| Property name | Description |
|---|---|
| kind | The resource type. |
| aliquots[] | List of barcodes of aliquots taken from this participant. |
| clinical_data | The clinical data about the participant. |
| clinical_data.ParticipantBarcode | Participant barcode. |
| clinical_data.Project | Project name, .eg. “TCGA”. |
| clinical_data.Study | Tumor type abbreviation, e.g. “BRCA”. |
| clinical_data.age_at_initial_pathologic_diagnosis | Age at which a condition or disease was first diagnosed in years. |
| clinical_data.anatomic_neoplasm_subdivision | Text term to describe the spatial location, subdivisions and/or anatomic site name of a tumor. |
| clinical_data.batch_number | Groups samples by the batch they were processed in. |
| clinical_data.bcr | Biospecimen core resource, e.g. “Nationwide Children’s Hospital”, “Washington University”. |
| clinical_data.clinical_M | Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. |
| clinical_data.clinical_N | Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. |
| clinical_data.clinical_T | Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. |
| clinical_data.clinical_stage | Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer. |
| clinical_data.colorectal_cancer | Text term to signify whether a patient has been diagnosed with colorectal cancer. |
| clinical_data.country | Text to identify the name of the state, province, or country in which the sample was procured. |
| clinical_data.days_to_birth | Time interval from a person’s date of birth to the date of initial pathologic diagnosis, represented as a calculated number of days. |
| clinical_data.days_to_initial_pathologic_diagnosis | Numeric value to represent the day of an individual’s initial pathologic diagnosis of cancer. |
| clinical_data.days_to_last_followup | Time interval from the date of last followup to the date of initial pathologic diagnosis, represented as a calculated number of days. |
| clinical_data.ethnicity | The text for reporting information about ethnicity based on the Office of Management and Budget (OMB) categories. |
| clinical_data.frozen_specimen_anatomic_site | Text description of the origin and the anatomic site regarding the frozen biospecimen tumor tissue sample. |
| clinical_data.gender | Text designations that identify gender. |
| clinical_data.histological_type | Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. |
| clinical_data.history_of_colon_polyps | 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). |
| clinical_data.history_of_neoadjuvant_treatment | Text term to describe the patient’s history of neoadjuvant treatment and the kind of treament given prior to resection of the tumor. |
| clinical_data.history_of_prior_malignancy | Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. |
| clinical_data.hpv_calls | Results of HPV tests. |
| clinical_data.hpv_status | Current HPV status. |
| clinical_data.icd_10 | The tenth version of the International Classification of Disease (ICD). |
| clinical_data.icd_o_3_histology | The third edition of the International Classification of Diseases for Oncology. |
| clinical_data.icd_o_3_site | The third edition of the International Classification of Diseases for Oncology. |
| clinical_data.lymphatic_invasion | A yes/no indicator to ask if malignant cells are present in small or thin-walled vessels suggesting lymphatic involvement. |
| clinical_data.lymphnodes_examined | The yes/no/unknown indicator whether a lymph node assessment was performed at the primary presentation of disease. |
| clinical_data.lymphovascular_invasion_present | The yes/no indicator to ask if large vessel (vascular) invasion or small, thin-walled (lymphatic) invasion was detected in a tumor specimen. |
| clinical_data.menopause_status | 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. |
| clinical_data.mononucleotide_and_dinucleotide_marker_panel_analysis_status | Text result of microsatellite instability (MSI) testing at using a mononucleotide and dinucleotide microsatellite panel. |
| clinical_data.mononucleotide_marker_panel_analysis_status | Text result of microsatellite instability (MSI) testing using a mononucleotide microsatellite panel. |
| clinical_data.neoplasm_histologic_grade | Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. |
| clinical_data.new_tumor_event_after_initial_treatment | Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. |
| clinical_data.number_of_lymphnodes_examined | The total number of lymph nodes removed and pathologically assessed for disease. |
| clinical_data.number_of_lymphnodes_positive_by_he | Numeric value to signify the count of positive lymph nodes identified through hematoxylin and eosin (H&E) staining light microscopy. |
