Data Dictionary

The ICGC ARGO Data Dictionary expresses the details of the data model, which adheres to specific formats and restrictions to ensure a standard of data quality. The following describes the attributes and permissible values for all of the fields within the clinical tsv files for the ARGO Data Platform.

0 New field0 Updated field0 Deleted field

15 files with 233 fields

Data Tier:

All

Attribute:

All

Sample Registration (sample_registration)

9 Fields

The collection of data elements required to register the required Donor-Specimen-Sample data to the ARGO Data Platform. Registration of samples is required before molecular and clinical data submission can proceed.

File Name Example: sample_registration[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

This is the unique id that is assigned to your program. If you have logged into the platform, this is the Program Id that you see in the Program Services area. For example, TEST-CA is a Program ID.

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

Examples:

90234, BLD_donor_89, AML-90,

gender

Description of the donor self-reported gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles.

Core

Required

TEXT

Female

Male

Other

submitter_specimen_id

Unique identifier of the specimen, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

Examples:

LAML_PO, 00445, THY_099-tumour,

specimen_tissue_source

Tissue source of the biospecimen.

Core

Required

TEXT

Blood derived - bone marrow

Blood derived - peripheral blood

Blood derived

Bone marrow

Bone

21 more

tumour_normal_designation

Description of specimens tumour/normal status for data processing.

Core

Required

TEXT

Normal

Tumour

specimen_type

Description of the kind of specimen that was collected with respect to tumour/normal tissue origin.

Core

Required

TEXT

Cell line - derived from metastatic tumour

Cell line - derived from normal

Cell line - derived from tumour

Cell line - derived from xenograft tumour

Metastatic tumour - additional metastatic

13 more

submitter_sample_id

Unique identifier of the sample, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

Examples:

hnc_12, CCG_34_94583, BRCA47832-3239,

sample_type

Description of the type of molecular sample used for testing.

Core

Required

TEXT

Amplified DNA

ctDNA

Other DNA enrichments

Other RNA fractions

polyA+ RNA

3 more

Donor (donor)

19 Fields

The collection of data elements related to a specific donor in an ARGO program.

File Name Example: donor[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

vital_status

Donor's last known state of living or deceased.

Core

Required

TEXT

Alive

Deceased

cause_of_death

Indicate the cause of a donor's death.

Core

Conditional

TEXT

Died of cancer

Died of other reasons

Unknown

Cause of death is only required to be submitted if the donor's vital_status is Deceased.

survival_time

Interval of how long the donor has survived since primary diagnosis, in days.

Core

Conditional

INTEGER

Survival_time is only required to be submitted if the donor's vital_status is Deceased.

primary_site

The text term used to describe the primary site of disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). This categorization groups cases into general categories.

Core

Required

TEXT

Accessory sinuses

Adrenal gland

Anus and anal canal

Base of tongue

Bladder

65 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

height

Indicate the donor's height, in centimeters (cm).

Extended

NUMBER

weight

Indicate the donor's weight, in kilograms (kg).

Extended

NUMBER

bmi

Indicate the donor's Body Mass Index (BMI) in kg/m².

Extended

NUMBER

genetic_disorders

Indicate presence of any hereditary genetic disorders. Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. (References: NCIt C3101. Genetic disorder names were standardized using Orphanet (https://www.orpha.net/) and NCI Thesaurus)

Extended

TEXT

Alpha-1-antitrypsin Deficiency

Ataxia Telangiectasia Syndrome

BAP1-related Tumor Predisposition Syndrome

Beckwith-Wiedemann Syndrome

Birt-Hogg-Dub Syndrome

40 more

If the genetic disorder term you use is not included in the controlled terminology, please contact us at https://platform.icgc-argo.org/contact to request it be added. To include multiple values, separate values with a pipe delimiter '|' within your file.

menopause_status

Indicate the donor's menopause status at the time of primary diagnosis. (Reference: caDSR CDE ID 2434914)

Extended

TEXT

Not applicable

Perimenopausal

Postmenopausal

Premenopausal

Unknown

age_at_menarche

Indicate the donor's age, in years, at which the first menstruation event occurred. (Reference: NCIt C19666)

Extended

INTEGER

number_of_pregnancies

Indicate the total number of pregnancy events experienced by the donor. (Reference: NCIt C106551)

Extended

INTEGER

number_of_children

Indicate the number of children the donor has birthed. (Reference: caDSR CDE ID 2486644)

Extended

INTEGER

hrt_type

Indicate the type of hormone replacement therapy (HRT) the donor has taken or is currently taking.

Extended

TEXT

Combination HRT

Estrogen-only HRT

Injectable

Never taken HRT

Not applicable

4 more

hrt_duration

If donor has taken hormone replacement therapy (HRT), indicate how long donor has been taking HRT, in months. (Reference: caDSR CDE ID 5365433)

Extended

Conditional

INTEGER

contraception_type

Indicate the type of hormonal contraception the donor has taken or is currently taking. (Reference: caDSR CDE ID 3264234)

Extended

TEXT

Combination pill

Contraceptive implant

Contraceptive patch

Injectable

Intrauterine device

7 more

contraception_duration

If donor has taken hormonal contraception, indicate duration of use, in months. (Reference: caDSR CDE ID 5206887)

Extended

Conditional

INTEGER

lost_to_followup_after_clinical_event_id

If the donor became lost to follow up, indicate the identifier of the clinical event (eg. submitter_primary_diagnosis_id, submitter_treatment_id or submitter_follow_up_id) after which the donor became lost to follow up.

Extended

TEXT

Specimen (specimen)

24 Fields

The collection of data elements related to a donor's specimen. A specimen is any material sample taken for testing, diagnostic or research purposes.

File Name Example: specimen[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_specimen_id

Unique identifier of the specimen, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_primary_diagnosis_id

Indicate the primary diagnosis event in the clinical timeline that this specimen acquisition was related to.

Required

TEXT

Values must meet the regular expression

pathological_tumour_staging_system

Specify the tumour staging system used to assess the cancer at the time the tumour specimen was resected. Pathological classification is based on the clinical stage information (acquired before treatment) and supplemented/modified by operative findings and pathological evaluation of the resected specimen.

