2007

Interoperability

• Data can be shared with any HL7 compliant clinical

software or Electronic Health Record

• Increased value of data entered by the patient

• Decreased workload for the clinician

• Clinical Decision Support helps the clinician provide the

best care possible

Surgeon General's My Family Health Portrait 45

Increased Quality of care with less workIncreased Quality of care with less work

EHRs/PHRs with a family history section that can import and export the full HL7 CG SIG Pedigree model

Source: AHIC recommendations for a core data set

Ideally all EHRs/PHRs will have a family history sectionthat can import and export the full HL7 CG SIG Pedigree model

• For more information

• Clinical Decision Support and HL7 CG SIG Pedigre model• Kevin S. Hughes, MD

– [email protected]• Amnon Shabo, PhD

– [email protected]

• My Family Health Portrait• Greg Feero, MD, PhD

– [email protected]

Looking for Adopters

amnon shabo (shvo), phd co-chair & facilitator, clinical genomics work group co-editor, cda r2...

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