Implementation Guide for CDA Release 2 Genetic Testing Report (GTR)

Transcription

1 Implementation Guide for CDA Release 2 Genetic Testing Report (GTR) (Universal Realm) Draft Standard For Trial Use September 2012 CDAR2_IG_GENTESTRPT_R1 (Developer Documentation)

2 Introduction 2

3 TOC 3 Contents Authors... 5 Acknowledgments... 7 Revision History...9 List of Figures List of Tables Chapter 1: INTRODUCTION Purpose Approach Scope Audience...17 Organization of This Guide...17 Templates Vocabulary and Value Sets Use of Templates...18 Originator Responsibilities...18 Recipient Responsibilities Note on Draft Standards...18 Conventions Used in This Guide...18 Conformance Requirements...18 Keywords...19 XML Examples Contents of the Ballot Package Chapter 2: DOCUMENT TEMPLATES...21 Genetic Testing Report...22 Chapter 3: SECTION TEMPLATES...39 Background Section Findings Section...41 Indications Section Interpretation Section Methodology Section Overall Interpretation Section Performers Section Recommendations Section References Section Specimen Section Summary Of Tests Performed Section...52 Summary Section Test Details Section...58 Test Information Section...65 Test Performed Section... 68

4 TOC 4 Chapter 4: CLINICAL STATEMENT TEMPLATES Clinical Genomic Statement...73 Clinical Genomic Statement Cytogenetics...75 Clinical Genomic Statement Gene Expression Clinical Genomic Statement Genetic Variation Clinical Genomic Statement Overall Interpretation...83 Cytogenetics Associated Observation Cells Analyzed Count...85 Cytogenetics Associated Observation Cells Count...86 Cytogenetics Associated Observation Cells Karyotyped Count Cytogenetics Associated Observation Colonies Count...87 Cytogenetics Associated Observation ISCN Band Level Genetic Variation Associated Observation Amino Acid Change Genetic Variation Associated Observation DNA Change Genetic Variation Associated Observation DNA Region Name...91 Genetic Variation Associated Observation Zygosity Genomic Associated Observation Genomic Observation Reference...93 Genomic Observations Organizer Genomic Source Class...94 Indication Observation Interpretive Phenotype Interpretive Phenotype Cytogenetics...96 Interpretive Phenotype Gene Expression Interpretive Phenotype Genetic Variation...97 Interpretive Phenotype Pharmacogenomic...98 Interpretive Phenotype Pharmacogenomic Drug Efficacy...99 Interpretive Phenotype Pharmacogenomic Drug Metabolism Overall Interpretive Phenotype Chromosome Analysis Overall Interpretive Phenotype Genetic Disease Overall Interpretive Phenotype Genetic Disease Carrier Overall Interpretive Phenotype Pharmacogenomic Drug Efficacy Overall Interpretive Phenotype Pharmacogenomic Drug Metabolism Test Performed Observation Chapter 5: OTHER CLASSES Chapter 6: VALUE SETS Allelic State Amino acid change type Chromosome analysis overall interpretation DNA sequence variation change type Drug efficacy analysis overall interpretation Drug Efficacy Sequence Variation Interpretation Drug metabolism analysis overall interpretation Drug metabolism sequence variation interpretation Genetic disease analysis overall carrier interpretation Genetic disease analysis overall interpretation Genetic disease sequence variation interpretation Genomic source class ISCN band level REFERENCES

5 Authors Primary Editor Co-Editor CG and SDWG Members Amnon Shabo, Ph.D. IBM Research Lab in Haifa Mollie Ullman-Cullere MS, MSE Department of Clinical Research Informatics Dana-Farber Cancer Institute If you're interested in contributing to the development of the GTR IG, please contact Amnon Shabo. Last Published: 10/05/2010 HL7 Version 3 Standard, 2005 Health Level Seven, Inc. All Rights Reserved. HL7 and Health Level Seven are registered trademarks of Health Level Seven, Inc. Reg. U.S. Pat & TM Off

6 Authors 6 Genetic Testing Report (GTR) Page 6

7 Acknowledgments We acknowledge the foundational work on HL7 Version 3 and the Reference Information Model (RIM), the HL7 domain committees, especially the work done by the Structured Documents Work Group on Clinical Document Architecture (CDA) itself. We acknowledge the efforts of the HL7 Clinical Genomics Work Group which has been developing v3 specifications for the past seven years as well as v2 implementation guide for genetic testing results message. Note that the LOINC codes developed within the v2 effort are utilized in this GTR IG. We acknowledge the efforts the MDHT tool developers who work closely and tirelessly with us to accommodate the requirements of the GTR. This material contains content from LOINC ( The LOINC table, LOINC codes, and LOINC panels and forms file are copyright , Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and available at no cost under the license at

