CGCI-HTMCP-CC: DICOM converted whole slide images from the Cancer Genome Characterization Initiative (CGCI) HIV+ Tumor Molecular Characterization Project (HTMCP) - Cervical 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 Office of Cancer Genomics at the National Cancer Institute sponsored a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel emerging sequencing technologies in cancer. The CGCI program included comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors.

As part of CGCI, the HIV+ Tumor Molecular Characterization Project (HTMCP) was a joint effort of the Office of Cancer Genomics (OCG) and the Office of HIV and AIDS Malignancy (OHAM). Its goals were to characterize HIV-associated cancers obtained from HIV-infected patients and compare them to the same types of cancers from patients without HIV infection. Approximately 34.2 million people are living with HIV worldwide. People infected with HIV have an elevated risk of cancer and mortality, and cancer is a ranking cause of death among people with HIV/AIDS. The Genome Sciences Center at the British Columbia Cancer Agency performed whole genome sequencing of 100 cases of paired tumor and germline DNA, along with transcriptome sequencing of HIV+ tumors.

Cervical cancer, a type of cancer that slowly forms in tissues of the cervix, is almost always caused by human papillomavirus (HPV) infection. In a thorough evaluation of various HPV-related malignancies, cervical cancer was selected for study based on its impact on mortality and on the prevalence of high quality source tissue.

This collection contains DICOM converted whole slide images from 211 of the 212 cases in the GDC CGCI-HTMCP-CC project (dbGaP accession phs000528). The proprietary format whole slide images were obtained from GDC and converted to DICOM Slide Microscopy (SM) format using idc-wsi-conversion. The 525 slides include specimens stained with H&E (hematoxylin and eosin, 217 slides) and p16 immunohistochemistry (217 slides), along with additional IHC markers for subsets of cases: BER-EP4 (15), MOC31 (15), P40 (15), P63 (15), CEA (5), ER (5), PR (5), Vimentin (5), TP53 (5), CD56 (2), Chromogranin (2), and Synaptophysin (2).

Diagnoses coded in ICD-O-3 include squamous cell carcinoma, large cell, nonkeratinizing NOS (129 patients), squamous cell carcinoma, keratinizing NOS (48), adenocarcinoma NOS (19), small cell carcinoma NOS (3), squamous cell carcinoma NOS (2), adenosquamous carcinoma (2), lymphoepithelial carcinoma (2), and other rare subtypes.

Data organization: DICOM PatientIDs correspond to GDC case IDs and can be used to link to genomic, transcriptomic, and clinical data in the GDC portal. Of 212 GDC cases, 211 have Tissue Slide images; the remaining case has no slide and is not represented in this collection. Most patients have multiple slides representing different stains (H&E + p16 as baseline, with additional IHC markers for subsets).

HTMCP-CC data is accessible at the NCI's Genomic Data Commons (GDC) via the GDC Data Portal. Please see the CGCI Use and Publication Guidelines for updated details on the sharing of any CGCI substudy data, including how to cite CGCI.

Files included

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

• cgci_htmcp_cc-idc_v24-aws.s5cmd: AWS download manifest
• cgci_htmcp_cc-idc_v24-gcs.s5cmd: GCS download manifest
• cgci_htmcp_cc-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:

1. Install idc-index: pip install --upgrade idc-index
2. 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 support@canceridc.dev or post on the IDC Forum.