Core

Conditional

TEXT

AJCC 8th edition

AJCC 7th edition

AJCC 6th edition

Ann Arbor staging system

Binet staging system

6 more

This field is only required if the specimen is a tumour.

pathological_t_category

The code to represent the stage of cancer defined by the size or contiguous extension of the primary tumour (T), according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Core

Conditional

TEXT

T1a

T1a1

T1a2

47 more

This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.

pathological_n_category

The code to represent the stage of cancer defined by whether or not the cancer has reached nearby lymph nodes (N), according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Core

Conditional

TEXT

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more

This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.

pathological_m_category

The code to represent the stage of cancer defined by whether there are distant metastases (M), meaning spread of cancer to other parts of the body, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Core

Conditional

TEXT

M0(i+)

M1a

M1a(0)

13 more

This field is required only if the selected pathological_tumour_staging_system is any edition of the AJCC cancer staging system.

pathological_stage_group

Specify the tumour stage, based on pathological_tumour_staging_system, used to assess the cancer at the time the tumour specimen was resected.

Core

Conditional

TEXT

Occult Carcinoma

Stage 0

Stage 0a

Stage 0is

Stage 1

78 more

This field depends on the selected pathological_tumour_staging_system, and is only required if the specimen is a tumour. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications

specimen_acquisition_interval

Interval between primary diagnosis and specimen acquisition, in days.

Core

Required

INTEGER

The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.

tumour_histological_type

The code to represent the histology (morphology) of neoplasms that is usually obtained from a pathology report, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.

Core

Conditional

TEXT

Values must meet the regular expression

Examples:

8260/3, 9691/36,

This field is only required if the specimen is a tumour.

specimen_anatomic_location

Indicate the ICD-O-3 topography code for the anatomic location of a specimen when it was collected. Refer to the guidelines provided in the ICD-O-3 manual at https://apps.who.int/iris/handle/10665/42344.

Core

Required

TEXT

Values must meet the regular expression

Examples:

C50.1, C18,

specimen_laterality

For cancer in a paired organ, indicate the side on which the specimen was obtained. (Reference caDSR CDE ID 2007875)

Extended

TEXT

Left

Not applicable

Right

Unknown

specimen_processing

Indicate the technique used to process specimen.

Extended

TEXT

Cryopreservation in liquid nitrogen (dead tissue)

Cryopreservation in dry ice (dead tissue)

Cryopreservation of live cells in liquid nitrogen

Cryopreservation - other

Formalin fixed & paraffin embedded

5 more

specimen_storage

Indicate the method of specimen storage for specimen that were not extracted freshly or immediately cultured.

Extended

TEXT

Cut slide

Frozen in -70 freezer

Frozen in liquid nitrogen

Frozen in vapour phase

Not Applicable

4 more

For specimens that were freshly extracted or immediately cultured, select Not Applicable.

reference_pathology_confirmed

Indicate whether the pathological diagnosis was confirmed by a (central) reference pathologist. (Reference caDSR CDE ID 2007007)

Core

Conditional

TEXT

Yes

Unknown

This field is only required if the specimen is a tumour.

tumour_grading_system

Specify the tumour staging system used to assess the description of a tumour based on how abnormal the tumour cells and the tumour tissue look under a microscope. Tumour grade is an indicator of how quickly a tumour is likely to grow.

Core

Conditional

TEXT

FNCLCC grading system

Four-tier grading system

Gleason grade group system

Grading system for GISTs

Grading system for GNETs

6 more

This field is only required if the specimen is a tumour.

tumour_grade

Grade of the tumour as assigned by the reporting tumour_grading_system.

Core

Conditional

TEXT

Low grade

High grade

13 more

This field depends on the selected tumour_grading_system, and is only required if the specimen is a tumour. Please refer to the documentation for Tumour Grading Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-grading-classifications

percent_tumour_cells

Indicate a value, in decimals, that represents the percent of tumour cells compared to the number of total cells in a specimen. (Reference: NCIt: C159484)

Core

Conditional

NUMBER

This field is only required if the specimen is a tumour.

percent_tumour_cells_measurement_method

Indicate method used to measure percent_tumour_cells.

Core

Conditional

TEXT

Genomics

Image analysis

Pathology estimate by percent nuclei

This field is only required if the specimen is a tumour.

percent_proliferating_cells

Indicate a value, in decimals, that represents the count of proliferating cells determined during pathologic review of the specimen.

Extended

Conditional

NUMBER

This field should only be submitted if the specimen is tumour.

percent_inflammatory_tissue

Indicate a value, in decimals, that represents the percent of a specimen that is positive for inflammatory markers, including the presence of capillary dilatation, edema and increased leukocytes. (Reference NCIt C159479)

Extended

Conditional

NUMBER

This field should only be submitted if the specimen is tumour.

percent_stromal_cells

Indicate a value, in decimals, that represents the percentage of reactive cells that are present in a tumour specimen but are not malignant such as fibroblasts, vascular structures, etc. (Reference caDSR CDE ID 2841241)

Extended

Conditional

NUMBER

This field should only be submitted if the specimen is tumour.

percent_necrosis

Indicate a value, in decimals, that represents the percent of cells undergoing necrosis compared to the number of total cells present in a tumour specimen. (Reference NCIt C159481)

Extended

Conditional

NUMBER

This field should only be submitted if the specimen is tumour.

Primary Diagnosis (primary_diagnosis)

19 Fields

The collection of data elements related to a donor's primary diagnosis. The primary diagnosis is the first diagnosed case of cancer in a donor. To submit multiple primary diagnoses for a single donor, submit multiple rows in the primary diagnosis file for this donor.

File Name Example: primary_diagnosis[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_primary_diagnosis_id

Unique identifier of the primary diagnosis event, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

age_at_diagnosis

Age that the donor was first diagnosed with cancer, in years. This should be based on the earliest diagnosis of cancer.

Core

Required

INTEGER

cancer_type_code

The code to represent the cancer type using the WHO ICD-10 code (https://icd.who.int/browse10/2019/en) classification.

Core

Required

TEXT

Values must meet the regular expression

Examples:

C41.1, C16.9, C00.5, D46.9,

cancer_type_additional_information

Additional details related to the cancer type that are not covered by the ICD-10 code provided in the cancer_type field.