8 Acknowledgments 8 Genetic Testing Report (GTR) Page 8

9 Revision History Rev Date By Whom Changes New 8 January 2009 Amnon Shabo New Draft 1 3 August 2010 Amnon Shabo CGWG review DSTU R1_O1 10 August 2010 Amnon Shabo CGWG review Draft For Comment R1_O2 March 2011 Amnon Shabo CGWG review Draft For Comment R1_O3 September 2011 Amnon Shabo CGWG review (note that reconciliation of negative comments has not been completed) Draft For Comment May 2012 Amnon Shabo Informal Review Draft Standard For Trial Use September 2012 Amnon Shabo Ballot

10 Revision History 10 Genetic Testing Report (GTR) Page 10

11 TOC 11 List of Figures Figure 1: Template name and "conforms to" appearance...18 Figure 2: Template-based conformance statements example...19 Figure 3: Conformance statements example (taken from the CCD IG) Figure 4: ClinicalDocument example...19 Figure 5: Genetic Testing Report example...23 Figure 6: Background Section example...40 Figure 7: Findings Section example Figure 8: Indications Section example Figure 9: Interpretation Section example Figure 10: Methodology Section example...44 Figure 11: Overall Interpretation Section example Figure 12: Performers Section example Figure 13: Recommendations Section example Figure 14: References Section example Figure 15: Specimen Section example Figure 16: Summary Section example...54 Figure 17: Test Details Section example Figure 18: Test Information Section example Figure 19: Clinical Genomic Statement example...74 Figure 20: Clinical Genomic Statement Cytogenetics example Figure 21: Clinical Genomic Statement Gene Expression example...79 Figure 22: Clinical Genomic Statement Genetic Variation example Figure 23: Clinical Genomic Statement Overall Interpretation example Figure 24: Cytogenetics Associated Observation Cells Analyzed Count example...86 Figure 25: Cytogenetics Associated Observation Cells Count example... 86

12 TOC 12 Figure 26: Cytogenetics Associated Observation Cells Karyotyped Count example Figure 27: Cytogenetics Associated Observation Colonies Count example Figure 28: Cytogenetics Associated Observation ISCN Band Level example...89 Figure 29: Genetic Variation Associated Observation Amino Acid Change example...90 Figure 30: Genetic Variation Associated Observation DNA Change example...91 Figure 31: Genetic Variation Associated Observation DNA Region Name example...91 Figure 32: Genetic Variation Associated Observation Zygosity example Figure 33: Genomic Associated Observation example Figure 34: Genomic Observation Reference example...93 Figure 35: Genomic Observations Organizer example Figure 36: Genomic Source Class example...95 Figure 37: Indication Observation example Figure 38: Interpretive Phenotype example...96 Figure 39: Interpretive Phenotype Cytogenetics example...97 Figure 40: Interpretive Phenotype Gene Expression example Figure 41: Interpretive Phenotype Genetic Variation example Figure 42: Interpretive Phenotype Pharmacogenomic example...99 Figure 43: Interpretive Phenotype Pharmacogenomic Drug Efficacy example Figure 44: Interpretive Phenotype Pharmacogenomic Drug Metabolism example Figure 45: Overall Interpretive Phenotype Chromosome Analysis example Figure 46: Overall Interpretive Phenotype Genetic Disease example Figure 47: Overall Interpretive Phenotype Genetic Disease Carrier example Figure 48: Overall Interpretive Phenotype Pharmacogenomic Drug Efficacy example Figure 49: Overall Interpretive Phenotype Pharmacogenomic Drug Metabolism example Figure 50: Test Performed Observation example...106

13 TOC 13 List of Tables Table 1: Contents of the Ballot Package...20

14 TOC 14

15 Chapter 1 INTRODUCTION Topics: Purpose Approach Scope Audience Organization of This Guide Use of Templates Conventions Used in This Guide Contents of the Ballot Package The purpose of this Implementation Guide (IG) is to specify a standard for Genetic Testing Reports. In this project, the Clinical Genomics Work Group develops a CDA Implementation Guide (IG) for genetic testing reports, with the support of the Structured Documents Work Group. Note that this spec has passed DSTU ballot but is still being refined based on reconciliation of negative ballot comments. Early adopters are welcome but should be aware that final spec could be different than the current version. A few complete GTR samples are provided in the package containing this guide but only the hearing loss sample has been adjusted to the latest structure. XML snippets are automatically generated by the editing tool and placed as figures demonstrating the various templates of this guide. Nevertheless, these XML snippets are often merely skeletal and may not be accurate contentwise. Therefore, for best viewing of the XML snippets, it is recommended to first go through the complete samples provided in the ballot package.

