HIV+ Tumor Molecular Characterization Project: Lung Cancer

Program Description

The CGCI program included comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors, including HIV-associated lung cancer. This project has been a joint effort between the Office of Cancer Genomics (OCG) (now CCG) 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 (22.9 million in Sub-Saharan Africa and over 1 million in the US, according to UNAIDS World AIDS Day Report, 2011). 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. It is important to understand why certain cancers, but not others, are increased in patients with HIV infection. Even though many HIV-associated cancers have a viral etiology, and immunodeficiency is believed to provide a permissive environment for viral oncogenesis, many questions remain even for those tumors that are induced by oncogenic viruses.

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. These platforms allow discovery of mutations both in coding and non-coding genomic regions, gene expression and genomic alterations (including translocations, insertions and deletions). Comparing tumors of cancer patients both with and without HIV-infection can provide insight into the potential function of this virus in certain cancers.

Lung cancer incidence is significantly increased among HIV-positive patients, including those on highly active antiretroviral therapy (HAART). Additionally, the tumor spectrum of Lung cancers in HIV+ patients is quite different from that seen in HIV-cases, suggesting a different biological development. Please visit the CGCI Program Page for more information on this and other CGCI studies.

Supplemental Data

• GDC Manifests
  • Controlled-Access Data - Download Manifest (2 Files)
  • Open-Access Data - Download Manifest (4 Files)
• miRNA
  • CGCI-HTMCP-LC miRNA-Seq Level 3 Data
• mRNA
  • CGCI-HTMCP-LC mRNA-Seq Level 3 Data
  • CGCI-HTMCP-LC mRNA-Seq Level 3 Data (Controlled)
• Whole Genome Sequencing
  • CGCI-HTMCP-LC WGS Level 3 Data
  • CGCI-HTMCP-LC WGS Level 3 Data (Controlled)
• Miscellaneous Files
  • CGCI-HTMCP-LC Sample Matrix Level 3 Data

Additional Resources

• Office of Cancer Genomics (link is external)

Instructions for Data Download

Open Access Data

1. Download the appropriate manifest file from the publication page
2. Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
   • GDC DTT ( Download, User's Guide)
   • GDC API ( User’s Guide)

Controlled Access Data

1. Download the appropriate manifest file from the publication page
2. Download a token from the GDC Data Portal
   • GDC Data Portal ( Launch, User’s Guide)
3. Use the manifest file and token to download data using the GDC DTT or the GDC API
   • GDC DTT ( Download, User’s Guide)
   • GDC API ( User’s Guide)

For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.