Extended

TEXT

basis_of_diagnosis

Indicate the most valid basis of how the primary diagnosis was identified. If more than one diagnosis technique was used, select the term that has the highest code number (see notes). (Reference: IACR Standard for Basis of Diagnosis http://www.iacr.com.fr/images/doc/basis.pdf)

Extended

TEXT

Clinical investigation

Clinical

Cytology

Death certificate only

Histology of a metastasis

3 more

0: Death certificate only: Information provided is from a death certificate. 1: Clinical: Diagnosis made before death. 2: Clinical investigation: All diagnostic techniques, including X-ray, endoscopy, imaging, ultrasound, exploratory surgery (such as laparotomy), and autopsy, without a tissue diagnosis. 4: Specific tumour markers: Including biochemical and/or immunologic markers that are specific for a tumour site. 5: Cytology: Examination of cells from a primary or secondary site, including fluids aspirated by endoscopy or needle; also includes the microscopic examination of peripheral blood and bone marrow aspirates. 6: Histology of a metastasis: Histologic examination of tissue from a metastasis, including autopsy specimens. 7: Histology of a primary tumour: Histologic examination of tissue from primary tumour, however obtained, including all cutting techniques and bone marrow biopsies; also includes autopsy specimens of primary tumour. 9: Unknown: No information on how the diagnosis has been made.

laterality

For cancer in a paired organ, indicate the side of the body on which the primary tumour or cancer first developed at the time of primary diagnosis. (Reference caDSR CDE ID 827)

Extended

TEXT

Bilateral

Left

Midline

Not a paired site

Right

2 more

lymph_nodes_examined_status

Indicate if lymph nodes were examined for metastases.

Core

Required

TEXT

Cannot be determined

No lymph nodes found in resected specimen

Not applicable

Yes

lymph_nodes_examined_method

Indicate the method used to examine lymph nodes.

Core

Conditional

TEXT

Imaging

Lymph node dissection/pathological exam

Physical palpation of patient

number_lymph_nodes_examined

The total number of lymph nodes tested for the presence of cancer. (Reference: caDSR CDE ID 3)

Extended

Conditional

INTEGER

This field should only be submitted if 'lymph_nodes_examined_status' is 'Yes'.

number_lymph_nodes_positive

The number of regional lymph nodes reported as being positive for tumour metastases. (Reference: caDSR CDE ID 6113694)

Core

Conditional

INTEGER

This field is only required if 'lymph_nodes_examined_status' is 'Yes'.

clinical_tumour_staging_system

Indicate the tumour staging system used to stage the cancer at the time of primary diagnosis (prior to treatment).

Core

TEXT

AJCC 8th edition

AJCC 7th edition

AJCC 6th edition

Ann Arbor staging system

Binet staging system

6 more

clinical_t_category

The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Core

Conditional

TEXT

T1a

T1a1

T1a2

47 more

This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.

clinical_n_category

The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Core

Conditional

TEXT

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more

This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.

clinical_m_category

The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined at time of primary diagnosis and prior to treatment, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual. MX is NOT a valid category and cannot be assigned.

Core

Conditional

TEXT

M0(i+)

M1a

M1a(0)

13 more

This field is required only if the selected clinical_tumour_staging_system is any edition of the AJCC cancer staging system.

clinical_stage_group

Stage group of the tumour, as assigned by the reporting clinical_tumour_staging_system, that indicates the overall prognostic tumour stage.

Core

Conditional

TEXT

Occult Carcinoma

Stage 0

Stage 0a

Stage 0is

Stage 1

78 more

This field is dependent on the selected clinical_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications

presenting_symptoms

Indicate presenting symptoms at time of primary diagnosis.

Extended

TEXT

Abdominal Pain

Anemia

Back Pain

Bloating

Cholangitis

21 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

performance_status

Indicate the donor's performance status grade at the time of primary diagnosis. (Reference: ECOG performance score grades from https://ecog-acrin.org/resources/ecog-performance-status).

Extended

TEXT

Grade 0

Grade 1

Grade 2

Grade 3

Grade 4

1 more

Grade 0: Fully active, able to carry on all pre-disease performance without restriction. Grade 1: Restricted in physically strenuous activity but ambulatory and able to carry out work of a light or sedentary nature (ie. Light house work, office work). Grade 2: Ambulatory and capable of all selfcare but unable to carry out any work activities; up and about more than 50% of waking hours. Grade 3: Capable of only limited selfcare; confined to bed or chair more than 50% of waking hours. Grade 4: Completely disabled; cannot carry on any selfcare; totally confined to bed or chair

Treatment (treatment)

22 Fields

The collection of data elements related to a donor's treatment at a specific point in the clinical record. To submit multiple treatments for a single donor, please submit treatment rows in the treatment file for this donor.

File Name Example: treatment[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_treatment_id

Unique identifier of the treatment, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_primary_diagnosis_id

Indicate the primary diagnosis event in the clinical timeline that this treatment was related to.

Required

TEXT

Values must meet the regular expression

treatment_type

Indicate the type of treatment regimen that the donor completed.

Core

Required

TEXT

Ablation

Bone marrow transplant

Chemotherapy

Endoscopic therapy

End of life care

8 more

Depending on the treatment_type(s) selected, additional treatment details may be required to be submitted. For example, if treatment_type includes 'Chemotherapy', the supplemental Chemotherapy treatment type file is required. To include multiple values, separate values with a pipe delimiter '|' within your file.

is_primary_treatment

Indicate if the treatment was the primary treatment following the initial diagnosis.

Core

Conditional

TEXT

Yes

line_of_treatment

Indicate the line of treatment if it is not the primary treatment.

Extended

Conditional

INTEGER

treatment_start_interval

The interval between the primary diagnosis and initiation of treatment, in days.

Core

Conditional

INTEGER

The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.

treatment_duration

The duration of treatment regimen, in days.

Core

Conditional

INTEGER

days_per_cycle

Indicate the number of days in a treatment cycle.

Extended

Conditional

INTEGER

number_of_cycles

Indicate the number of treatment cycles.

Extended

Conditional

INTEGER

treatment_intent

Indicate the purpose of the treatment, or the desired effect or outcome resulting from the treatment. (Reference: mCODE/FHIR)

Core

Conditional

TEXT

Curative

Diagnostic

Forensic

Guidance

Palliative

3 more

treatment_setting

Indicate the treatment setting, which describes the treatment's purpose in relation to the primary treatment. (Reference: NCIt C124308)

Core

Conditional

TEXT

Adjuvant

Advanced/Metastatic

Conditioning

Induction

Maintenance

5 more

response_to_treatment_criteria_method

Indicate the criteria used to assess the donor's response to the applied treatment regimen.

Core

Conditional

TEXT

ELN Dohner AML 2017 Oncology Response Criteria

IWG Cheson AML 2003 Oncology Response Criteria

iRECIST

RECIST

Response Assessment in Neuro-Oncology (RANO)

1 more

response_to_treatment

The donor's response to the applied treatment regimen.

