CDDP-EAGLE-1: DICOM converted whole slide images from the Environment And Genetics in Lung cancer Etiology (EAGLE) study

Abstract: The role of smoking has been well-documented in lung cancer for over 50 years. Less
well-understood is why only 15-20 percent of smokers are afflicted with lung cancer and a small
proportion of lung cancer occurs in the absence of smoking. A key goal of the EAGLE Study was to
understand the role of inherited variation in smokers with lung cancer.

This dataset corresponds to a collection of images and/or image-derived data available from the
National Cancer Institute Imaging Data Commons (IDC).
This dataset was converted into DICOM representation and ingested by the IDC team.
You can explore and visualize the corresponding images using the
IDC Portal.
You can use the manifests included in this Zenodo record to download the collection following
the Download instructions below.

The Environment And Genetics in Lung cancer Etiology (EAGLE) study is a large, multicenter,
population-based case-control study conducted in the Lombardy region of Italy from 2002 to 2005.
The study enrolled over 2,000 incident lung cancer cases (ages 35-79) from 13 hospitals and over
2,000 matched population-based controls, to investigate the role of inherited genetic variation
and environmental factors in lung cancer etiology.

This collection contains DICOM converted whole slide images of H&E-stained (hematoxylin and
eosin) frozen sections of primary lung tumor tissue from 49 of the 50 EAGLE lung adenocarcinoma
cases available in the
GDC CDDP_EAGLE-1 project
(dbGaP accession phs001239). The original Aperio SVS slide images were converted to DICOM Slide
Microscopy (SM) format using
idc-wsi-conversion.

Diagnoses include adenocarcinoma NOS (24 cases), adenocarcinoma with
mixed subtypes (13), acinar cell carcinoma (8), clear cell adenocarcinoma (2), and solid
carcinoma (2), coded in ICD-O-3.

Data organization: DICOM PatientIDs correspond to GDC case IDs
(e.g. CDDP_EAGLE-1-CDDP_00002) and can be used to link to genomic and clinical
data in the GDC portal.
Of 50 cases in GDC, 49 have Tissue Slide images; the remaining case has no slide and is not
represented in this collection.

The EAGLE study was led by Maria Teresa Landi, M.D., Ph.D. (NCI Division of Cancer Epidemiology
and Genetics) in collaboration with EPOCA at the University of Milan. Please see the EAGLE Study page
and the
dbGaP study page to learn
more about the study and to obtain any supporting metadata for this
collection.

Files included

A manifest file's name indicates the IDC data release in which a version of collection data was first introduced. For example, cddp_eagle_1-idc_v22-aws.s5cmd corresponds to the contents of the cddp_eagle_1 collection introduced in IDC data release v22.

cddp_eagle_1-idc_v24-aws.s5cmd: AWS download manifest

cddp_eagle_1-idc_v24-gcs.s5cmd: GCS download manifest

cddp_eagle_1-idc_v24-dcf.dcf: DCF download manifest

Manifest files ending in -aws.s5cmd reference files in Amazon Web Services (AWS) buckets; -gcs.s5cmd reference files in Google Cloud Storage. The actual files are identical and mirrored between AWS and GCP.

Download instructions

Each manifest file includes instructions in its header on how to download the included files.

To download the files using .s5cmd manifests:

Install idc-index:
pip install --upgrade idc-index

Download the files referenced by a manifest included in this dataset:
idc download manifest.s5cmd

To download files using a .dcf manifest, see the manifest header.

For questions or help, contact [e-mail]
or post on the IDC Forum.