16 INTRODUCTION 16 Purpose Genetic tests have recently become an important tool in clinical care that further personalizes the care processes based on the patient individual genetic makeup. Genetic testing methods are diverse and span from testing for known germline mutations in the context of single-gene disorders, to full sequencing of genes in tumor tissues looking for somatic variations in cancer cells. We also see the emerging use of gene expression testing in clinical care and it is expected to see a growing use of research techniques adjusted to healthcare. As a consequence of that diversity and the constantly growing number of techniques yielding new result formats less familiar to clinicians, we see existing report formats having emphasis on detailed but easy-to-understand interpretations of the testing results along with recommendations. These interpretations may originate from the laboratory or they may be created by a clinician specializing in genetic/genomic medicine. This work also supports, communication within the report itself, detailed information on the tests performed including references to the appropriate scientific studies and publications in a format that looks quite often like a short abstract in a scientific journal. Within the clinical environment, genetic test results typically flow from the genetic testing laboratory into the electronic health record (EHR). From the EHR these results may flow into another EHR or a personal health record (PHR). In some realms the first transmission of this data (from the laboratory into the EHR) is performed using the Laboratory message standard. Clinical Genomics has written an implementation guide which extends this standard for the support of clinical genetics (HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 1 (US Realm) ). In some realms, the second transmission of this data (EHR to EHR/PHR) is performed using the CCD message model (a constrained version of the CDA model). As such for the healthcare specific message, this implementation guide will minimally detail how certain data sets defined in the above mentioned implementation guide would be included using the CDA model as appropriate to the level of granularity of this human-readable report. Note: The producers of GTR documents include genetic laboratories as well as clinical geneticists or any clinician who needs to create a report summarizing genetic testing results (and is capable and authorized to do so). In addition, all roles in a research environment that needs to summarize genetic assays are included in the scope. Approach The following GTR IG design principles are based on requirements analysis through collecting requirements from various stake-holders of genetic testing reports. Convey findings and emphasize interpretations and recommendations (in the clinical environment, interpretations should be related to clinically relevant findings) Provide in-line information on tests performed Represent interpretation by utilizing patterns of genotype-phenotype associations in the HL7 v3 Clinical Genomics and implement them as harmonized clinical statement entry-level templates in this IG Represent a 'genetic study' by allowing different types of testing's to be included in the same GTR report, e.g., genetic variations, cytogenetics, gene expression etc.,all possibly contributing to the "overall interpretation" based on the interpretations of the discrete testings. Reference HL7 Clinical Genomics instances as the place holders of raw data (personal evidences) similarly to referencing images In particular, the GTR is organized as follows: The layout of the GTR starts with a summary section and ends with general information about the test performed; In between these two sections there are the specialized sections (represented by TestDetailsSection)describing specific genetic testing performed The rendered portion of the GTR (aka "narrative") is placed in the text attributes of sections and sub-sections The structured portion of the GTR is carried by the "ClinicalGenomicStatement" template. At its core, it has a genomic observation, optionally associated on the one side with indications for performing this observation and on the other side with interpretations of that observation Genetic Testing Report (GTR) Page 16

17 INTRODUCTION 17 A number of ClinicalGenomicStatement's can be placed in the TestDetailsSection which serves as a blueprint for specialized sections describing genetic variations, cytogenetics, gene expression, etc. Interpretations of a genomic observation are placed in sub-templates of the InterpretivePhenotypeObservation (an abstract class), for example, InterpretivePhenotypeObservationGeneticVariation The summary section has the following sub-sections: indications, summary of test performed, specimen, overall interpretation and recommendations. Regarding the tests performed section, it is similar to the TestPerformedSection, but can hold several tests (with concise descriptions) in contrast to the TestPerformedSection residing in each specific testing section and could have more detail about that specific test Sections that don't have a sub-template of "ClinicalGenomicStatement" or of "InterpretivePhenotypeObservation", merely carry narrative content A TestInformationSection can appear in each of the specific test sections if more detail is needed or if each test has its own description and there is no general description of all tests Notes: 1. The XML figures (snippets) are generated automatically the editing tool (MDHT); if they are empty or merely skeletal, please refer to the complete XML samples enclosed in the ballot package 2. Constraints on the value attribute have been described in free text similar to Object Constraining Language (OCL) statements. In later releases of this guide, all constraints will be represented in OCL and thus could be validated Scope The scope of this project is to define a Universal CDA Implementation Guide that can accommodate the needs described above which could then be further refined to specific genetic testing reports, either realm specific or method-specific or any other set of restrictions. In addition, this IG will strive to serve both research and clinical environment as much as possible. Audience The audience for this document includes software developers and implementers who wish to enable information exchange of genetic testing reports that can be both human readable and machine-processable. Organization of This Guide Templates Templates are organized by document (see Document Templates), by section (see Section Templates), and by clinical statements (see Clinical Statement Templates). Within a section, templates are arranged hierarchically, where a more specific template is nested under the more generic template that it conforms to. See Templates by Containment for a listing of the higher level templates by containment; the appendix Templates Used in This Guide includes a table of all of the templates Organized Hierarchically. Vocabulary and Value Sets Vocabularies recommended in this guide are from standard vocabularies. The LOINC codes developed within the v2 genetic testing results message are used in this IG as optional value sets. When further constraining this IG to the US Realm, it would be possible to mandate the use of these LOINC value sets. Of note, these LOINC codes have been successfully piloted within the clinical genetic laboratory and EHR. In addition, these terms have been added to the NCI-t (U.S. National Cancer Institute's Thesaurus, see: ncit.nci.nih.gov/ Genetic Testing Report (GTR) Page 17

