preview

Takes a JSON object of filters in the request body and returns a “preview” of the cohort that would result from passing a similar request to the cohort save endpoint. This preview consists of two lists: the lists of participant (aka patient) barcodes, and the list of sample barcodes. Authentication is not required. Example:

$ curl https:/api-dot-isb-cgc.appspot.com/_ah/api/cohort_api/v1/preview_cohort -d ‘{“Study”: “BRCA,OV”}’ -H “Content-Type: application/json”

Access control: To call this method, you must have the following roles:

• None

Request

HTTP request

POST https://api-dot-isb-cgc.appspot.com/_ah/api/cohort_api/v1/preview_cohort

Parameters

None

Request body

In the request body, supply a metadata resource:

{
        'adenocarcinoma_invasion ': string,
        'age_at_initial_pathologic_diagnosis ': string,
        'anatomic_neoplasm_subdivision ': string,
        'avg_percent_lymphocyte_infiltration ': float,
        'avg_percent_monocyte_infiltration ': float,
        'avg_percent_necrosis ': float,
        'avg_percent_neutrophil_infiltration ': float,
        'avg_percent_normal_cells ': float,
        'avg_percent_stromal_cells ': float,
        'avg_percent_tumor_cells ': float,
        'avg_percent_tumor_nuclei ': float,
        'batch_number ': integer,
        'bcr ': string,
        'clinical_M ': string,
        'clinical_N ': string,
        'clinical_stage ': string,
        'clinical_T ': string,
        'colorectal_cancer ': string,
        'country ': string,
        'country_of_procurement ': string,
        'days_to_birth ': integer,
        'days_to_collection ': integer,
        'days_to_death ': integer,
        'days_to_initial_pathologic_diagnosis ': integer,
        'days_to_last_followup ': integer,
        'days_to_submitted_specimen_dx ': integer,
        'Study ': string,
        'ethnicity ': string,
        'frozen_specimen_anatomic_site ': string,
        'gender ': string,
        'height ': integer,
        'histological_type ': string,
        'history_of_colon_polyps ': string,
        'history_of_neoadjuvant_treatment ': string,
        'history_of_prior_malignancy ': string,
        'hpv_calls ': string,
        'hpv_status ': string,
        'icd_10 ': string,
        'icd_o_3_histology ': string,
        'icd_o_3_site ': string,
        'lymph_node_examined_count ': integer,
        'lymphatic_invasion ': string,
        'lymphnodes_examined ': string,
        'lymphovascular_invasion_present ': string,
        'max_percent_lymphocyte_infiltration ': integer,
        'max_percent_monocyte_infiltration ': integer,
        'max_percent_necrosis ': integer,
        'max_percent_neutrophil_infiltration ': integer,
        'max_percent_normal_cells ': integer,
        'max_percent_stromal_cells ': integer,
        'max_percent_tumor_cells ': integer,
        'max_percent_tumor_nuclei ': integer,
        'menopause_status ': string,
        'min_percent_lymphocyte_infiltration ': integer,
        'min_percent_monocyte_infiltration ': integer,
        'min_percent_necrosis ': integer,
        'min_percent_neutrophil_infiltration ': integer,
        'min_percent_normal_cells ': integer,
        'min_percent_stromal_cells ': integer,
        'min_percent_tumor_cells ': integer,
        'min_percent_tumor_nuclei ': integer,
        'mononucleotide_and_dinucleotide_marker_panel_analysis_status': string,
        'mononucleotide_marker_panel_analysis_status ': string,
        'neoplasm_histologic_grade ': string,
        'new_tumor_event_after_initial_treatment ': string,
        'number_of_lymphnodes_examined ': integer,
        'number_of_lymphnodes_positive_by_he ': integer,
        'ParticipantBarcode ': string,
        'pathologic_M ': string,
        'pathologic_N ': string,
        'pathologic_stage ': string,
        'pathologic_T ': string,
        'person_neoplasm_cancer_status ': string,
        'pregnancies ': string,
        'preservation_method ': string,
        'primary_neoplasm_melanoma_dx ': string,
        'primary_therapy_outcome_success ': string,
        'prior_dx ': string,
        'Project ': string,
        'psa_value ': float,
        'race ': string,
        'residual_tumor ': string,
        'SampleBarcode ': string,
        'tobacco_smoking_history ': string,
        'total_number_of_pregnancies ': integer,
        'tumor_tissue_site ': string,
        'tumor_pathology ': string,
        'tumor_type ': string,
        'weiss_venous_invasion ': string,
        'vital_status ': string,
        'weight ': integer,
        'year_of_initial_pathologic_diagnosis ': string,
        'SampleTypeCode ': string,
        'has_Illumina_DNASeq ': string,
        'has_BCGSC_HiSeq_RNASeq ': string,
        'has_UNC_HiSeq_RNASeq ': string,
        'has_BCGSC_GA_RNASeq ': string,
        'has_UNC_GA_RNASeq ': string,
        'has_HiSeq_miRnaSeq ': string,
        'has_GA_miRNASeq ': string,
        'has_RPPA ': string,
        'has_SNP6 ': string,
        'has_27k ': string,
        'has_450k ': string
}

