Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
@namespace("org.gel.models.participant.avro")
/**
This protocol defines the Common things between participant models
*/
protocol CommonParticipant {
enum TissueSource {BMA_TUMOUR_SORTED_CELLS, CT_GUIDED_BIOPSY, ENDOSCOPIC_BIOPSY, ENDOSCOPIC_ULTRASOUND_GUIDED_BIOPSY,
ENDOSCOPIC_ULTRASOUND_GUIDED_FNA, LAPAROSCOPIC_BIOPSY, LAPAROSCOPIC_EXCISION, MRI_GUIDED_BIOPSY, NON_GUIDED_BIOPSY,
SURGICAL_RESECTION, STEREOTACTICALLY_GUIDED_BIOPSY, USS_GUIDED_BIOPSY, NON_STANDARD_BIOPSY, NOT_SPECIFIED}
enum diseaseType {ADULT_GLIOMA, BLADDER, BREAST, CARCINOMA_OF_UNKNOWN_PRIMARY, CHILDHOOD, COLORECTAL, ENDOCRINE,
ENDOMETRIAL_CARCINOMA, HAEMONC, HEPATOPANCREATOBILIARY, LUNG, MALIGNANT_MELANOMA, NASOPHARYNGEAL, ORAL_OROPHARYNGEAL,
OVARIAN, PROSTATE, RENAL, SARCOMA, SINONASAL, TESTICULAR_GERM_CELL_TUMOURS, UPPER_GASTROINTESTINAL, OTHER,
NON_HODGKINS_B_CELL_LYMPHOMA_LOW_MOD_GRADE, CLASSICAL_HODGKINS, NODULAR_LYMPHOCYTE_PREDOMINANT_HODGKINS, T_CELL_LYMPHOMA}
/**
NOTE: This has been changed completely, the previous tumour type has been split into TumourPresentation and PrimaryOrMetastatic
*/
enum TumourType {BRAIN_TUMOUR, HAEMATOLOGICAL_MALIGNANCY_SOLID_SAMPLE, HAEMATOLOGICAL_MALIGNANCY_LIQUID_SAMPLE, SOLID_TUMOUR_METASTATIC, SOLID_TUMOUR_PRIMARY, SOLID_TUMOUR, UNKNOWN}
enum ProgrammePhase {CRUK, OXFORD, CLL, IIP, MAIN, EXPT}
enum Product {DNA, RNA}
enum TumourContent {High, Medium, Low}
enum HaematologicalCancerLineage {MYELOID, LYMPHOID, UNKNOWN}
enum TumourPresentation {FIRST_PRESENTATION, RECURRENCE, UNKNOWN}
enum PrimaryOrMetastatic {PRIMARY, METASTATIC, UNKNOWN, NOT_APPLICABLE}
/**
Sex
*/
enum Sex {MALE, FEMALE, UNKNOWN}
/**
The source of the sample
NOTE: IN GMS, BONE_MARROW_ASPIRATE_TUMOUR_CELLS and BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS are deprecated as they have been separated into their respective biotypes
*/
enum SampleSource {AMNIOTIC_FLUID, BLOOD, BONE_MARROW, BONE_MARROW_ASPIRATE_TUMOUR_CELLS, BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS, BUCCAL_SWAB, CHORIONIC_VILLUS_SAMPLE, FIBROBLAST, FLUID, FRESH_TISSUE_IN_CULTURE_MEDIUM, OTHER, SALIVA, TISSUE, TUMOUR, URINE}
/**
Karyotipic Sex
*/
enum PersonKaryotipicSex {UNKNOWN, XX, XY, XO, XXY, XXX, XXYY, XXXY, XXXX, XYY, OTHER}
/**
In 100K, preparation Method of sample
NOTE: In GMS, this field is deprecated in favour of StorageMedium and Method
*/
enum PreparationMethod {ASPIRATE, CD128_SORTED_CELLS, CD138_SORTED_CELLS, EDTA, FF, FFPE, LI_HEP, ORAGENE}
/**
In GMS, Method is defined as how the sample was taken directly from the patient
*/
enum Method {ASPIRATE, BIOPSY, NOT_APPLICABLE, RESECTION, SORTED_OTHER, UNKNOWN, UNSORTED, CD138_SORTED}
/**
In GMS, storage medium of sample
*/
enum StorageMedium {EDTA, FF, LI_HEP, ORAGENE, FFPE}
/**
Penetrance assumed in the analysis
*/
enum Penetrance {complete, incomplete}
/**
This defines a yes/no/unknown case
*/
enum TernaryOption {yes, no, unknown}
/**
This is the list of ethnicities in ONS16
* `D`: Mixed: White and Black Caribbean
* `E`: Mixed: White and Black African
* `F`: Mixed: White and Asian
* `G`: Mixed: Any other mixed background
* `A`: White: British
* `B`: White: Irish
* `C`: White: Any other White background
* `L`: Asian or Asian British: Any other Asian background
* `M`: Black or Black British: Caribbean
* `N`: Black or Black British: African
* `H`: Asian or Asian British: Indian
* `J`: Asian or Asian British: Pakistani
* `K`: Asian or Asian British: Bangladeshi
* `P`: Black or Black British: Any other Black background
* `S`: Other Ethnic Groups: Any other ethnic group
* `R`: Other Ethnic Groups: Chinese
* `Z`: Not stated
*/
enum EthnicCategory {D, E, F, G, A, B, C, L, M, N, H, J, K, P, S, R, Z}
/**
* A British, Mixed British
* B Irish
* C Any other White background
* C2 Northern Irish