18 INTRODUCTION 18 Use of Templates When valued in an instance, the template identifier (templateid) signals the imposition of a set of templatedefined constraints. The value of this attribute provides a unique identifier for the templates in question. Originator Responsibilities An originator can apply a templateid to assert conformance with a particular template. In the most general forms of CDA exchange, an originator need not apply a templateid for every template that an object in an instance document conforms to. This implementation guide asserts when templateids are required for conformance. Recipient Responsibilities A recipient may reject an instance that does not contain a particular templateid (e.g., a recipient looking to receive only GTR documents can reject an instance without the appropriate templateid). A recipient may process objects in an instance document that do not contain a templateid (e.g., a recipient can process entries that contain Observation acts within a Problems section, even if the entries do not have templateids). Note on Draft Standards The requirements as laid out in the body of this document are subject to change per the policy on implementation guides (see section 13.02" Draft Standard for Trial Use Documents" within the HL7 Governance and Operations Manual, ). Conventions Used in This Guide Conformance Requirements Conformance statements are grouped and identified by the name of the template, along with the templateid and the context of the template (e.g., ClinicalDocument, section, observation), which specifies the element under constraint. If a template is a specialization of another template, its first constraint indicates the more general template. In all cases where a more specific template conforms to a more general template, asserting the more specific template also implies conformance to the more general template. An example is shown below. Template name [<type of template>: templateid <XXXX.XX.XXX.XXX>] Description of the template will be here Conforms to <The template name> Template (templateid: XXXX<XX>XXX>YYY). 2. SHALL contain = <AAA> <code display name> (CodeSystem: <XXX> Class) STATIC (CONF:<number>) Figure 1: Template name and "conforms to" appearance The conformance verb keyword at the start of a constraint ( SHALL, SHOULD, MAY, etc.) indicates business conformance, whereas the cardinality indicator (0..1, 1..1, 1..*, etc.) specifies the allowable occurrences within an instance. Thus, " MAY contain 0..1" and " SHOULD contain 0..1" both allow for a document to omit the particular component, but the latter is a stronger recommendation that the component be included if it is known. The following cardinality indicators may be interpreted as follows: Genetic Testing Report (GTR) Page 18

19 INTRODUCTION as zero to one present 1..1 as one and only one present 2..2 as two must be present 1..* as one or more present 0..* as zero to many present Value set bindings adhere to HL7 Vocabulary Working Group best practices, and include both a conformance verb ( SHALL, SHOULD, MAY, etc.) and an indication of DYNAMIC vs. STATIC binding. The use of SHALL requires that the component be valued with a member from the cited value set; however, in every case any HL7 "null" value such as other (OTH) or unknown (UNK) may be used. Each constraint is uniquely identified (e.g., "CONF:605") by an identifier placed at or near the end of the constraint. These identifiers are not sequential as they are based on the order of creation of the constraint. 1. SHALL contain [1..1] component/structuredbody (CONF:4082). a. This component/structuredbody SHOULD contain [0..1] component (CONF:4130) such that it a. SHALL contain [1..1] Reporting Parameters section (templateid: ) (CONF:4131). b. This component/structuredbody SHALL contain [1..1] component (CONF:4132) such that it a. SHALL contain [1..1] Patient data section - NCR (templateid: ) (CONF:4133). Figure 2: Template-based conformance statements example 1. The value for "Observation in a problem observation SHALL be "EVN" ActMood STATIC. (CONF: 814). 2. A problem observation SHALL include exactly one Observation / statuscode. (CONF: 815). 3. The value for "Observation / statuscode" in a problem observation SHALL be "completed" ActStatus STATIC. (CONF: 816). 4. A problem observation SHOULD contain exactly one Observation / effectivetime, to indicate the biological timing of condition (e.g. the time the condition started, the onset of the illness or symptom, the duration of a condition). (CONF: 817). Figure 3: Conformance statements example (taken from the CCD IG) Keywords The keywords SHALL, SHALL NOT, SHOULD, SHOULD NOT, MAY, and NEED NOT in this document are to be interpreted as described in the HL7 Version 3 Publishing Facilitator's Guide: SHALL: an absolute requirement SHALL NOT: an absolute prohibition against inclusion SHOULD/SHOULD NOT: valid reasons to include or ignore a particular item, but must be understood and carefully weighed MAY/NEED NOT: truly optional; can be included or omitted as the author decides with no implications XML Examples XML samples appear in various figures in this document in a fixed-width font. Portions of the XML content may be omitted from the content for brevity, marked by an ellipsis ( ) as shown in the example below. <ClinicalDocument xmlns= urn:h17-org:v3 >... </ClinicalDocument> Figure 4: ClinicalDocument example Genetic Testing Report (GTR) Page 19

