Clinical Data

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.

TierDescription
1Demographics, Diagnosis, Exposure, Treatment, Follow-up, Molecular Test and Family History
2Disease-agnostic extensions to the GDC
3Disease-specific extensions to the GDC
4HTAN 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

Tier 3 Clinical Data

Describes clinical data elements identified as required to be included in the HTAN data model and specific to an atlas, and not covered in a previous tier.

Data Schema:
Attribute
Label
Description
Demographics
Demographics
Individual biomedical demographics attributes
Diagnosis
Diagnosis
Individual's diagnosis
Exposure
Exposure
Individual's exposure to carcenogens
Family History
FamilyHistory
Individual's family cancer history
Follow Up
FollowUp
Individual's follow up exams
Molecular Test
MolecularTest
Individual's clinical molecular test data
Therapy
Therapy
Individual's first line of therapy or treatment
Clinical Data Tier 2
ClinicalDataTier2
Cancer related clinical data
Acute Lymphoblastic Leukemia Tier 3
AcuteLymphoblasticLeukemiaTier3
Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3
Brain Cancer Tier 3
BrainCancerTier3
Brain cancer specific attributes in Clinical Data Tier 3
Breast Cancer Tier 3
BreastCancerTier3
Breast cancer specific attributes in Clinical Data Tier 3
Colorectal Cancer Tier 3
ColorectalCancerTier3
Colorectal cancer specific attributes in Clinical Data Tier 3
Lung Cancer Tier 3
LungCancerTier3
Lung cancer specific attributes in Clinical Data Tier 3
Melanoma Tier 3
MelanomaTier3
Melanoma specific attributes in Clinical Data Tier 3
Ovarian Cancer Tier 3
OvarianCancerTier3
Ovarian cancer specific attributes in Clinical Data Tier 3
Pancreatic Cancer Tier 3
PancreaticCancerTier3
Pancreatic cancer specific attributes in Clinical Tier Data 3
Prostate Cancer Tier 3
ProstateCancerTier3
Prostate cancer specific attributes in Clinical Data Tier 3
Sarcoma Tier 3
SarcomaTier3
Sarcoma specific attributes in Clinical Data Tier 3