* C3 Other white, white unspecified
* CA English
* CB Scottish
* CC Welsh
* CD Cornish
* CE Cypriot (part not stated)
* CF Greek
* CG Greek Cypriot
* CH Turkish
* CJ Turkish Cypriot
* CK Italian
* CL Irish Traveller
* CM Traveller
* CN Gypsy/Romany
* CP Polish
* CQ All republics which made up the former USSR
* CR Kosovan
* CS Albanian
* CT Bosnian
* CU Croatian
* CV Serbian
* CW Other republics which made up the former Yugoslavia
* CX Mixed white
* CY Other white European, European unspecified, European mixed
* D White and Black Caribbean
* E White and Black African
* F White and Asian
* G Any other mixed background
* GA Black and Asian
* GB Black and Chinese
* GC Black and White
* GD Chinese and White
* GE Asian and Chinese
* GF Other Mixed, Mixed Unspecified
* H Indian or British Indian
* J Pakistani or British Pakistani
* K Bangladeshi or British Bangladeshi
* L Any other Asian background
* LA Mixed Asian
* LB Punjabi
* LC Kashmiri
* LD East African Asian
* LE Sri Lanka
* LF Tamil
* LG Sinhalese
* LH British Asian
* LJ Caribbean Asian
* LK Other Asian, Asian unspecified
* M Caribbean
* N African
* P Any other Black background
* PA Somali
* PB Mixed Black
* PC Nigerian
* PD Black British
* PE Other Black, Black unspecified
* R Chinese
* S Any other ethnic group
* S1 Ashkenazi
* S2 Sephardi
* SA Vietnamese
* SB Japanese
* SC Filipino
* SD Malaysian
* SE Any Other Group
* Z Not stated
*/
enum ClinicalEthnicity {A,B,C,C2,C3,CA,CB,CC,CD,CE,CF,CG,CH,CJ,CK,CL,CM,CN,CP,CQ,CR,CS,CT,CU,CV,CW,CX,CY,D,E,F,G,GA,GB,GC,GD,GE,GF,H,J,K,L,LA,LB,LC,LD,LE,LF,LG,LH,LJ,LK,M,N,P,PA,PB,PC,PD,PE,R,S,S1,S2,SA,SB,SC,SD,SE,Z}
/**
1K Genomes project populations
*/
enum KgPopCategory {ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD, IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, YRI}
/**
1K Genomes project super populations
*/
enum KgSuperPopCategory {AFR, AMR, EAS, EUR, SAS}
/**
Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations
*/
record ChiSquare1KGenomesPhase3Pop {
/**
1K Super Population
*/
KgSuperPopCategory kgSuperPopCategory;
/**
1K Population
*/
union {null, KgPopCategory} kgPopCategory;
/**
Chi-square test for goodness of fit of this sample to this 1000 Genomes Phase 3 population
*/
double chiSquare;
}
/**
This defines a date record
*/
record Date{
/**
Format YYYY
*/
int year;
/**
Format MM. e.g June is 06
*/
union {null, int} month;
/**
Format DD e.g. 12th of October is 12
*/
union {null, int} day;
}
/**
An analysis panel
*/
record AnalysisPanel {
/**
The specific disease that a panel tests
*/
string specificDisease;
/**
The name of the panel
*/
string panelName;
/**
Id of the panel
*/
union {null, string} panelId;
/**
The version of the panel
*/
union {null, string} panelVersion;
/**
Deprecated
*/
union {null, string} reviewOutcome;
/**
Deprecated
*/
union {null, string} multipleGeneticOrigins;
}
/**
Ancestries, defined as Ethnic category(ies) and Chi-square test
*/
record Ancestries {
/**
Mother's Ethnic Origin
*/
union{null, EthnicCategory} mothersEthnicOrigin;
/**
Mother's Ethnic Origin Description
*/
union{null, string} mothersOtherRelevantAncestry;
/**
Father's Ethnic Origin
*/
union{null, EthnicCategory} fathersEthnicOrigin;
/**
Father's Ethnic Origin Description
*/
union{null, string} fathersOtherRelevantAncestry;
/**
Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations
*/
union{null, array} chiSquare1KGenomesPhase3Pop;
}
/**
clinicalEthnicities supersedes Ancestries in GMS
*/
enum GenericConsent {yes, no, undefined, not_applicable}
/**
Consent Status for GMS
*/
record GmsConsentStatus {
/**
Is this individual consented to the programme? It could simply be a family member that is not consented
but for whom affection status is known
*/
GenericConsent programmeConsent;
/**
Consent for feedback of primary findings?