Core

Conditional

TEXT

Complete remission

Complete remission with incomplete hematologic recovery (CRi)

Complete remission without minimal residual disease (CRMRD-)

Complete response

Cytogenetic complete remission (CRc)

21 more

This field depends on the selected response_to_treatment_criteria_method. Please refer to the documentation for Response to Treatment Criteria: http://docs.icgc-argo.org/docs/submission/dictionary-overview#response-to-treatment-criteria

outcome_of_treatment

Indicate the donor's outcome of the prescribed treatment.

Extended

Conditional

TEXT

Treatment completed as prescribed

Treatment incomplete due to technical or organizational problems

Treatment incomplete because patient died

Patient choice (stopped or interrupted treatment)

Physician decision (stopped or interrupted treatment)

5 more

toxicity_type

If the treatment was terminated early due to acute toxicity, indicate whether it was due to hematological toxicity or non-hematological toxicity.

Extended

Conditional

TEXT

Hematological

Non-hematological

Not applicable

Unknown

hematological_toxicity

Indicate the hematological toxicities which caused early termination of the treatment. (Codelist reference: NCI-CTCAE (v5.0))

Extended

Conditional

TEXT

Anemia - Grade 3

Anemia - Grade 4

Anemia - Grade 5

Neutropenia - Grade 3

Neutropenia - Grade 4

5 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

non-hematological_toxicity

Indicate the non-hematological toxicities which caused early termination of the treatment. (Codelist reference: NCI-CTCAE (v5.0))

Extended

Conditional

TEXT

Cardiac disorders - Grade 1

Cardiac disorders - Grade 2

Cardiac disorders - Grade 3

Cardiac disorders - Grade 4

Cardiac disorders - Grade 5

25 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

adverse_events

Report any treatment related adverse events. (Codelist reference: NCI-CTCAE (v5.0))

Extended

Conditional

TEXT

Abdominal distension

Abdominal infection

Abdominal pain

Abdominal soft tissue necrosis

Abducens nerve disorder

834 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

clinical_trials_database

If the donor is a participant in a clinical trial, indicate the clinical trial database where the clinical trial is registered.

Extended

TEXT

NCI Clinical Trials

EU Clinical Trials Register

Not applicable

Unknown

If the clinical trials database you use is not included in the controlled terminology, please contact us at https://platform.icgc-argo.org/contact to request it be added.

clinical_trial_number

Based on the clinical_trial_database, indicate the unique NCT or EudraCT clinical trial identifier of which the donor is a participant.

Extended

Conditional

TEXT

Chemotherapy (chemotherapy)

11 Fields

The collection of data elements describing the details of a chemotherapy treatment regimen completed by a donor. To submit multiple treatment drugs for a single regimen, submit multiple rows in the chemotherapy file.

File Name Example: chemotherapy[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_treatment_id

Unique identifier of the treatment, as assigned by the data provider.

Required

TEXT

Values must meet the regular expression

drug_rxnormcui

The unique RxNormID assigned to the treatment regimen drug.

Core

Required

TEXT

This field uses standardized vocabulary from the RxNorm database (https://www.nlm.nih.gov/research/umls/rxnorm), provided by the NIH. You can search for RX Norm values through the web interface (https://mor.nlm.nih.gov/RxNav/) or API (https://mor.nlm.nih.gov/download/rxnav/RxNormAPIs.html). For example, to find the rxnormcui based on drug name, you can use: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=leucovorin or https://mor.nlm.nih.gov/RxNav/search?searchBy=String&searchTerm=leucovorin

drug_name

Name of agent or drug administered to donor as part of the treatment regimen.

Core

Required

TEXT

chemotherapy_drug_dose_units

Indicate units used to record chemotherapy drug dose.

Core

Required

TEXT

mg/m2

IU/m2

ug/m2

g/m2

mg/kg

prescribed_cumulative_drug_dose

Indicate the total prescribed cumulative drug dose in the same units specified in chemotherapy_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

actual_cumulative_drug_dose

Indicate the total actual cumulative drug dose in the same units specified in chemotherapy_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

dose_intensity_reduction

Indicate if there was a significant reduction in dose intensity.

Extended

TEXT

Yes

Unknown

dose_intensity_reduction_event

If there was a signficiant reduction in dose intensity, indicate which event caused it.

Extended

TEXT

Dose reduction

Dose delay or dose omission

Both

This field should only be submitted if 'dose_intensity_reduction' is 'Yes'

dose_intensity_reduction_amount

If there was a significant reduction in dose intensity, indicate the amount.

Extended

TEXT

<20%

20-49%

>=50%

Unknown

This field should only be submitted if 'dose_intensity_reduction' is 'Yes'

Hormone Therapy (hormone_therapy)

8 Fields

The collection of data elements describing the details of a hormone treatment therapy completed by a donor. To submit multiple treatment drugs for a single regimen, submit multiple rows in the hormone_therapy file.

File Name Example: hormone_therapy[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_treatment_id

Unique identifier of the treatment, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

drug_rxnormcui

The unique RxNormID assigned to the treatment regimen drug.

Core

Required

TEXT

drug_name

Name of agent or drug administered to donor as part of the treatment regimen.

Core

Required

TEXT

hormone_drug_dose_units

Indicate the units used to record hormone drug dose.

Core

Required

TEXT

mg/m2

IU/m2

ug/m2

g/m2

mg/kg

prescribed_cumulative_drug_dose

Indicate the total prescribed cumulative drug dose in the same units specified in hormone_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

actual_cumulative_drug_dose

Indicate the total actual cumulative drug dose in the same units specified in hormone_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

Radiation (radiation)

8 Fields

The collection of data elements describing the details of a radiation treatment completed by a donor.

File Name Example: radiation[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_treatment_id

Unique identifier of the treatment, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

radiation_therapy_modality

Indicate the method of radiation treatment or modality.

Core

Required

TEXT

Electron

Heavy Ions

Photon

Proton

radiation_therapy_type

Indicate type of radiation therapy administered.

Core

Required

TEXT

External

Internal

Internal application includes Brachytherapy.

radiation_therapy_fractions

Indicate the total number of fractions delivered as part of treatment.

Core

Required

INTEGER

radiation_therapy_dosage

Indicate the total dose given in units of Gray (Gy).

Core

Required

NUMBER

anatomical_site_irradiated

Indicate body region where radiation therapy was administered. (Reference: Cancer Care Ontario)

Core

Required

TEXT

Abdomen

Body

Brain

Chest

Head

9 more

Immunotherapy (immunotherapy)

9 Fields

The collection of data elements describing the details of an immunotherapy treatment completed by a donor.

File Name Example: immunotherapy[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_treatment_id

Unique identifier of the treatment, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

immunotherapy_type

Indicate the type of immunotherapy administered to donor.

