**HL7 Clinical Genomics Genotype Models\
Co-Chair, Amnon Shabo, PhD**\
IBM Research Lab in Haifa, Israel\
Phone: 972-54-714070\
Email: <shabo@il.ibm.com>

**\
**Several HL7 organizational members (e.g., IBM, Mayo Clinic, Cap
Gemini, Ernst & Young) have initiated the Clinical Genomics Special
Interest Group whose scope is the actual use of genomic data in
healthcare practice.

The main specifications developed by the HL7 Clinical Genomics SIG are
the Genotype models which include the GeneticLocus and GeneticLoci
models.

The GeneticLocus model is intended to be used as a shared component in
any HL7 specification that conveys genomic data. It embeds various types
of genomic data relating to a chromosomal locus including sequence
variations, gene expression and proteomics.

The GeneticLocus model utilizes existing bioinformatics markups that are
commonly used by the genomic community (e.g., MAGE-ML for gene
expression data or BSML for DNA sequences).

Those bioinformatics markups represent the raw genomic data and are
encapsulated in HL7 objects. On the other hand, only portions of the raw
and mass genomic data are relevant to clinical practice. To that end,
the full-blown bioinformatics markup schemas have been constrained and
areas describing pure research data were excluded. More importantly, the
GeneticLocus model also includes \"specialized\" HL7 objects (e.g.,
SequenceVariation of SNP type) that hold those portions of the raw
genomic data that seem to be significant to clinical practice. Those
specialized objects have attributes that represent the essential genomic
data along with optional annotation.

They are populated through a \"bubbling-up\" process that specialized
applications carry out within an EHR environment where such application
are foreseen to be useful for healthcare practice. The \"bubbling-up\"
process should take into account the goals of clinical care, the patient
specific history and the most current knowledge about relevant
clinical-genomic correlations. Once populated, those specialized objects
can be associated with clinical phenotypes, represented either
internally within the GeneticLocus model or elsewhere, for example, as
diagnoses, allergies and adverse drug events residing in the patient
medical records.

**HL7 Family History Model**

**Co-Chair, Amnon Shabo, PhD**\
IBM Research Lab in Haifa, Israel\
Phone: 972-54-714070\
Email: <shabo@il.ibm.com>

The HL7 Clinical Genomics group has developed the Family History model
which is based on a use case relevant to PHR, as it involves the patient
key in their family history which then gets into the medical records
maintained by healthcare providers. This data set would assist in
evaluating the patient for potential risk, especially when it includes
genetic data in addition to the clinical data. There are other
simplified family history models within HL7, however to capture the type
of family data needed for many types cancers, the HL7 Family history
model is more comprehensive. This model can be used for both simple
(i.e., no genetic data) family histories and those that genetic data is
relevant.

There is an ongoing implementation project of the HL7 Family History
model where IBM Haifa Research is involved. It is carried out by
Massachusetts General Hospital and the University of Massachusetts.
Transformations were developed between the proprietary data format like
CaGene and the Avon Tablet System Program used in Mass General as well
as the General Surgeon Family History tool. The HL7 Clinical Genomics
Family History model utilizes the GeneticLocus core model for
representing high-resolution genetic data (described further in this
document).

A number of family history applications are in use by healthcare
professionals as well as by patients. Each has its own proprietary data
format for family history health information, thus making it difficult
to exchange the information. By using a standard representation,
disparate family history applications will be able to exchange an
individual's family history. This standard needs to hold the pedigree
structure as well as an appropriate representation of clinical-genomic
correlated data.

One of the clear use cases is in breast and ovarian cancers that run in
families. These cancers are associated with variations in the BRCA
genes. A complete family history can be assessed for potential risk,
supporting clinical decision in genetic counseling and at the point of
care. Family history data might involve accessing other family members\'
medical history, which raises ethical issues relating to privacy within
families. In addition, patients are sometimes expected or even
encouraged to enter their family history directly (PHR), and the
challenge is how to incorporate patient-entered data into
legally-authenticated medical records held by healthcare providers.

An example for such program is the US Surgeon General Family History Web
Tool (see <https://familyhistory.hhs.gov/>) which is available for
citizens to document their family history. Here is an abridged
storyboard of what presented in the HL7 Clinical Genomics domain: Ms.
Martha Francis is 48 years old. Her mother had ovarian cancer and was
found to have a deleterious BRCA1 mutation. She has two sisters, a
husband and a daughter. She is not of Ashkenazi Jewish descent. She
makes an appointment at a Risk Clinic. The Clinic instructs the patient
to use the Surgeon General\'s Family History Tool to prepare for the
visit. She downloads the Surgeon General\'s Family History Tool onto her
computer at home, and enters her family history. She then exports the
data as an HL7 MESSAGE, places it on Portable Media (CD, Flash drive)
and brings it to her Risk Clinic appointment. The counselor at the risk
clinic (Nurse Geneticist, Nurse Practitioner, Genetic Counselor, MD,
etc.) imports the HL7 MESSAGE into CAGENE, a pedigree drawing program
that runs risk models. The counselor edits the data after confirming and
clarifying various issues with the patient, and adds additional
information that had not been entered at home. The patient is considered
to be at high risk, and she is told she is a candidate for genetic
testing. This includes a thorough discussion of the pros and cons of
testing. The patient decides not to have testing, and leaves.