20 INTRODUCTION 20 XPath expressions are used in the narrative and conformance requirements to identify elements because they are familiar to many XML implementers. Contents of the Ballot Package Table 1: Contents of the Ballot Package Filename CDAR2_IG_GENTESTRPT_R1_D2_2012SEP Description This guide CDA Genetic Testing Report (GTR) Samples (.xml files) A GTR sample on hearing loss genetic variation tests; A few more GTR samples are included on DCM, Warfarin and cytogenetics but have not been adjusted to the latest structure, however the differences are minor and they can illustrate the use of GTR in various cases; NOTE: the samples are provided in order to illustrate the GTR structure and are not necessarily accurate content-wise cda.xsl Changes from previous ballot.doc A generic stylesheet for displaying the content of the sample document in HTML A Word document summarizing main changes made after GTR ballot cycles Genetic Testing Report (GTR) Page 20

21 Chapter 2 DOCUMENT TEMPLATES Topics: Genetic Testing Report This section contains the document level constraints for CDA documents that are compliant with this implementation guide.

22 DOCUMENT TEMPLATES 22 Genetic Testing Report [ClinicalDocument: templateid ] The GeneticTestingReport is a document template and thus serves as the root template for the GTR Implementation Guide. Its organization is described in the Approach section of this document. The sub-sections residing here constitute the backbone of the GTR. A specific genetic test is described in the TestDetailsSection which serves as a blueprint specialized sections describing testing like genetic variation or gene expression. 1. SHALL contain exactly one [1..1] code/@code=" " Genetic analysis summary report (CodeSystem: LOINC) (CONF-GTR-1) 2. SHALL contain exactly one [1..1] title (CONF-GTR-7) Default title is "Genetic Testing Report". 3. SHALL contain exactly one [1..1] component a. Contains exactly one [1..1] Summary Section (templateid: ) 4. Contains at least one [1..*] component a. Contains exactly one [1..1] Test Details Section (templateid: ) 5. Contains zero or one [0..1] component a. Contains exactly one [1..1] Test Information Section (templateid: ) 6. Sections and subsections SHALL have a title and the title SHALL NOT be empty. Text of a section title can specialize the section code by being more specific, for example, a hearing loss genetic testing report. 7. Sections SHALL appear in the order they are presented in this guide. Thus, SummarySection which SHALL appear first and TestInformationSection which SHOULD appear last. In between, TestDetailsSection can be repeated per the no. of genetic tests performed. Note that a TestInformationSection can appear in each of the specific test sections. 1. Contains exactly one [1..1] typeid with data type Infrastructure Root Type Id 2. Contains exactly one [1..1] id with data type II 3. SHALL contain exactly one [1..1] code/@code=" " Genetic analysis summary report (CodeSystem: LOINC) (CONF-GTR-1) 4. SHALL contain exactly one [1..1] title (CONF-GTR-7) Default title is "Genetic Testing Report". 5. Contains exactly one [1..1] effectivetime with data type TS 6. Contains exactly one [1..1] confidentialitycode with data type CE 7. Contains at least one [1..*] recordtarget, where its type is Record Target a. Contains exactly one [1..1] Record Target 8. Contains at least one [1..*] author, where its type is Author a. Contains exactly one [1..1] Author 9. Contains exactly one [1..1] custodian, where its type is Custodian a. Contains exactly one [1..1] Custodian 10. Contains exactly one [1..1] component, where its type is Component2 a. Contains exactly one [1..1] Component2 11. SHALL contain exactly one [1..1] component a. Contains exactly one [1..1] Summary Section (templateid: ) 12. Contains at least one [1..*] component a. Contains exactly one [1..1] Test Details Section (templateid: ) 13. Contains zero or one [0..1] component Genetic Testing Report (GTR) Page 22

23 DOCUMENT TEMPLATES 23 a. Contains exactly one [1..1] Test Information Section (templateid: ) 14. Sections and subsections SHALL have a title and the title SHALL NOT be empty. Text of a section title can specialize the section code by being more specific, for example, a hearing loss genetic testing report. 15. Sections SHALL appear in the order they are presented in this guide. Thus, SummarySection which SHALL appear first and TestInformationSection which SHOULD appear last. In between, TestDetailsSection can be repeated per the no. of genetic tests performed. Note that a TestInformationSection can appear in each of the specific test sections. <?xml version="1.0" encoding="utf-8"?> <ClinicalDocument xmlns:xsi=" xmlns="urn:hl7-org:v3" xsi:schemalocation="urn:hl7-org:v3 CDA.xsd"> <typeid root=" " extension="pocd_hd000040"/> <templateid root=" "/> <id root=" " extension="c266"/> <code code=" " codesystem=" " codesystemname="loinc" displayname="genetic analysis summary report"/> <title>genetic Testing Report</title> <effectivetime value=" "/> <confidentialitycode code="r" codesystem=" "/> <languagecode code="en-us"/> <setid root=" " extension="bb35"/> <versionnumber value="1"/> <recordtarget> <patientrole> <id root=" " extension=" "/> <patient> <name use="l"> <given>john</given> <given>q.</given> <family>doe</family> </name> <administrativegendercode code="m" codesystem=" " codesystemname="administrativegender" displayname="male"/> <birthtime value=" "/> </patient> <providerorganization> <id root=" "/> <name>the New Genetic Testing Laboratory</name> </providerorganization> </patientrole> </recordtarget> <author> <functioncode code="aut" displayname="author (originator)"/> <time/> <assignedauthor> <id root=" " extension="author123"/> <code code="aut" displayname="author"/> <assignedperson> <name>jean Geome</name> </assignedperson> <representedorganization> <id root=" " extension="2dd "/> </representedorganization> </assignedauthor> </author> <custodian> <assignedcustodian> <representedcustodianorganization> <id root=" "/> Genetic Testing Report (GTR) Page 23

