Clinical

The Clinical table contains one row per TCGA participant (aka patient or donor). Each TCGA participant is uniquely represented by a TCGA barcode of length 12, eg TCGA-2G-AAM4. (For more information on how TCGA barcodes were created and how to “read” a TCGA barcode, click on the preceding link.)

Clinical Feature Selection

In the first pass, any XML features with the tag procurement\_status=Completed which were found to exist in at least 20% of the participants in any one Disease (aka tumor-type) were considered for selection. A few important features related to smoking, pregnancy, etc were added to the list during a manual-curation pass.

Selected fields from the both the clinical, auxiliary, ssf, and omf XML files were then extracted and loaded into the BigQuery table.

Additionally, only the most recent follow-up information was included (for cases where multiple follow-up sections existed in the clinical XML file).

XML Parsing

Each clinical XML file is divided into admin and case blocks, and each of these were processed separately.

While iterating through the case block of information, all elements (XML tags) and their values were collected. For follow-up blocks, only the most recent (based on sequence number) sub-block elements were kept.

In the final pass, case elements and follow-up elements were carefully merged with preference given to follow-up elements.

Transforms

Different survival-related fields are completed based on the value of the vital_status field:

  • for all patients with vital_status=Alive:
    • days_to_last_known_alive should not be NULL
    • days_to_last_known_alive is set to days_to_last_followup
    • days_to_death is set to NULL
  • for all patients with vital_status=Dead:
    • days_to_death should not be NULL (if it is NULL, and days_to_last_followup is not NULL, then vital_status is set to “Alive”
    • days_to_last_known_alive  is set to days_to_death
    • days_to_last_followup is set to NULL
  • pregnancies and total_number_of_pregnancies were merged into a single pregnancies field. Counts above four are represented as 4+ (e.g: [0,1,2,3,4+])
  • number\_of\_lymphnodes\_examined and lymph\_node\_examined\_count were merged into a single number\_of\_lymphnodes\_examined field
  • country and country_of_procurement were merged into a
    single country field

The following fields were extracted from the ssf XML file:

  • histological\_type
  • country
  • other\_dx
  • tobacco\_smoking\_history
  • gleason\_score\_combined
  • history\_of\_neoadjuvant\_treatment

The following fields were extracted from the omf XML file:

  • other\_malignancy\_malignancy\_type
  • other\_malignancy\_anatomic\_site
  • other\_malignancy\_histological\_type

When an auxiliary XML file exists for a participant, and the batch numbers in both the clinical XML and the auxiliary XML file match, the following fields are extracted from the auxiliary XML file and added to the Clinical table:

  • hpv\_calls,
  • hpv\_status,
  • mononucleotide\_and\_dinucleotide\_marker\_panel\_analysis\_status,

Finally, the patient BMI was calculated based on the height and weight values (when both were present) and was added to the Clinical table.

Have feedback or corrections? You can file an issue here or email us at feedback@isb-cgc.org.