HTAN Clinical Data Standard

Overview

This page describes the data tiers and data collection for the HTAN clinical data standard.

Description of Model

HTAN clinical data consists of four tiers. Tier 1 is in alignment with the Genomic Data Commons (GDC) guidelines for clinical data, while Tier 2, 3 and 4 are extensions to this model.

Tier

Description

1

Demographics, Diagnosis, Exposure, Treatment, Follow-up, Molecular Test and Family History

2

Disease-agnostic extensions to the GDC

3

Disease-specific extensions to the GDC

4

HTAN Research Network Atlas-specific clinical data elements not covered in a previous tier and that are recognized as a requirement by the atlas. These are attributes specific to an atlas

Tier 1 Clinical Data

To establish consistency across HTAN atlases and tumor types, the HTAN Tier 1 clinical data consists of GDC clinical data elements defined as Required, Preferred and Optional. The HTAN CDE Dictionary contains a comprehensive list of elements attributed as Required, Preferred and Optional.

  • Required CDE: Data submitters must provide a value for this attribute; “Unknown”, “Not Reported” or “null” are valid values for many of these attributes if the required information is missing for a subset of patients
  • Preferred CDE: Data submitters are strongly recommended to provide values for this attribute
  • Optional CDE: Data submitters can populate this attribute based on availability of the data requested

Tier 2 Clinical Data

Describes disease-agnostic extensions to the GDC not included in Tier 1 Clinical Data that were suggested for inclusion by the HTAN Research Network. These suggested CDEs were compared to NCI standards described in the caDSR system and the most similar CDE was selected for inclusion in the HTAN Clinical Data model. If no comparable CDE was found for a particular element, an HTAN-specific CDE was developed.

Tier 3 Clinical Data

Describes disease-specific extensions to the GDC not included in Tier 1 Clinical Data that were suggested for inclusion by the HTAN Research Network. These suggested CDEs were compared to NCI standards described in the caDSR system and the most similar CDE was selected for inclusion in the HTAN Clinical Data model. If no comparable CDE was found for a particular element, an HTAN-specific CDE was developed.

Attributes are divided by tumor type:

  • Melanoma-specific
  • Lung pre-cancer and cancer-specific Colorectal pre-cancer and cancer-specific
  • Breast pre-cancer and cancer-specific
  • Neuroblastoma-specific
  • Glioma-specific
  • Pancreatic pre-cancer and cancer-specific
  • Acute lymphoblastic leukemia-specific
  • Sarcoma-specific
  • Ovarian pre-cancer and cancer-specific
  • Prostate pre-cancer and cancer-specific