avro.gel_participant_6_2_0.ExitQuestionnaire.avdl Maven / Gradle / Ivy
@namespace("org.gel.models.report.avro")
/**
This protocol defines ExitQuestionnaires
*/
protocol ExitQuestionnaires {
import idl "CommonInterpreted.avdl";
enum CaseSolvedFamily {yes, no, partially, unknown}
enum PhenotypesSolved {yes, no, partially, unknown}
enum SegregationQuestion {yes, no}
enum ReportingQuestion {yes, no, na}
enum ConfirmationDecision {yes, no, na}
enum ConfirmationOutcome {yes, no, na}
enum Actionability {yes, no, not_yet, na}
// TODO: refactor with VariantClassification in CommonInterpreted.avdl
enum ACMGClassification {pathogenic_variant, likely_pathogenic_variant, variant_of_unknown_clinical_significance, likely_benign_variant, benign_variant, not_assessed, na}
enum ClinicalUtility {none, change_in_medication, surgical_option, additional_surveillance_for_proband_or_relatives, clinical_trial_eligibility, informs_reproductive_choice, unknown, other}
enum FamilyHistoryCondition {yes, no, unknown}
enum FamilyHistoryPatient {yes, no, unknown}
enum FamilyHistoryFamily {yes, no, unknown}
/**
The family level questions
*/
record FamilyLevelQuestions{
/**
Have the results reported here explained the genetic basis of the family’s presenting phenotype(s)?
*/
CaseSolvedFamily caseSolvedFamily;
/**
Have you done any segregation testing in non-participating family members?
*/
SegregationQuestion segregationQuestion;
/**
Comments regarding report
*/
string additionalComments;
}
/**
The variant level questions
*/
record VariantLevelQuestions{
/**
Variant coordinates
*/
VariantCoordinates variantCoordinates;
/**
Did you carry out technical confirmation of this variant via an alternative test?
*/
ConfirmationDecision confirmationDecision;
/**
Did the test confirm that the variant is present?
*/
ConfirmationOutcome confirmationOutcome;
/**
Did you include the variant in your report to the clinician?
*/
ReportingQuestion reportingQuestion;
/**
What ACMG pathogenicity score (1-5) did you assign to this variant?
*/
ACMGClassification acmgClassification;
/**
Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers
*/
string publications;
}
/**
Structural variant level questions
*/
record StructuralVariantLevelQuestions{
/**
Structural variant type
*/
StructuralVariantType variantType;
/**
Variant coordinates
*/
Coordinates coordinates;
/**
Did you carry out technical confirmation of this variant via an alternative test?
*/
ConfirmationDecision confirmationDecision;
/**
Did the test confirm that the variant is present?
*/
ConfirmationOutcome confirmationOutcome;
/**
Did you include the variant in your report to the clinician?
*/
ReportingQuestion reportingQuestion;
/**
What ACMG pathogenicity score (1-5) did you assign to this variant?
*/
ACMGClassification acmgClassification;
/**
Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers
*/
string publications;
}
/**
The variant level questions
*/
record ShortTandemRepeatLevelQuestions{
/**
Variant coordinates
*/
Coordinates coordinates;
/**
Did you carry out technical confirmation of this variant via an alternative test?
*/
ConfirmationDecision confirmationDecision;
/**
Did the test confirm that the variant is present?
*/
ConfirmationOutcome confirmationOutcome;
/**
Did you include the variant in your report to the clinician?
*/
ReportingQuestion reportingQuestion;
/**
What ACMG pathogenicity score (1-5) did you assign to this variant?
*/
ACMGClassification acmgClassification;
/**
Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers
*/
string publications;
}
/**
The variant group level questions
*/
record VariantGroupLevelQuestions{
/**
This value groups variants that together could explain the phenotype according to the mode of inheritance used.
(e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in
the same group (i.e.: reported together). This value is an integer unique in the whole report.
These values are only relevant within the same report.
*/
int variantGroup;
/**
Variant level questions for each of the variants in the group
*/
union {null, array} variantLevelQuestions;
/**
STR level questions for each of the variants in the group
*/
union {null, array} shortTandemRepeatLevelQuestions;
/**
Structural level questions for each of the variants in the group
*/
union {null, array} structuralVariantLevelQuestions;
/**
Is evidence for this variant/variant pair sufficient to use it for clinical purposes such as prenatal diagnosis or predictive testing?
*/
Actionability actionability;
/**
Has the clinical team identified any changes to clinical care which could potentially arise as a result of this variant/variant pair?
*/
array clinicalUtility;
/**
Did you report the variant(s) as being partially or completely causative of the family's presenting phenotype(s)?
*/
PhenotypesSolved phenotypesSolved;
/**
If you indicated that the variant(s) only partially explained the family’s presenting phenotypes, please indicate which HPO terms you are confident that they DO explain
*/
union {null, array} phenotypesExplained;
}
/**
The additional findings variant group level questions
*/
record AdditionalFindingsVariantGroupLevelQuestions{
/**
This value groups variants that together could explain the phenotype according to the mode of inheritance used.