Core

Required

TEXT

Cell-based

Immune checkpoint inhibitors

Monoclonal antibodies other than immune checkpoint inhibitors

Other immunomodulatory substances

drug_rxnormcui

The unique RxNormID assigned to the treatment regimen drug.

Core

Required

TEXT

drug_name

Name of agent or drug administered to donor as part of the treatment regimen.

Core

Required

TEXT

immunotherapy_drug_dose_units

Indicate units used to record immunotherapy drug dose.

Core

Required

TEXT

mg/m2

IU/m2

ug/m2

g/m2

mg/kg

prescribed_cumulative_drug_dose

Indicate the total prescribed cumulative drug dose in the same units specified in immunotherapy_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

actual_cumulative_drug_dose

Indicate the total actual cumulative drug dose in the same units specified in immunotherapy_drug_dose_units.

Core

Conditional

NUMBER

Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted.

Surgery (surgery)

18 Fields

The collection of data elements related to a donor's surgical treatment at a specific point in the clinical record. To submit multiple surgeries, submit multiple rows in the Surgery file. If a specimen was resected during surgery, indicate the unique identifier of the specimen in the 'submitter_specimen_id' field. If multiple specimens were resected during a single surgical procedure, submit each 'submitter_specimen_id' as a new row with the same 'submitter_treatment_id' and 'surgery_type' values.

File Name Example: surgery[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_specimen_id

If a specimen was resected during surgery, indicate the unique identifier of the specimen here. This submitter_specimen_id should exist in the Specimen file.

TEXT

Values must meet the regular expression

Please refer to documentation for instructions on how to submit a specimen that was resected during surgery: https://docs.icgc-argo.org/docs/submission/submitting-clinical-data#submitting-data-in-surgery-file

submitter_treatment_id

Unique identifier of the treatment, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

surgery_type

Indicate the type of surgical procedure that was performed. (References: SNOMED, NCIt, UMLS)

Core

Required

TEXT

Axillary Clearance

Axillary lymph nodes sampling

Biopsy

Bypass Gastrojejunostomy

Cholecystectomy

48 more

surgery_site

Indicate the ICD-O-3 topography code for the anatomic site where the surgical procedure was performed, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3).

Core

Conditional

TEXT

Values must meet the regular expression

Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344. This field is not required if a specimen was resected during surgery (ie. if `submitter_specimen_id` is submitted) since anatomic site is collected in the Specimen table.

surgery_location

Indicate whether the surgical procedure was done at the primary, local recurrence or metastatic location.

Core

Conditional

TEXT

Local recurrence

Metastatic

Primary

This field is not required if a specimen was resected during surgery (ie. if `submitter_specimen_id` is submitted) since type of specimen is collected in the Specimen table.

tumour_length

Indicate the length of the tumour, in millimetres (mm).

Extended

NUMBER

tumour_width

Indicate the width of the tumour, in millimetres (mm).

Extended

NUMBER

greatest_dimension_tumour

Indicate the greatest dimension or diameter of the tumour, in millimetres (mm). (Reference: NCIt C157135)

Extended

NUMBER

tumour_focality

Indicate the characterization of the location of the tumour. (Reference: NCIt: C157425)

Extended

TEXT

Cannot be assessed

Multifocal

Not applicable

Unifocal

Unknown

residual_tumour_classification

Indicate the absence or presence of residual tumour after treatment. In some cases treated with surgery and/or with neoadjuvant therapy there will be residual tumour at the primary site after treatment because of incomplete resection or local and regional disease that extends beyond the limit of ability of resection. (Reference: AJCC 8th ed.)

Extended

TEXT

Not applicable

1 more

RX (Presence of residual tumour cannot be assessed), R0 (no residual tumour), R1 (microscopic residual tumour), R2 (macroscopic residual tumour)

margin_types_involved

Indicate the margin type(s) involved.

Extended

TEXT

Circumferential resection margin

Common bile duct margin

Distal margin

Not applicable

Proximal margin

1 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

margin_types_not_involved

Indicate the margin type(s) not involved.

Extended

TEXT

Circumferential resection margin

Common bile duct margin

Distal margin

Not applicable

Proximal margin

1 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

margin_types_not_assessed

Indicate the margin type(s) that cannot be assessed.

Extended

TEXT

Circumferential resection margin

Common bile duct margin

Distal margin

Not applicable

Proximal margin

1 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

lymphovascular_invasion

Indicate the absence or presence of lymphovascular invasion (LVI). LVI includes lymphatic invasion, vascular invasion and lymphovascular invasion. (Reference: AJCC 8th ed.)

Extended

TEXT

Absent

Both lymphatic and small vessel and venous (large vessel) invasion

Lymphatic and small vessel invasion only

Not applicable

Present

2 more

perineural_invasion

A morphologic finding referring to a tumour that has spread along and infiltrated nerve fibers. Indicate the presence or absence of perineural invasion. (Reference: NCIt: C48260, ICCR)

Extended

TEXT

Absent

Cannot be assessed

Not applicable

Present

Unknown

extrathyroidal_extension

Indicate the involvement of perithyroidal soft tissues by direct extension from the thyroid primary. (Reference: AJCC 8th Ed.)

Extended

TEXT

Absent

Cannot be assessed

Not applicable

Present

Unknown

Follow Up (follow_up)

22 Fields

The collection of data elements related to a specific follow-up visit to a donor. A follow-up is defined as any point of contact with a patient after primary diagnosis. To submit multiple follow-ups for a single donor, please submit multiple rows in the follow-up file for this donor.

File Name Example: follow_up[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_follow_up_id

Unique identifier for a follow-up event in a donor's clinical record, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

interval_of_followup

Interval from the primary diagnosis date to the follow-up date, in days.

Core

Required

INTEGER

The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.

disease_status_at_followup

Indicate the donor's disease status at time of follow-up. (Reference: RECIST)

Core

Required

TEXT

Complete remission

Distant progression

Loco-regional progression

No evidence of disease

Partial remission

3 more

submitter_primary_diagnosis_id

Indicate if the follow-up is related to a specific primary diagnosis event in the clinical timeline.

TEXT

Values must meet the regular expression

submitter_treatment_id

Indicate if the follow-up is related to a specific treatment event in the clinical timeline.

TEXT

Values must meet the regular expression

weight_at_followup

Indicate the donor's weight, in kilograms (kg), at the time of follow-up.

Extended

NUMBER

relapse_type

Indicate the donor's relapse type.