RD: Primary Findings
Cancer: PrimaryFindings is somatic + pertinent germline findings
*/
GenericConsent primaryFindingConsent;
/**
Research Consent
*/
GenericConsent researchConsent;
/**
Consent for secondary health related findings?
*/
GenericConsent healthRelatedFindingConsent;
/**
Consent for carrier status check?
*/
GenericConsent carrierStatusConsent;
/**
Consent for pharmacogenomics consent as secondary findings?
*/
GenericConsent pharmacogenomicsFindingConsent;
}
/**
Consent Status for 100k program
*/
record ConsentStatus {
/**
Is this individual consented to the programme?
It could simply be a family member that is not consented but for whom affection status is known
*/
boolean programmeConsent=false;
/**
Consent for feedback of primary findings?
*/
boolean primaryFindingConsent=false;
/**
Consent for secondary finding lookup
*/
boolean secondaryFindingConsent=false;
/**
Consent for carrier status check?
*/
boolean carrierStatusConsent=false;
}
/**
Inbreeding coefficient
*/
record InbreedingCoefficient {
/**
This is the sample id against which the coefficient was estimated
*/
string sampleId;
/**
Name of program used to calculate the coefficient
*/
string program;
/**
Version of the programme
*/
string version;
/**
Where various methods for estimation exist, which method was used.
*/
string estimationMethod;
/**
Inbreeding coefficient ideally a real number in [0,1]
*/
double coefficient;
/**
Standard error of the Inbreeding coefficient
*/
union {null, double} standardError;
}
/**
Familiar relationship from pedrigree
*/
enum FamiliarRelationship {TwinsMonozygous, TwinsDizygous, TwinsUnknown, FullSibling, FullSiblingF,
FullSiblingM, Mother, Father, Son, Daughter, ChildOfUnknownSex, MaternalAunt, MaternalUncle,
MaternalUncleOrAunt, PaternalAunt, PaternalUncle, PaternalUncleOrAunt, MaternalGrandmother,
PaternalGrandmother, MaternalGrandfather, PaternalGrandfather, DoubleFirstCousin, MaternalCousinSister,
PaternalCousinSister, MaternalCousinBrother, PaternalCousinBrother, Cousin, Spouse, Other,
RelationIsNotClear, Unrelated, Unknown}
/**
In GMS, Previous Treatment of Patient
*/
record PreviousTreatment{
union {null, string} previousTreatmentType;
union {null, string} previousTreatmentName;
union {null, Date} previousTreatmentDate;
}
record ClinicalIndication{
/**
GUID of Clinical Indication for the Referral
*/
string clinicalIndicationUid;
/**
Code of Clinical Indication, e.g. (RT-13)
*/
string clinicalIndicationCode;
/**
Clinical Indication Full Name
*/
string clinicalIndicationFullName;
/**
Clinical Indication version number
*/
union {null, string} clinicalIndicationVersionNumber;
}
record Morphology{
/**
The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)
*/
union {null, string} id;
/**
The ontology term name
*/
union {null, string} name;
/**
Optional value for the ontology term, the type of the value is not checked
(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*/
union {null, string} value;
/**
Ontology version
*/
union {null, string} version;
}
record Topography{
/**
The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)
*/
union {null, string} id;
/**
The ontology term name
*/
union {null, string} name;
/**
Optional value for the ontology term, the type of the value is not checked
(i.e.: we could set the pvalue term to "significant" or to "0.0001")
*/
union {null, string} value;
/**
Ontology version
*/
union {null, string} version;
}
/**
A germline sample
*/
record GermlineSample {
/**
Sample identifier (e.g, LP00012645_5GH))
*/
string sampleId;
/**
Lab sample identifier
*/
string labSampleId;
/**
LDP Code (Local Delivery Partner)
*/
union {null, string} LDPCode;
/**
Source of the sample
*/