(e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in
the same group (i.e.: reported together). This value is an integer unique in the whole report.
These values are only relevant within the same report.
*/
int variantGroup;
/**
Variant level questions for each of the variants in the group
*/
union {null, array} variantLevelQuestions;
/**
STR level questions for each of the variants in the group
*/
union {null, array} shortTandemRepeatLevelQuestions;
/**
Structural level questions for each of the variants in the group
*/
union {null, array} structuralVariantLevelQuestions;
/**
Does this patient have a positive family history relevant to this condition?
*/
FamilyHistoryCondition familyHistoryCondition;
/**
Was this variant previously known to be present in this patient/family?
*/
/**
In patient:
*/
FamilyHistoryPatient familyHistoryPatient;
/**
In family:
*/
FamilyHistoryFamily familyHistoryFamily;
/**
Has the clinical team identified any changes to clinical care which could potentially arise as a result of this variant/variant pair?
*/
array clinicalUtility;
}
/**
The rare disease program exit questionnaire
*/
record RareDiseaseExitQuestionnaire{
/**
The date when the questionnaire was submitted
*/
string eventDate;
/**
The person that submitted the questionnaire
*/
string reporter;
/**
The set of questions at family level
*/
FamilyLevelQuestions familyLevelQuestions;
/**
The list of variant group level variants (ungrouped variants are to be set in single variant group)
*/
array variantGroupLevelQuestions;
}
/*
-------------------------------------------------
ADDITIONAL FINDINGS EXIT QUESTIONNAIRE
-------------------------------------------------
*/
record AdditionalFindingsExitQuestionnaire{
/**
The date when the questionnaire was submitted
*/
string eventDate;
/**
The person that submitted the questionnaire
*/
string reporter;
/**
The list of variant group level variants (ungrouped variants are to be set in single variant group)
*/
array additionalFindingsVariantGroupLevelQuestions;
}
/*
-------------------------------------------------
CANCER EXIT QUESTIONNAIRE
-------------------------------------------------
*/
/**
An enumeration for Which parts of the WGA were reviewed?:
* `domain_1`: Domain 1 only
* `domain_1_and_2`: Domains 1 and 2
* `domain_1_2_and_suplementary`: Domains 1, 2 and supplementary analysis
*/
enum ReviewedParts {domain_1, domain_1_and_2, domain_1_2_and_suplementary, somatic_if_relevant}
/**
Are the variants actionable?
* `yes`: yes
* `no`: no
*/
enum CancerActionableVariants {yes, no}
/**
The variant actionabilities:
* `predicts_therapeutic_response`: Predicts therapeutic response
* `prognostic`: Prognostic
* `defines_diagnosis_group`: Defines diagnosis group
* `eligibility_for_trial`: Eligibility for trial
* `other`: Other (please specify)
*/
enum CancerActionabilitySomatic {predicts_therapeutic_response, prognostic, defines_diagnosis_group, eligibility_for_trial, other}
/**
An enumeration Variant Actionability:
* `predicts_therapeutic_response`: Predicts therapeutic response
* `prognostic`: Prognostic
* `defines_diagnosis_group`: Defines diagnosis group
* `eligibility_for_trial`: Eligibility for trial
* `germline_susceptibility`: Germline susceptibility
* `other`: Other (please specify)
*/
enum CancerActionability {germline_susceptibility, predicts_therapeutic_response, prognostic, defines_diagnosis_group, eligibility_for_trial, other}
/**
Variant usability for somatic variants:
* `already_actioned`: Already actioned (i.e. prior to receiving this WGA)
* `actioned_result_of_this_wga`: actioned as a result of receiving this WGA
* `not_yet_actioned`: not yet actioned, but potentially actionable in the future
*/
enum CancerUsabilitySomatic {already_actioned, actioned_result_of_this_wga, not_yet_actioned}
/**
Variant usability for germline variants:
* `already_actioned`: Already actioned (i.e. prior to receiving this WGA)
* `actioned_result_of_this_wga`: actioned as a result of receiving this WGA
*/
enum CancerUsabilityGermline {already_actioned, actioned_result_of_this_wga}
/**
Was the variant validated with an orthogonal technology?