Core

Conditional

TEXT

Distant recurrence/metastasis

Local recurrence

Local recurrence and distant metastasis

Progression (liquid tumours)

This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.

relapse_interval

If the donor was clinically disease free following primary treatment and then relapse or recurrence or progression (for liquid tumours) occurred afterwards, then this field will indicate the length of disease free interval, in days.

Core

Conditional

INTEGER

This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.

method_of_progression_status

Indicate the method(s) used to confirm the donor's progression or relapse or recurrence disease status. (Reference: caDSR CDE ID 6161031)

Core

Conditional

TEXT

Biomarker in liquid biopsy (e.g. tumour marker in blood or urine)

Biopsy

Blood draw

Bone marrow aspirate

Core biopsy

19 more

This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence. To include multiple values, separate values with a pipe delimiter '|' within your file.

anatomic_site_progression_or_recurrence

Indicate the ICD-O-3 topography code for the anatomic site(s) where disease progression, relapse or recurrence occurred, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.

Core

Conditional

TEXT

Values must meet the regular expression

Examples:

C50.1|C18,

recurrence_tumour_staging_system

Specify the tumour staging system used to stage the cancer at time of retreatment for recurrence or disease progression. This may be represented as rTNM in the medical report.

Extended

Conditional

TEXT

AJCC 8th edition

AJCC 7th edition

AJCC 6th edition

Ann Arbor staging system

Binet staging system

6 more

This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.

recurrence_t_category

The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

T1a

T1a1

T1a2

47 more

This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.

recurrence_n_category

The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more

This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.

recurrence_m_category

The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined at the time of retreatment for a recurrence or disease progression, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

M0(i+)

M1a

M1a(0)

13 more

This field is required only if the selected recurrence_tumour_staging_system is any edition of the AJCC cancer staging system.

recurrence_stage_group

The code to represent the stage group of the tumour, as assigned by the reporting recurrence_tumour_staging_system, that indicates the overall prognostic tumour stage (ie. Stage I, Stage II, Stage III etc.) at the time of retreatment for a recurrence or disease progression.

Extended

Conditional

TEXT

Occult Carcinoma

Stage 0

Stage 0a

Stage 0is

Stage 1

78 more

This field is dependent on the selected recurrence_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications

posttherapy_tumour_staging_system

Specify the tumour staging system used to stage the cancer after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery. This may be represented as ypTNM or ycTNM in the medical report.

Extended

TEXT

AJCC 8th edition

AJCC 7th edition

AJCC 6th edition

Ann Arbor staging system

Binet staging system

6 more

posttherapy_t_category

The code to represent the extent of the primary tumour (T) based on evidence obtained from clinical assessment parameters determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

T1a

T1a1

T1a2

47 more

This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.

posttherapy_n_category

The code to represent the stage of cancer defined by the extent of the regional lymph node (N) involvement for the cancer based on evidence obtained from clinical assessment parameters determined determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

N0a

N0a (biopsy)

N0b

N0b (no biopsy)

21 more

This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.

posttherapy_m_category

The code to represent the stage of cancer defined by the extent of the distant metastasis (M) for the cancer based on evidence obtained from clinical assessment parameters determined after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery, according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.

Extended

Conditional

TEXT

M0(i+)

M1a

M1a(0)

13 more

This field is required only if the selected posttherapy_tumour_staging_system is any edition of the AJCC cancer staging system.

posttherapy_stage_group

The code to represent the stage group of the tumour, as assigned by the reporting posttherapy_tumour_staging_system, that indicates the overall prognostic tumour stage (ie. Stage I, Stage II, Stage III etc.) after treatment for patients receiving systemic and/or radiation therapy alone or as a component of their initial treatment, or as neoadjuvant therapy before planned surgery.

Extended

Conditional

TEXT

Occult Carcinoma

Stage 0

Stage 0a

Stage 0is

Stage 1

78 more

This field is dependent on the selected posttherapy_tumour_staging_system. Please refer to the documentation for Tumour Staging Classifications: http://docs.icgc-argo.org/docs/submission/dictionary-overview#tumour-staging-classifications

Exposure (exposure)

15 Fields

The collection of data elements related to a donor's clinically relevant information not immediately resulting from genetic predispositions.

File Name Example: exposure[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

tobacco_smoking_status

Indicate donor's self-reported smoking status and history. (Reference: caDSR CDE ID 2181650)

Extended

TEXT

Current reformed smoker for <= 15 years

Current reformed smoker for > 15 years

Current reformed smoker, duration not specified

Current smoker

Lifelong non-smoker (<100 cigarettes smoked in lifetime)

2 more

Current smoker: Has smoked 100 cigarettes in their lifetime and who currently smokes. Includes daily smokers and non-daily smokers (also known as occassional smokers). Current reformed smoker for >15 years: A person who currently does not smoke and has been a non-smoker for more than 15 years, but has smoked at least 100 cigarettes in their life. Current reformed smoker for <= 15 years: A person who currently does not smoke and has been a non-smoker for less than 15 years, but has smoked at least 100 cigarettes in their life. Current reformed smoker, duration not specified: A person who currently does not smoke and has been a non-smoker for unspecified time, but has smoked at least 100 cigarettes in their lifetime. Smoking history not documented: Smoking history has not be recorded or is unknown.

tobacco_type

Indicate the type(s) of tobacco used by donor. (Reference: NCIt CDE C177629)

Extended

Conditional

TEXT

Chewing Tobacco

Cigar

Cigarettes

Electronic cigarettes

Not applicable

5 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

pack_years_smoked

This field applies to cigarettes. Indicate the smoking intensity in Pack Years, where the number of pack years is defined as the number of cigarettes smoked per day times (x) the number of years smoked divided (/) by 20. (Reference: caDSR CDE ID 2955385)

Extended

Conditional

NUMBER

alcohol_history

Indicate if the donor has consumed at least 12 drinks of any alcoholic beverage in their lifetime. (Reference: caDSR CDE ID 2201918)

Extended

TEXT

Yes

Not applicable

Unknown

alcohol_consumption_category

Describe the donor's current level of alcohol use as self-reported by the donor. (Reference: caDSR CDE ID 3457767)

Extended

TEXT

Daily Drinker

None

Not applicable

Occasional Drinker (< once a month)

Social Drinker (> once a month, < once a week)

2 more

alcohol_type

Indicate the type(s) of alcohol the donor consumes. (Reference: NCIt CDE C173647)

Extended

Conditional

TEXT

Beer

Liquor

Not applicable

Other

Unknown

1 more

To include multiple values, separate values with a pipe delimiter '|' within your file.

opiate_use

Indicate if the donor has ever used opium or other opiates like opium juice, heroin, or Sukhteh regularly (at least weekly over a 6-month period).

