preparing for the collection of external family history

Preparing for the Collection of External Family History & Genetic Test Result Data

February 27, 2008

HL7 Theater at HIMSS 2008

Grant M. Wood

Senior IT Strategist

Intermountain Healthcare Clinical Genetics Institute

What does it all mean?

There was just one problem at all the parties, press conferences, and publications celebrating the completion of the Human Genome Project (again

and again and again) — healthcare providers do not have the knowledge, education, and informatics tools to implement clinical genetics, genomics,

proteomics, metabolics, and epigenetics into personalized medicine

Genetic Testing Becoming Common

The good news from human genome research is that tests to determine people's genetic susceptibility to many common and deadly diseases are already, or soon will be, available.

Are Healthcare Systems Prepared?

The bad news is that most health care systems risk being overwhelmed unless they start preparing for the complex and costly demands of genetic screening programs

A Personalized Medicine story

A patient is concerned about a family history of breast cancer or cardiovascular disease

She follows the Surgeon General program to collect family history

- And takes the paper copy to her doctor

- And makes her husband also take a copy for his doctor

The question is –

Will the family health history data ever be stored and shared electronically with other healthcare providers?

Will the data be available to help their children? Grandchildren?


They have many choices to enter data –

1. In an employer Personal Health Record

2. In a health plan Personal Health Record

3. Or in their health system Patient Portal / PHR

They use a family history tool on Microsoft HealthVault –Will it also be recorded in the EHR of their healthcare provider?


She pays for a breast cancer test from Myriad?

They spend money on -

Will the family history and genomic data get to their EHR so that their healthcare providers can use it?

They do genealogy online – Shouldn’t they also do family health history at the same time?

Value of Family History in Clinical Care

Family History remains the best and least expensive genetic ‘test’currently available for use. A major effort will entail developing ways to obtain this information in a standardized format, store the information in the electronic medical record, apply risk stratification and develop messages to clinicians that will alter patient care based on the information obtained.

HL7 Family Health History model

• The model can be used for family health history data storage in an EHR.

• It is fundamentally designed for

1. the interoperability of family history data between clinical information systems,

2. and provide structured data for clinical decision support.

HL7 Family Health History Data Model

Sample XML – Family History <relative><code code="NMTH" /> <relationshipHolder>  <deceasedInd value="true" /> </relationshipHolder>  <subjectOf1><deceasedEstimatedAge><value value="72" /> </deceasedEstimatedAge></subjectOf1><subjectOf2><clinicalObservation>  <code code="V1043" codeSystemName="ICD" displayName="HX OF OVARIAN MALIGNANCY" />

 <subject><dataEstimatedAge><value value="40" /> </dataEstimatedAge></subject></clinicalObservation></subjectOf2></relative>

Sample XML – Genetic test data in family history

 <subjectOf2><geneticLocus moodCode="EVN"><component1><individualAllele moodCode="EVN"><text>breast cancer 2, early onset</text> <value code="U43746" displayName="BRCA2" codeSystemName="HUGO" /> <component3><sequenceVariation moodCode="EVN"><value xsi:type="CE" code="185delAG" /> <interpretationCode code="DELETERIOUS" />

Sample XML – DNA sequence data in family history

<code code="BSMLcon3" /> <value mediaType="text/xml"><bsml:Bsml xmlns:bsml="urn:bsml.org"><bsml:Definitions><bsml:Sequences><bsml:Sequence id="seq1" molecule="dna" ic-acckey="U14680 REGION: 101..199" db-

source="GenBank" title="BRCA1, exon 2" representation="raw" local-acckey="this could be used by the genetic lab"><bsml:Seq-data>GCTCCCA CTCCATGAGG TATTTCTTCA CATCCGTGTC

CCGGCCCGGC CGCGGGGAGC CCCGCTTCAT CGCCGTGGGC TACGTGGACG ACACGCAGTT CGTGCGGTTC GACAGCGACG CCGCGAGCCA GAGGATGGAG CCGCGGGCGC CGTGGATAGA GCAGGAGGGG CCGGAGTATT GGGACCAGGA GACACGGAAT GTGAAGGCCC AGTCACAGAC TGACCGAGTG GACCTGGGGA CCCTGCGCGG CTACTACAAC CAGAGCGAGG CCG</bsml:Seq-data> </bsml:Sequence>

HL7 Current Implementation

Kevin Hughes MD, surgeon at Massachusetts General Hospital, has developed a breast cancer risk application that uses HL7 messages to import family history data from the Surgeon General tool

And sends data to Progeny via an HL7 message to draw a pedigree

And sends data to CaGene via an HL7 message to calculate risk score

The system is freely available at Hughesriskapps.com

HL7 Genetic Variation Data Model

The Genetic Variation model specifies the structure and semantics for the transmission of information created during single or multiple gene testing and analysis - such as SNP probes, sequencing and genotype arrays that focus on small scale genetic changes, usually in the coding region(s) of one or a small number of genes.