24 DOCUMENT TEMPLATES 24 </representedcustodianorganization> </assignedcustodian> </custodian> <legalauthenticator> <time value=" "/> <signaturecode code="s"/> <assignedentity> <id root=" " extension="abcd " displayable="true"/> <code code="aut" displayname="author"/> <assignedperson> <name>jean Genome</name> </assignedperson> <representedorganization> <id root=" " extension="2dd " displayable="true"/> <name>the New Genetic Testing Laboratory</name> </representedorganization> </assignedentity> </legalauthenticator> <documentationof> <serviceevent> <id root=" " extension="abcd-1234"/> </serviceevent> </documentationof> <component> <structuredbody> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="summary report"/> <title>summary</title> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="indication for"/> <title>indications</title> <text> <list> <content ID="a2">Indication: Profound sensorineural hearing loss</ content> </list> </text> <entry> <templateid root=" "/> <id root=" "/> <code code="mthu008863" codesystem=" " codesystemname="loinc" displayname="indications description"/> <effectivetime value="1950"/> <value xsi:type="cd" code="c26973" codesystemname="nci Thesaurus" displayname="sensory Hearing Loss"/> </entry> </section> </component> <component> <section> <templateid root=" "/> Genetic Testing Report (GTR) Page 24

25 DOCUMENT TEMPLATES 25 <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="specimen description"/> <title>specimen and Genomic Source Class</title> <text> <list> Peripheral Blood Genomic source class: Germline </list> </text> <entry> <templateid root=" "/> <code code=" " codesystemname="loinc" displayname="genomic source class"/> <value xsi:type="cd" code="la6683-2" codesystemname="loinc" displayname="germline"/> <specimen> <templateid root=" "/> <specimenrole> <specimenplayingentity> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="peripheral blood specimen"/> </specimenplayingentity> </specimenrole> </specimen> </entry> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="genetic test"/> <title>summary of Tests Performed</title> <text> <list> <content ID="a1"> GJB2 Full Gene Test <content ID="a5"> GJB6-D13S1830 deletion terminology <content ID="a3"> Mitochondrial Hearing Loss Mutation Test </list> </text> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="assessment section"/> <title>overall Interpretation</title> <text> Genetic Testing Report (GTR) Page 25

26 DOCUMENT TEMPLATES 26 <list> <content stylecode="bold">inconclusive. DNA sequencing detected two changes in the GJB2 gene, 79G>A (V27I) and 109G>A (V37I). The V27I change has been reported as a benign variant (references) and is not believed to cause hearing loss. The V37I mutation has been previously reported in patients with hearing loss. This mutation, in homozygosity or combined with another GJB2 disease causing mutation, typically results in a mild to moderate hearing loss (Cryns et al. 2005). Mutations in both copies of the GJB2 gene are necessary to assume that GJB2 is responsible for the hearing loss. Although two mutations were identified in this patient, we would assume that the combination of a benign variant and a mild pathogenic mutation would result in a mild to moderate hearing loss rather than a moderately-severe one, as in this patient. It is most likely that the hearing loss in this patient is the result of the V37I mutation and an unknown second pathogenic mutation. It should be noted that a second mutation is not identified in a large percentage (10-50%) of patients with nonsyndromic hearing loss and GJB2 mutations (del Castillo et al. 2003). GJB6-D13S1830 Deletion: A PCR-based analysis of the GJB6-D13S1830 region of chromosome 13 was performed and did not detect the deletion. This test does not assess the DNA sequence of the GJB6 gene or detect other mutations that could affect the expression of the gene. Mitochondrial Hearing Loss mutations: Targeted bidirectional sequencing of mitochondrial DNA 1555 and 7445 regions did not detect the presence of these mutations. Although this test examines all regions known to contain pathogenic mutations in these genes, it does not include sequencing of the 5' end of the MTRNR1 gene. </list> </text> <entry> <templateid root=" "/> <id root=" "/> <code code=" " codesystemname="loinc" displayname="genetic analysis summary panel"/> <statuscode code="completed"/> <entryrelationship typecode="subj"> <organizer classcode="battery" moodcode="evn"> <statuscode code="completed"/> <component> <id root=" "/> <code/> </component> <component> <id root=" "/> <code/> Genetic Testing Report (GTR) Page 26