Parameter name	Value	Description
adenocarcinoma_invasion	string
age_at_initial_pathologic_diagnosis	string	Age at which a condition or disease was first diagnosed. (in years)
anatomic_neoplasm_subdivision	string	Text term to describe the spatial location, subdivisions and/or anatomic site name of a tumor.
avg_percent_lymphocyte_infiltration	float	Average in the series of numeric values to represent the percentage of lymphocyte infiltration in a malignant tumor sample or specimen.
avg_percent_monocyte_infiltration	float	Average in the series of numeric values to represent the percentage of monocyte infiltration in a malignant tumor sample or specimen.
avg_percent_necrosis	float	Average in the series of numeric values to represent the percentage of cell death in a malignant tumor sample or specimen.
avg_percent_neutrophil_infiltration	float	Average in the series of numeric values to represent the percentage of neutrophil infiltration in a malignant tumor sample or specimen.
avg_percent_normal_cells	float	Average in the series of numeric values to represent the percentage of normal cells in a malignant tumor sample or specimen.
avg_percent_stromal_cells	float	Average in the series of numeric values to represent the percentage of stromal cells in a malignant tumor sample or specimen.
avg_percent_tumor_cells	float	Average in the series of numeric values to represent the percentage of tumor cells in a malignant tumor sample or specimen.
avg_percent_tumor_nuclei	float	Average in the series of numeric values to represent the percentage of tumor nuclei in a malignant tumor sample or specimen.
batch_number	integer	groups samples by the batch they were processed in
bcr	string	A TCGA center where samples are carefully catalogued, processed, quality-checked and stored along with participant clinical information.
clinical_M	string	Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
clinical_N	string	Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
clinical_stage	string	Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis ...
clinical_T	string	Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
colorectal_cancer	string	Text term to signify whether a patient has been diagnosed with colorectal cancer.
country	string	Text to identify the name of the state, province, or country in which the sample was procured.
country_of_procurement	string	Text to identify the name of the state, province, or country in which the sample was procured.
days_to_birth	integer	Time interval from a person’s date of birth to the date of initial pathologic diagnosis, represented as a calculated number of days.
days_to_collection	integer
days_to_death	integer	Time interval from a person’s date of death to the date of initial pathologic diagnosis, represented as a calculated number of days.
days_to_initial_pathologic_diagnosis	integer	Numeric value to represent the day of an individual’s initial pathologic diagnosis of cancer.
days_to_last_followup	integer	Time interval from the date of last followup to the date of initial pathologic diagnosis, represented as a calculated number of days.
days_to_submitted_specimen_dx	integer	Time interval from the date of diagnosis of the submitted sample to the date of initial pathologic diagnosis, represented as a calculated number of d...
Study	string	A disease study is the sum of results from all experiments for a specific cancer type (or tumor type) that TCGA is tasked to study. Within the projec...
ethnicity	string	The text for reporting information about ethnicity based on the Office of Management and Budget (OMB) categories.
frozen_specimen_anatomic_site	string	Text description of the origin and the anatomic site regarding the frozen biospecimen tumor tissue sample.
gender	string	Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal ro...
height	integer	The height of the patient in centimeters.
histological_type	string	Text term for the structural pattern of cancer cells used to define a microscopic diagnosis.
history_of_colon_polyps	string	Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report(s).
history_of_neoadjuvant_treatment	string	Text term to describe the patient’s history of neoadjuvant treatment and the kind of treament given prior to resection of the tumor.
history_of_prior_malignancy	string	Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence.
hpv_calls	string	Results of HPV tests
hpv_status	string	Current HPV status