* `not_indicated_for_patient_care`: No: not indicated for patient care at this time
* `no_orthologous_test_available`: No: no orthologous test available
* `test_performed_prior_to_wga`: Yes: test performed prior to receiving WGA (eg using standard-of-care assay such as panel testing, or sanger sequencing)
* `technical_validation_following_WGA`: Yes: technical validation performed/planned following receiving this WGA
*/
enum CancerTested {not_indicated_for_patient_care, no_orthologous_test_available, test_performed_prior_to_wga, technical_validation_following_wga}
/**
An enumeration Variant tested:
* `not_indicated_for_patient_care`: No: not indicated for patient care at this time
* `no_orthologous_test_available`: No: no orthologous test available
* `test_performed_prior_to_wga`: Yes: test performed prior to receiving WGA (eg using standard-of-care assay such as panel testing, or sanger sequencing)
* `technical_validation_following_wga`: Yes: technical validation performed/planned following receiving this WGA
* `na`: N/A
*/
enum CancerTestedAdditional {not_indicated_for_patient_care, no_orthologous_test_available, test_performed_prior_to_wga, technical_validation_following_wga, na}
/**
The questions for the cancer program exit questionnaire at case level
*/
record CancerCaseLevelQuestions{
/**
Total time taken to review/collate evidence for variants (hours).
Include all literature review time, consultation with relevant experts etc.
*/
double total_review_time;
/**
Time taken to discuss case at MDT (hours).
*/
double mdt1_time;
/**
If the case is discussed at a 2nd MDT please enter time here (hours).
*/
union {null, double} mdt2_time;
/**
Total time to design ALL validation assay(s) for case (hours).
Only applicable if it is necessary to design a new assay to validate the variant.
*/
union {null, double} validation_assay_time;
/**
Technical Laboratory Validation. Total time for validation test wet work for all variants (hours).
*/
union {null, double} wet_validation_time;
/**
Analytical Laboratory Validation. Total time for analysis of validation results for all variants (hours).
*/
union {null, double} analytical_validation_time;
/**
Primary Reporting. Time taken to complete primary reporting stage (hours).
*/
double primary_reporting_time;
/**
Report Authorisation. Time taken to check and authorise report (hours).
*/
double primary_authorisation_time;
/**
Report Distribution.
Please enter, where possible/accessible how long it takes for the result to be conveyed to the patient.
E.g. via letter from the clinician (days).
*/
double report_distribution_time;
/**
Total time from result to report.
The total time taken from when the analysis of the WGS results started to a report being received
by the patient include any 'waiting' time (days).
*/
double total_time;
/**
Which parts of the WGA were reviewed?
*/
ReviewedParts reviewedInMdtWga;
/**
Were potentially actionable variants detected?
*/
CancerActionableVariants actionableVariants;
}
/**
The questions for the cancer program exit questionnaire for germline variants
*/
record CancerGermlineVariantLevelQuestions{
/**
Variant coordinates following format `chromosome:position:reference:alternate`
*/
VariantCoordinates variantCoordinates;
/**
Type of potential actionability:
*/
array variantActionability;
union {null, string} otherVariantActionability;
/**
How has/will this potentially actionable variant been/be used?
*/
CancerUsabilityGermline variantUsability;
/**
Has this variant been tested by another method (either prior to or following receipt of this WGA)?
*/
CancerTested variantTested;
/**
Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA;
*/
string validationAssayType;
}
record AdditionalVariantsQuestions{
/**
Chr: Pos Ref > Alt
*/
VariantCoordinates variantCoordinates;
/**
Type of potential actionability:
*/
array variantActionability;
union {null, string} otherVariantActionability;
/**
How has/will this potentially actionable variant been/be used?
*/
CancerUsabilitySomatic variantUsability;
/**
Has this variant been tested by another method (either prior to or following receipt of this WGA)?
*/
CancerTestedAdditional variantTested;
/**
Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA;
*/
string validationAssayType;
}
/**
The questions for the cancer program exit questionnaire for somatic variants
*/
record CancerSomaticVariantLevelQuestions{
/**
Variant coordinates following format `chromosome:position:reference:alternate`
*/
VariantCoordinates variantCoordinates;
/**
Type of potential actionability:
*/
array variantActionability;
/**
Other information about variant actionability
*/
union {null, string} otherVariantActionability;
/**
How has/will this potentially actionable variant been/be used?
*/
CancerUsabilitySomatic variantUsability;
/**
Has this variant been tested by another method (either prior to or following receipt of this WGA)?
*/
CancerTested variantTested;
/**
Please enter validation assay type e.g Pyrosequencing, NGS panel, COBAS, Sanger sequencing. If not applicable enter NA;
*/
string validationAssayType;
}
/**
The cancer program exit questionnaire
*/
record CancerExitQuestionnaire{
/**
The date when the questionnaire was submitted
*/
string eventDate;
/**
The person that submitted the questionnaire
*/
string reporter;
/**
The case level questions
*/
CancerCaseLevelQuestions caseLevelQuestions;
/**
The questions for somatic variants
*/
union {null, array} somaticVariantLevelQuestions;
/**
The questions for germline variants
*/
union {null, array} germlineVariantLevelQuestions;
/**
Please enter any additional comments you may have about the case here.
*/
union {null, string} additionalComments;
/**
Other actionable variants or entities.
Please provide other (potentially) actionable entities: e.g domain 3 small variants or SV/CNV, mutational signatures, mutational burden
*/
union {null, array} otherActionableVariants;
}
}
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