HL7 Genetic Variation Data Model

The model facilitates the electronic transmission of genetic testing results and interpretations from –

• Genetic testing laboratories to medical practitioners, electronic health records, personal health records and associated clinical decision support systems able to receive and process such information

• Genetic testing laboratories to drug and medical device companies that have ordered such information as part of a clinical trial

• Drug and medical device companies to regulatory agencies that need to review such information as part of a new drug or device marketing application

HL7 Genetic Variation model

Sample XML - Genetic Variation<geneticLocus moodCode="EVN"><effectiveTime value="20071218"/><value code="HGNC:6501" displayName="LAMP2 - lysosomal-associated membrane protein 2" codeSystemName="HGNC"><translation code="NT_011786.15" codeSystemName="NCBI-NUCLEOTIDE Genomic Reference Sequence Accession"/><translation code="NM_013995.1" codeSystemName="NCBI-NUCLEOTIDE Transcription Reference Sequence Accession"/></value><component3><sequenceVariation moodCode="EVN"><value xsi:type="II" assigningAuthorityName="LMM-GVIE" extension="82933"/><interpretationCode displayName="Unknown Signficance"/><derivedFrom><associatedProperty><code code="X00505-1" codeSystemName="LOINC" displayName="DNA Region"/><value xsi:type="ST">c.1171</value><derivedFrom><associatedProperty><code code="X00504-1" codeSystemName="LOINC" displayName="DNA Region Name"/><value xsi:type="ST">Exon 9B</value><derivedFrom><associatedProperty><code code="X00507-1" codeSystemName="LOINC" displayName="DNA Change"/><value xsi:type="ST">c.1171G>A</value><derivedFrom><associatedProperty><code code="X00508-1" codeSystemName="LOINC" displayName="DNA Change Type"/><value xsi:type="ST">Substitution</value></associatedProperty></derivedFrom>

Sample XML - Genetic Variation

<derivedFrom><associatedProperty><code code="X00509-1" codeSystemName="LOINC" displayName="Amino Acid Change"/><value xsi:type="ST">V391I</value></associatedProperty></derivedFrom><derivedFrom><associatedProperty><code code="X00510-1" codeSystemName="LOINC" displayName="Amino Acid Change Type"/><value xsi:type="ST">Missense</value></associatedProperty></derivedFrom><derivedFrom><associatedProperty><code code="X00500-1" codeSystemName="LOINC" displayName="Genomic Source Class"/><value xsi:type="CE" code="Germline"/></associatedProperty></derivedFrom><component><associatedObservation moodCode="EVN"><code code="X00511-1" codeSystemName="LOINC" displayName="Allelic State"/><value xsi:type="CE" code="Homozygous"/></associatedObservation></component></sequenceVariation></component3></geneticLocus>

Personalized Medicine Use Case

Scientists find genes that could predict Type 2 diabetesInternational scientists identified five different genetic variations tied to adult-onset diabetes and believed to be responsible for 70% of the genetic risk for the diabetes, also known as Type 2. One of the lead scientists says the findings "mean we can create a good genetic test to predict people's risk of developing this type of diabetes.“

1. Family history risk assessment2. Order genetic test3. Test interpretation4. Store results (sequence data, alleles, codons,

SNP’s also called variations or mutations)5. Pharmacogenomics for targeted drugs

Invitation and challenge

Since becoming a normative HL7 standard in 2007, the family history model has also been approved as an ANSI standard. HL7 Clinical Genomics is now calling on all commercial vendors and those who have developed “in-house” systems to implement this data model and electronic messaging standard in their clinical products and applications.

Invitation and challenge

HL7 Clinical Genomics is also calling on forward thinking organizations to test and comment on the Genetic Variation model, as we work towards establishing the final standard at the end of 2008.

Additional information and contact infoVisit the HL7 Clinical Genomics web site at:http://www.hl7.org/Special/committees/clingenomics/index.cfm

Contact the co-chairs:Amnon Shabo [email protected] Hughes MDPartners [email protected] Ullman-Cullere Harvard-Partners Center for Genetics and [email protected] [email protected]

• Contact Grant WoodIntermountain Healthcare Clinical Genetics [email protected]

Preparing for the Collection of External Family History & Genetic Test Result Data

Thanks!

HL7 Theater at HIMSS 2008

preparing for the collection of external family history

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