icd_10	string	The tenth version of the International Classification of Disease (ICD), published by the World Health Organization in 1992._A system of numbered cate...
icd_o_3_histology	string	The third edition of the International Classification of Diseases for Oncology, published in 2000, used principally in tumor and cancer registries fo...
icd_o_3_site	string	The third edition of the International Classification of Diseases for Oncology, published in 2000, used principally in tumor and cancer registries fo...
lymph_node_examined_count	integer
lymphatic_invasion	string	a yes/no indicator to ask if malignant cells are present in small or thin-walled vessels suggesting lymphatic involvement.
lymphnodes_examined	string	the yes/no/unknown indicator whether a lymph node assessment was performed at the primary presentation of disease.
lymphovascular_invasion_present	string	the yes/no indicator to ask if large vessel (vascular) invasion or small, thin-walled (lymphatic) invasion was detected in a tumor specimen.
max_percent_lymphocyte_infiltration	integer	Maximum in the series of numeric values to represent the percentage of lymphcyte infiltration in a malignant tumor sample or specimen.
max_percent_monocyte_infiltration	integer	Maximum in the series of numeric values to represent the percentage of monocyte infiltration in a malignant tumor sample or specimen.
max_percent_necrosis	integer	Maximum in the series of numeric values to represent the percentage of cell death in a malignant tumor sample or specimen.
max_percent_neutrophil_infiltration	integer	Maximum in the series of numeric values to represent the percentage of neutrophil infiltration in a malignant tumor sample or specimen.
max_percent_normal_cells	integer	Maximum in the series of numeric values to represent the percentage of normal cells in a malignant tumor sample or specimen.
max_percent_stromal_cells	integer	Maximum in the series of numeric values to represent the percentage of stromal cells in a malignant tumor sample or specimen.
max_percent_tumor_cells	integer	Maximum in the series of numeric values to represent the percentage of tumor cells in a malignant tumor sample or specimen.
max_percent_tumor_nuclei	integer	Maximum in the series of numeric values to represent the percentage of tumor nuclei in a malignant tumor sample or specimen.
menopause_status	string	Text term to signify the status of a woman’s menopause, the permanent cessation of menses, usually defined by 6 to 12 months of amenorrhea.
min_percent_lymphocyte_infiltration	integer	Minimum in the series of numeric values to represent the percentage of lymphcyte infiltration in a malignant tumor sample or specimen.
min_percent_monocyte_infiltration	integer	Minimum in the series of numeric values to represent the percentage of monocyte infiltration in a malignant tumor sample or specimen.
min_percent_necrosis	integer	Minimum in the series of numeric values to represent the percentage of cell death in a malignant tumor sample or specimen.
min_percent_neutrophil_infiltration	integer	Minimum in the series of numeric values to represent the percentage of neutrophil infiltration in a malignant tumor sample or specimen.
min_percent_normal_cells	integer	Minimum in the series of numeric values to represent the percentage of normal cells in a malignant tumor sample or specimen.
min_percent_stromal_cells	integer	Minimum in the series of numeric values to represent the percentage of stromal cells in a malignant tumor sample or specimen.
min_percent_tumor_cells	integer	Minimum in the series of numeric values to represent the percentage of tumor cells in a malignant tumor sample or specimen.
min_percent_tumor_nuclei	integer	Minimum in the series of numeric values to represent the percentage of tumor nuclei in a malignant tumor sample or specimen.
mononucleotide_and_dinucleotide_marker_panel_analysis_status	string	Text result of microsatellite instability (MSI) testing at using a mononucleotide and dinucleotide microsatellite panel.
mononucleotide_marker_panel_analysis_status	string	Text result of microsatellite instability (MSI) testing using a mononucleotide microsatellite panel.
neoplasm_histologic_grade	string	Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.
new_tumor_event_after_initial_treatment	string	Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.
number_of_lymphnodes_examined	integer	the total number of lymph nodes removed and pathologically assessed for disease.