Extended

TEXT

Never

Not applicable

Unknown

Yes, currently

Yes, only in the past

hot_drinks_consumption

Indicate if the donor regularly drinks tea, coffee, or other hot drinks.

Extended

TEXT

Never

Not applicable

Unknown

Yes, currently

Yes, only in the past

red_meat_frequency

Indicate how frequently the donor eats red meat. Examples of red meat include beef, veal, pork, lamb, mutton, horse, or goat meat.

Extended

TEXT

Never

Less than once a month

1-3 times a month

Not applicable

Once or twice a week

3 more

processed_meat_frequency

Indicate how frequently the patient eats processed meat. Examples of processed meat include hams, salamis, or sausages.

Extended

TEXT

Never

Less than once a month

1-3 times a month

Not applicable

Once or twice a week

3 more

soft_drinks_frequency

Indicate the frequency of soft drink consumption by the donor.

Extended

TEXT

Never

Less than once a month

1-3 times a month

Not applicable

Once or twice a week

3 more

exercise_frequency

Indicate how many times per week the donor exercises for at least 30 minutes. (Reference: NCIt CDE C25367)

Extended

TEXT

Never

Less than once a month

1-3 times a month

Not applicable

Once or twice a week

3 more

exercise_intensity

Indicate the intensity of exercise. (Reference: NCIt CDE C25539)

Extended

Conditional

TEXT

Low: No increase in the heart beat, and no perspiration

Moderate: Increase in the heart beat slightly with some light perspiration

Not applicable

Vigorous: Increase in the heart beat substantially with heavy perspiration

Unknown

Family History (family_history)

11 Fields

The collection of data elements describing a donor's familial relationships and familial cancer history.

File Name Example: family_history[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

family_relative_id

Unique identifier of the relative, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

This field is required to ensure that family members are identified in unique records. Ids can be as simple as an incremented numeral to ensure uniqueness.

relative_with_cancer_history

Indicate if donor has any genetic relatives with a history of cancer. (Reference: NCIt C159104, caDSR CDE ID 6161023)

Extended

TEXT

Yes

Unknown

relationship_type

Indicate genetic relationship of the relative to the donor. (Reference: caDSR CDE ID 2179937)

Extended

TEXT

Aunt

Brother

Cousin

Daughter

Father

25 more

gender_of_relative

The self-reported gender of related individual.

Extended

TEXT

Female

Male

Other

Unknown

age_of_relative_at_diagnosis

The age (in years) when the donor's relative was first diagnosed. (Reference: caDSR CDE ID 5300571)

Extended

Conditional

INTEGER

cancer_type_code_of_relative

The code to describe the malignant diagnosis of the donor's relative with a history of cancer using the WHO ICD-10 code (https://icd.who.int/browse10/2019/en) classification.

Extended

Conditional

TEXT

Values must meet the regular expression

Examples:

C41.1, C16.9, C00.5, D46.9,

relative_vital_status

Relative's last known state of living or deceased.

Extended

TEXT

Alive

Deceased

Unknown

cause_of_death_of_relative

Indicate the cause of the death of the relative.

Extended

Conditional

TEXT

Died of cancer

Died of other reasons

Unknown

relative_survival_time

Indicate how long, in days, the relative survived from the time they were diagnosed with cancer.

Extended

Conditional

INTEGER

Biomarker (biomarker)

30 Fields

The collection of data elements describing a donor's biomarker tests. A biomarker is a biological molecule found in blood, other body fluids, or tissues that is indicative of the presence of cancer in the body. Each row should include one or more biomarker test(s) associated with a particular clinical event (submitter_specimen_id, submitter_primary_diagnosis_id, submitter_treatment_id or submitter_follow_up_id field). If the biomarker test is not associated with a particular clinical event, then indicate the time interval at which the biomarker test was performed (test_interval field).

File Name Example: biomarker[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

submitter_specimen_id

Unique identifier of the specimen, assigned by the data provider.

TEXT

Values must meet the regular expression

Only one of ['submitter_specimen_id', 'submitter_primary_diagnosis_id', 'submitter_treatment_id', 'submitter_follow_up_id'] is required. If the biomarker test is not associated with a specimen or primary diagnosis, treatment or follow up event, then the 'test_interval' field will be required.

submitter_primary_diagnosis_id

If the biomarker test was done at the time of primary diagnosis, then indicate the associated submitter_primary_diagnosis_id here.

TEXT

Values must meet the regular expression

submitter_treatment_id

If the biomarker test was done at the initiation of a specific treatment regimen, indicate the associated submitter_treatment_id here.

TEXT

Values must meet the regular expression

submitter_follow_up_id

If the biomarker test was done during a follow-up event, then indicate the associated submitter_follow_up_id here.

TEXT

Values must meet the regular expression

test_interval

If the biomarker test was not associated with a specific specimen or follow-up, primary diagnosis or treatment event, then indicate the interval of time since primary diagnosis that the biomarker test was performed at, in days.

INTEGER

This field is required if the biomarker test is not associated with a specimen or primary diagnosis, treatment or follow-up event. The associated primary diagnosis is used as the reference point for this interval. To calculate this, find the number of days since the date of primary diagnosis.

ca19-9_level

Indicate the level of carbohydrate antigen 19-9 (CA19-9). Carbohydrate antigen 19-9 testing is useful to monitor the response to treatment in pancreatic cancer patients. (Reference: LOINC: 24108-3)

Extended

INTEGER

crp_levels

Indicate the quantitative measurement of the amount of CRP, an inflammatory marker, in the blood in mg/L. Used for screening and monitoring for inflammatory disease, infections, and for cardiovascular disease risk assessment. (Reference: NCIt C64548, LOINC 30522-7)

Extended

INTEGER

ldh_level

Indicate the level of lactate dehydrogenase (LDH), in IU/L. An increased amount of LDH in the blood may be a sign of tissue damage and some types of cancer. (Reference: NCI)

Extended

INTEGER

anc

Indicate the value for a hematology laboratory test for the absolute number of neutrophil cells present in a sample of peripheral blood from a donor, in cells/uL. The ANC may be used to check for infection, inflammation, leukemia and other conditions. Cancer treatment such as chemotherapy may reduce the ANC. (Reference: caDSR CDE ID: 2180198)

Extended

INTEGER

alc

Indicate the absolute number of lymphocytes (ALC) found in a given volume of blood, as cells/uL. Lymphocytes help fight off infections and an altered cellular immune function has been demonstrated in patients with cancer. (Reference: NCIt: C113237)

Extended

INTEGER

brca_carrier

Indicate whether donor is a carrier of a mutation in a BRCA gene. A mutation in this gene is associated with an increased risk of familial breast and ovarian cancer.