union {null, SampleSource} source;
/**
Product of the sample
*/
union {null, Product} product;
/**
Preparation method
NOTE: In GMS, this has been deprecated in favour of Method and storageMedium
*/
union {null, PreparationMethod} preparationMethod;
/**
Genomics England programme phase
*/
union {null, ProgrammePhase} programmePhase;
/**
The time when the sample was received. In the format YYYY-MM-DDTHH:MM:SS+0000
*/
union {null,string} clinicalSampleDateTime;
union {null,string} participantId;
/**
Participant UId of the sample
*/
union {null, string} participantUid;
union {null,string} sampleUid;
union {null,string} maskedPid;
/**
In GMS, this is how the sample was extracted from the participant
*/
union {null, Method} method;
/**
In GMS, this is what solvent/medium the sample was stored in
*/
union {null, StorageMedium} storageMedium;
/**
In GMS, this is the sampleType as entered by the clinician in TOMs
*/
union {null, string} sampleType;
/**
In GMS, this is the sampleState as entered by the clinician in TOMs
*/
union {null, string} sampleState;
}
/**
A tumour sample
*/
record TumourSample {
/**
Sample identifier (e.g, LP00012645_5GH))
*/
string sampleId;
/**
Lab sample identifier
*/
string labSampleId;
/**
LDP Code (Local Delivery Partner)
*/
union {null, string} LDPCode;
/**
This is the ID of the tumour from which this tumour sample was taken from
*/
union {null, string} tumourId;
/**
Genomics England programme phase
*/
union {null, string} programmePhase;
/**
Disease type.
NOTE: Deprecated in GMS
*/
union {null, diseaseType} diseaseType;
/**
Disease subtype.
NOTE: Deprecated in GMS
*/
union {null, string} diseaseSubType;
/**
True or false if this sample is of type: Haematological Cancer
*/
union {null, boolean} haematologicalCancer;
/**
This is the Haematological cancer lineage of the tumourSample if this sample is from a haematological cancer
*/
union {null, HaematologicalCancerLineage} haematologicalCancerLineage;
/**
The time when the sample was received. In the format YYYY-MM-DDTHH:MM:SS+0000
*/
union {null, string} clinicalSampleDateTime;
/**
Tumor type.
NOTE: Deprecated in GMS in tumourSample but available in tumour record
*/
union {null, string} tumourType;
/**
This is the tumour content
*/
union {null, TumourContent} tumourContent;
/**
This is the tumour content percentage
*/
union {null, float} tumourContentPercentage;
/**
Source of the sample
*/
union {null, SampleSource} source;
/**
The preparation method of the sample
NOTE: Deprecated in GMS in replace of Method and storageMedium record
*/
union {null, PreparationMethod} preparationMethod;
/**
The tissue source of the sample.
NOTE: DEPRECATED IN GMS in replace of method record
*/
union {null, string} tissueSource;
/**
Product of the sample
*/
union {null, Product} product;
/**
Morphology according to the sample taken
*/
union {null, array} sampleMorphologies;
/**
Topography according to the sample taken
*/
union {null, array} sampleTopographies;
/**
In GMS, this is the GUID of the sample
*/
union {null, string} sampleUid;
/**
Participant Id of the sample
*/
union {null, string} participantId;
/**
Participant UId of the sample
*/
union {null, string} participantUid;
/**
In GMS, this is the maskedPID
*/
union {null, string} maskedPid;
/**
In GMS, this is how the sample was extracted from the participant
*/
union {null, Method} method;
/**
In GMS, this is what solvent/medium the sample was stored in
*/
union {null, StorageMedium} storageMedium;
/**
In GMS, this is the sampleType as entered by the clinician in TOMs
*/
union {null, string} sampleType;
/**
In GMS, this is the sampleState as entered by the clinician in TOMs
*/
union {null, string} sampleState;
}
}