number_of_lymphnodes_positive_by_he	integer	Numeric value to signify the count of positive lymph nodes identified through hematoxylin and eosin (H&E) staining light microscopy.
ParticipantBarcode	string	The barcode assigned by TCGA to the Participant
pathologic_M	string	Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the reg...
pathologic_N	string	The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC’s Cance...
pathologic_stage	string	The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.
pathologic_T	string	Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American ...
person_neoplasm_cancer_status	string	The state or condition of an individual’s neoplasm at a particular point in time.
pregnancies	string	Value to describe the number of full-term pregnancies that a woman has experienced.
preservation_method	string
primary_neoplasm_melanoma_dx	string	Text indicator to signify whether a person had a primary diagnosis of melanoma.
primary_therapy_outcome_success	string	Measure of Success
prior_dx	string	Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence
Project	string	The study for which the data was generated.
psa_value	float	The lab value that represents the results of the most recent (post-operative) prostatic-specific antigen (PSA) in the blood.
race	string	The text for reporting information about race based on the Office of Management and Budget (OMB) categories.
residual_tumor	string	Text terms to describe the status of a tissue margin following surgical resection.
SampleBarcode	string	The barcode assigned by TCGA to a sample from a Participant
tobacco_smoking_history	string	Category describing current smoking status and smoking history as self-reported by a patient.
total_number_of_pregnancies	integer
tumor_tissue_site	string	Text term that describes the anatomic site of the tumor or disease.
tumor_pathology	string
tumor_type	string	Text term to identify the morphologic subtype of papillary renal cell carcinoma.
weiss_venous_invasion	string	The result of an assessment using the Weiss histopathologic criteria.
vital_status	string	the survival state of the person registered on the protocol.
weight	integer	the weight of the patient measured in kilograms.
year_of_initial_pathologic_diagnosis	string	Numeric value to represent the year of an individual’s initial pathologic diagnosis of cancer.
SampleTypeCode	string	the type of the sample tumor or normal tissue cell or blood sample provided by a participant.
has_Illumina_DNASeq	string	Indicates if a sample has gene sequencing data. “True”, “False”, or “None”.
has_BCGSC_HiSeq_RNASeq	string	Indicates if a sample has RNA sequencing data from the IlluminaHiSeq platform and the BCGSC pipeline. “True”, “False”, or “None”.
has_UNC_HiSeq_RNASeq	string	Indicates if a sample has RNA sequencing data from the IlluminaHiSeq platform and the UNC pipeline. “True”, “False”, or “None”.
has_BCGSC_GA_RNASeq	string	Indicates if a sample has RNA sequencing data from the IlluminaGA platform and the BCGSC pipeline. “True”, “False”, or “None”.
has_UNC_GA_RNASeq	string	Indicates if a sample has RNA sequencing data from the IlluminaGA platform and the UNC pipeline. “True”, “False”, or “None”.
has_HiSeq_miRnaSeq	string	Indicates if a sample has microRNA data from the IlluminaHiSeq platform. “True”, “False”, or “None”.
has_GA_miRNASeq	string	Indicates if a sample has microRNA data from the IlluminaGA platform. “True”, “False”, or “None”.
has_RPPA	string	Indicates if a sample has protein array data. “True”, “False”, or “None”.
has_SNP6	string	Indicates if a sample has copy number data. “True”, “False”, or “None”.
has_27k	string	Indicates if a sample has methylation data from the Illumina 27k platform. “True”, “False”, or “None”.
has_450k	string	Indicates if a sample has methylation data from the Illumina 450k platform. “True”, “False”, or “None”.

Response

If successful, this method returns a response body with the following structure:

{
  "kind": "cohort_api#cohortsItem",
  "patient_count": string,
  "patients": [string],
  "sample_count": string,
  "samples": [string],
}

Property name	Value	Description
kind	cohort_api#cohortsItem	The resource type.
patient_count	string	Number of participants in this cohort.
patients[]	list	List of participant barcodes in this cohort.
sample_count	string	Number of samples in this cohort.
samples[]	list	List of sample barcodes in this cohort.

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