Extended

TEXT

BRCA1

BRCA2

Both BRCA1 and BRCA2

Not applicable

1 more

er_status

Indicate the expression of estrogen receptor (ER). (Reference: NAACCR 3827)

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

er_allred_score

Indicate the Allred score for estrogen receptor. The Allred score is based on the percentage of cells that stain positive by immunohistochemistry (IHC) for estrogen receptor (ER) and the intensity of that staining. (Reference: NAACCR: 3828, caDSR CDE ID 2725288)

Extended

TEXT

Total ER Allred score of 1

Total ER Allred score of 2

Total ER Allred score of 3

Total ER Allred score of 4

Total ER Allred score of 5

5 more

er_percent_positive

Indicate a value, in decimals, that represents the percent of cells staining estrogen receptor positive by immunohistochemistry (IHC).

Extended

NUMBER

her2_ihc_status

Indicate the expression of human epidermal growth factor receptor-2 (HER2) assessed by immunohistochemistry (IHC). (Reference: AJCC 8th Edition, Chapter 48)

Extended

TEXT

Cannot be determined

Equivocal

Negative

Not applicable

Positive

1 more

Negative: 0 or 1+ staining, Equivocal: 2+ staining, Positive: 3+ staining

her2_ish_status

Indicate the expression of human epidermal growth factor receptor-2 (HER2) assessed by in situ hybridization (ISH). (Reference: NAACCR: 3854)

Extended

TEXT

Cannot be determined

Equivocal

Positive

Negative

Not applicable

1 more

pr_status

Indicate the expression of progesterone receptor (PR). (Reference: NAACCR 3915)

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

pr_allred_score

Indicate the Allred score for progesterone receptor. The Allred score is based on the percentage of cells that stain positive by IHC for the progesterone receptor (PR) and the intensity of that staining. (Reference: NAACCR 3916)

Extended

TEXT

Total PR Allred score of 1

Total PR Allred score of 2

Total PR Allred score of 3

Total PR Allred score of 4

Total PR Allred score of 5

5 more

pr_percent_positive

Indicate a value, in decimals, that represents the percent of cells staining progesterone receptor positive by immunohistochemistry (IHC).

Extended

NUMBER

pd-l1_status

Indicate the immunohistochemical test result that refers to the over-expression or lack of expression of programmed death ligand 1 (PD-L1) in a tissue sample of a primary or metastatic malignant neoplasm. (Reference NCIt: C122807)

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

alk_ihc_status

Indicate the expression of anaplastic lymphoma receptor tyrosine kinase (ALK) as assessed by immunohistochemistry (IHC). Abnormalities of ALK can be present in lung cancers.

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

alk_ihc_intensity

Indicate the intensity of anaplastic lymphoma receptor tyrosine kinase (ALK) as assessed by immunohistochemistry (IHC). Abnormalities of ALK can be present in lung cancers.

Extended

TEXT

0 (No stain)

alk_fish_status

Indicate the expression of anaplastic lymphoma receptor tyrosine kinase (ALK) as assessed by fluorescence in situ hybridization (FISH). Abnormalities of ALK can be present in lung cancers.

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

ros1_ihc_status

Indicate the expression of receptor lymphoma kinase (ROS1) as assessed by immunohistochemistry (IHC). Gene fusions involving ROS1 can be present in lung cancers.

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

pan-trk_ihc_status

Indicate the expression of Pan-TRK as assessed by immunohistochemistry (IHC). Pan-TRK IHC screens for neurotrophic tyrosine kinase receptor (NTRK) fusions which have been described in many cancers including lung, thyroid and colorectal cancers.

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

ret_fish_status

Indicate the expression of gene arrangement involving the RET proto-oncogene (RET1) as assessed by fluorescence in situ hybridization (FISH). RET gene rearrangements are associated with several different neoplastic conditions. (Reference: NCIt C46005)

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

hpv_ihc_status

Indicate the expression of Human papillomavirus (HPV) p16 as assessed by immunohistochemistry (IHC).

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

hpv_dna_status

Indicate the expression of Human papillomavirus (HPV) as assessed using a laboratory test in which cells are scraped from the cervix to look for DNA of HPV. (Reference: NCIt C93141)

Extended

TEXT

Cannot be determined

Negative

Not applicable

Positive

Unknown

Comorbidity (comorbidity)

8 Fields

The collection of data elements related to a donor's comorbidities. A donor's comorbidities are any medical conditions (e.g diabetes, prior cancer malignancies) that have existed or may occur during the clinical course of the donor who has the index disease under study. To submit multiple comorbidities for a single donor, submit multiple rows in the comorbidity file for this donor.

File Name Example: comorbidity[-optional-extension].tsv

program_id

Unique identifier of the ARGO program.

Required

TEXT

submitter_donor_id

Unique identifier of the donor, assigned by the data provider.

Required

TEXT

Values must meet the regular expression

prior_malignancy

Prior malignancy affecting donor.

Extended

TEXT

Yes

Unknown

laterality_of_prior_malignancy

If donor has history of prior malignancy, indicate laterality of previous diagnosis. (Reference: caDSR CDE ID 4122391)

Extended

Conditional

TEXT

Bilateral

Left

Midline

Not applicable

Right

2 more

age_at_comorbidity_diagnosis

Indicate the age of comorbidity diagnosis, in years.

Extended

Conditional

INTEGER

comorbidity_type_code

Indicate the code for the comorbidity using the WHO ICD-10 code classification (https://icd.who.int/browse10/2019/en).

Required

Conditional

TEXT

Values must meet the regular expression

Examples:

E10, C50.1, I11, M06,

This field is required because it should have a cancer or non-cancer ICD-10 code. This field is marked 'Conditional' because it depends on the value of the `prior_malignancy` field. Both these fields will need to be consistent. If `prior_malignancy` is `Yes`, then an ICD-10 code related to cancer is expected in this field. If `prior_malignancy` is `No`, then an ICD-10 code related to a non-cancer condition is expected in this field.

comorbidity_treatment_status

Indicate if the patient is being treated for the comorbidity (this includes prior malignancies).

Extended

Conditional

TEXT

Yes

Unknown

comorbidity_treatment

Indicate treatment details for the comorbidity (this includes prior malignancies).

Extended

Conditional

TEXT