27 DOCUMENT TEMPLATES 27 </component> <component> <id root=" "/> <code/> </component> <component> <id root=" "/> <code/> </component> </organizer> <entryrelationship typecode="rson"> <observation classcode="cond" moodcode="evn"> <id root=" "/> <code/> <entryrelationship typecode="sprt"> <observation classcode="obs" moodcode="def"> <templateid root=" "/> <code code=" " codesystemname="loinc" displayname="genetic disease analysis overall interpretation"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="la9663-1" displayname="inconclusive"/> </entry> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="plan section"/> <title>recommendations</title> <text> <list> Although some cases may represent a coincidental carrier state, all of the studies have concluded that there are likely to be other genetic mutations that have not yet been identified. Genetic counseling is recommended for this patient and his/her family members. </list> </text> </section> </component> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="report"/> <title>genetic Variations</title> Genetic Testing Report (GTR) Page 27

28 DOCUMENT TEMPLATES 28 <entry> <templateid root=" "/> <id root=" "/> <code code=" " codesystemname="loinc" displayname="dna Analysis Discrete Sequence Variant Panel"/> <statuscode code="completed"/> <effectivetime value=" "/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="gene Identifier"/> <value xsi:type="cd" code="gjb2" codesystemname="hugo"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="transcript Reference Sequence Identifier"/> <value xsi:type="cd" code="nm_ " codesystem="refseq" codesystemname="ncbi Reference Sequence"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Sequence Variation Identifier"/> <value xsi:type="cd" code="rs " codesystemname="dbsnp"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Sequence Variation"/> <value xsi:type="cd" code="109g>a" codesystemname="hgvs nomenclature for the description of sequence variations"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Sequence Variation Type"/> <value xsi:type="cd" code="la6690-7" codesystemname="loinc" displayname="substitution"/> <entryrelationship typecode="subj"> <templateid root=" "/> <code code=" " codesystemname="loinc" displayname="amino Acid Change"/> <value xsi:type="cd" code="val37ile"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="amino acid change type"/> <value xsi:type="cd" code="la6698-0" displayname="missense"/> <entryrelationship typecode="subj"> Genetic Testing Report (GTR) Page 28

29 DOCUMENT TEMPLATES 29 <code code=" " codesystemname="loinc" displayname="dna Region Name"/> <value xsi:type="st">exon 2</value> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname=" Allelic State"/> <value xsi:type="cd" code="la6705-3" codesystemname="loinc" displayname="homozygous"/> <entryrelationship typecode="rson"> <id root=" "/> <code/> <entryrelationship typecode="sprt"> <observation classcode="obs" moodcode="def"> <code code=" " codesystemname="loinc" displayname="genetic disease sequence variation interpretation"/> <value xsi:type="cd" code="la6668-3" codesystemname="loinc" displayname="pathogenic"/> </entry> <entry> <templateid root=" "/> <id root=" "/> <code code=" " codesystemname="loinc" displayname=" DNA Analysis Discrete Sequence Variant Panel"/> <statuscode code="completed"/> <effectivetime value=" "/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="gene Identifier"/> <value xsi:type="cd" code="gjb2" codesystemname="hugo"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="transcript Reference Sequence Identifier"/> <value xsi:type="cd" code="nm_ " codesystem="refseq" codesystemname="ncbi Reference Sequence"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Sequence Variation Identifier"/> <value xsi:type="cd" code="rs " codesystemname="dbsnp"/> <entryrelationship typecode="subj"> Genetic Testing Report (GTR) Page 29

30 DOCUMENT TEMPLATES 30 <code code=" " codesystemname="loinc" displayname="dna Sequence Variation"/> <value xsi:type="cd" code="79g>a" codesystemname="hgvs nomenclature for the description of sequence variations"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Sequence Variation Type"/> <value xsi:type="cd" code="la6690-7" codesystemname="loinc" displayname="substitution"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="amino Acid Change"/> <value xsi:type="cd" code="val27ile"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="amino acid change type"/> <value xsi:type="cd" code="la6698-0" displayname="missense"/> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname="dna Region Name"/> <value xsi:type="st">exon 2</value> <entryrelationship typecode="subj"> <code code=" " codesystemname="loinc" displayname=" Allelic State"/> <value xsi:type="cd" code="la6706-1" codesystemname="loinc" displayname="heterozygous"/> <entryrelationship typecode="rson"> <id root=" "/> <code/> <entryrelationship typecode="sprt"> <observation classcode="obs" moodcode="def"> <code code=" " codesystemname="loinc" displayname="genetic disease sequence variation interpretation"/> <value xsi:type="cd" code="la6675-8" codesystemname="loinc" displayname="benign"/> </entry> <component> <section> <templateid root=" "/> Genetic Testing Report (GTR) Page 30