| clinical_data.pathologic_M | Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the reg... |
| clinical_data.pathologic_N | 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... |
| clinical_data.pathologic_stage | 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. |
| clinical_data.pathologic_T | Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American ... |
| clinical_data.person_neoplasm_cancer_status | The state or condition of an individual’s neoplasm at a particular point in time. |
| clinical_data.pregnancies | Value to describe the number of full-term pregnancies that a woman has experienced. |
| clinical_data.primary_neoplasm_melanoma_dx | Text indicator to signify whether a person had a primary diagnosis of melanoma. |
| clinical_data.primary_therapy_outcome_success | Measure of Success |
| clinical_data.prior_dx | Text term to describe the patient’s history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. |
| clinical_data.race | The text for reporting information about race based on the Office of Management and Budget (OMB) categories. |
| clinical_data.residual_tumor | Text terms to describe the status of a tissue margin following surgical resection. |
| clinical_data.tobacco_smoking_history | Category describing current smoking status and smoking history as self-reported by a patient. |
| clinical_data.tumor_tissue_site | Text term that describes the anatomic site of the tumor or disease. |
| clinical_data.tumor_type | Text term to identify the morphologic subtype of papillary renal cell carcinoma. |
| clinical_data.vital_status | The survival state of the person registered on the protocol. |
| clinical_data.weiss_venous_invasion | The result of an assessment using the Weiss histopathologic criteria. |
| clinical_data.year_of_initial_pathologic_diagnosis | Numeric value to represent the year of an individual’s initial pathologic diagnosis of cancer. |
| samples[] | List of barcodes of samples taken from this participant. |
| Column Name | Description |
|---|---|
| CLINICAL_NO | Unique identifier for a clinical sample. Oracle sequence generated number. |
| PATIENT_NO | Link to patient table. |
| SAMPLE_SOURCE | Source of the sample (surgery, biopsy, etc.). |
| SAMPLE_STATE | State of the sample (fresh, frozen, etc.). |
| GRANULARITY | Granularity of the sample (grossly dissected, sorted cells, etc.). |
| TUMOR_TYPE | Type of the tumor. |
| MARGINS | Conditions of the margins (Coded: +=positive, -=negative, 0=not applicable, U=unknown). |
| ANGIO_INVASION | Whether there was angio invasion (Coded: Y=Yes, N=No, U=Unknown). |
| FOCAL | Focal (Coded: Uni, Multiple, Unknown). |
| POST_OP | Post operative. |
| RECURRENCE | Tumor recurrence (Coded: Distant, Local, Biochemical, Regional, None, Unknown). |
| NOTEBOOK_ID | Notebook identifier containing original data on the clinical sample. |
| NOTEBOOK_PAGE | Notebook page number. |
| DATE_CREATED | Date record was entered into the database (default=SYSDATE, YYYY-MM-DD). |
| CREATED_BY | Person who entered the record into the database. |
| DATE_MODIFIED | Date record was last updated (default=SYSDATE, YYYY-MM-DD). |
| MODIFIED_BY | Person who last modified the record. |
| CLINICAL_SAMPLE_ID | Identifier to another database. |
| SAMPLE_SIZE | Size of the sample. |
| SAMPLE_SIZE_UNITS | Units of the sample size (Coded: cc=cubic centimeters, cm=centimeters, grams, none). |
| TIME_PM | Time to post-mortem (hours) for sample removal. |
| ORGAN | Organ from which the sample came. |
| PRIOR_TREATMENT | Type of prior treatment (CHEMO, REDIO, HORMONAL, NONE, etc.). |
| CLINICAL_T | Clinical tumor. |
| CLINICAL_N | Clinical node. |
| CLINICAL_DM | Clinical distal metastasis. |
| TUMOR_GRADE | Tumor grade. |
| TUMOR_SIZE | Size of the tumor. |
| TUMOR_SIZE_UNITS | Units of tumor size (Coded: cc=cubic centimeters, cm=centimeters, grams, none). |
| TIME_DO | Time from diagnosis to the operation (days). |
| TOTAL_LN | Total number of lymph nodes. |
| POSITIVE_LN | Total number of positive lymph nodes. |
| PATH_T | Pathological tumor. |
| PATH_N | Pathological node. |
| PATH_DM | Pathological distal metastasis. |
| TIME_OR | Time from operation to recurrence (days). |
| NOTEBOOK_LOCATION | Notebook location. |
| SAMPLE_NOTES | Additional notes on the clinical sample. |
REF:
https://puma.princeton.edu/cgi-bin/tools/viewSchema.pl?table=CLINICAL_SAMPLE
http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/progapi/progapi3_tcga/cases_get.html
NCI Dictionary of Cancer Terms
https://www.cancer.gov/publications/dictionaries/cancer-terms?search=clinical
如何利用TCGA数据库进行深度癌症研究及发大牛文章？
http://www.bio-equip.com/showarticle.asp?ID=453086429
http://www.yiqi.com/pt7004/file_100.html
TCGA博客文章
http://www.bio-info-trainee.com/tag/tcga