31 DOCUMENT TEMPLATES 31 <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="genetic test"/> <title>tests Performed</title> <text> <list> GJB2 Full Gene Test </list> </text> <entry> <templateid root=" "/> <code displayname="test Performed"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="cx26full" codesystem=" " codesystemname="loinc" displayname="connexin 26 Full Gene Test"> <originaltext> <reference value="#a1"/> </originaltext> </value> <entryrelationship typecode="rson"> <observation classcode="cond" moodcode="evn"> <id root=" "/> <code/> </entry> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="results section"/> <title>findings</title> <text> <list> DNA MUTATIONS: Heterozygous 109G>A (V37I), Exon 2, GJB2, Pathogenic INCIDENTAL VARIANTS: Heterozygous 79G>A (V27I), Exon 2, GJB2, Benign </list> </text> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="assessment section"/> <title>interpretation</title> Genetic Testing Report (GTR) Page 31

32 DOCUMENT TEMPLATES 32 <text> <list> Mutations interpretation <list> V37I - Pathogenic V27I - Benign </list> Details: DNA sequencing detected two mutations in the GJB2 gene, 79G>A (V27I) and 109G>A (V37I). The V27I mutation has been reported as a benign variant (references) and is not believed to cause hearing loss. The V37I mutation has been previously reported in patients with hearing loss. This mutation, in homozygosity or combined with another GJB2 disease causing mutation, typically results in a mild to moderate hearing loss (Cryns et al. 2005). Mutations in both copies of the GJB2 gene are necessary to assume that GJB2 is responsible for the hearing loss. Although two mutations were identified in this patient, we would assume that the combination of a benign variant and a mild pathogenic mutation would result in a mild to moderate hearing loss rather than a moderately-severe one, as in this patient. It is most likely that the hearing loss in this patient is the result of the V37I mutation and an unknown second pathogenic mutation. It should be noted that a second mutation is not identified in a large percentage (10-50%) of patients with nonsyndromic hearing loss and GJB2 mutations (del Castillo et al. 2003). </list> </text> </section> </component> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="report"/> <title>genetic Variations</title> <entry> <observation classcode="cond" moodcode="evn"> <templateid root=" "/> <id root=" "/> <code code=" " displayname="dna region of interest"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="gjb6-d13s1830"/> <entryrelationship typecode="comp"> <observation classcode="obs" moodcode="evn" negationind="true"> <code code=" " displayname="dna Sequence Variation type"/> <value xsi:type="cd" code="la6692-3" displayname="deletion"/> </entry> Genetic Testing Report (GTR) Page 32

33 DOCUMENT TEMPLATES 33 <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="genetic test"/> <title>tests Performed</title> <text> <list> GJB6-D13S1830 Deletion Test </list> </text> <entry> <templateid root=" "/> <code displayname="test Performed"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="tbd" codesystem=" " codesystemname="loinc" displayname="connexin 30 Deletion Test"> <originaltext> <reference value="#a5"/> </originaltext> </value> <entryrelationship typecode="rson"> <observation classcode="cond" moodcode="evn"> <id root=" "/> <code/> </entry> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="results section"/> <title>findings</title> <text> <list> Negative. </list> </text> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="assessment section"/> <title>interpretation</title> <text> <list> Genetic Testing Report (GTR) Page 33

34 DOCUMENT TEMPLATES 34 GJB6-D13S1830 Deletion: A PCR-based analysis of the GJB6- D13S1830 region of chromosome 13 was performed and did not detect the deletion. This test does not assess the DNA sequence of the GJB6 gene or detect other mutations that could affect the expression of the gene. </list> </text> </section> </component> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="report"/> <title>genetic Variations</title> <entry> <templateid root=" "/> <id root=" "/> <code code=" " displayname="gene identifier"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="mtts1"/> <entryrelationship typecode="comp"> <observation classcode="obs" moodcode="evn" negationind="true"> <code/> </entry> <entry> <code code=" " displayname="gene identifier"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="mtrnr1"/> <entryrelationship typecode="comp"> <observation classcode="obs" moodcode="evn" negationind="true"> <code/> </entry> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="genetic test"/> <title>tests Performed</title> <text> <list> Mitochondrial Hearing Loss Genes Test </list> </text> Genetic Testing Report (GTR) Page 34

35 DOCUMENT TEMPLATES 35 <entry> <templateid root=" "/> <code displayname="test Performed"/> <statuscode code="completed"/> <effectivetime value=" "/> <value xsi:type="cd" code="tbd" codesystem=" " codesystemname="loinc" displayname="mtts1 and MTRNR1 Genes Test"> <originaltext> <reference value="#a3"/> </originaltext> </value> <entryrelationship typecode="rson"> <observation classcode="cond" moodcode="evn"> <id root=" "/> <code/> </entry> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="results section"/> <title>findings</title> <text> <list> Negative. </list> </text> </section> </component> <component> <section> <templateid root=" "/> <code code=" " codesystem=" " codesystemname="snomed-ct" displayname="assessment section"/> <title>interpretation</title> <text> <list> DNA sequencing did not detect the presence of any mutations in the MTTS1 and MTRNR1 genes. Although this test examines all regions known to contain pathogenic mutations in these genes, it does not include sequencing of the 5' end of the MTRNR1 gene. </list> </text> </section> </component> </section> </component> <component> <section> Genetic Testing Report (GTR) Page 35