NCI's Genome Characterization Pipeline

  • Resize font
  • Print
  • Email
  • Facebook
  • Twitter
  • Google+
  • Pinterest

NCI’s Center for Cancer Genomics (CCG) coordinates research teams across the United States and Canada to produce rich cancer genomic and clinical datasets for the cancer research community. CCG implements this collaborative effort through an efficient and standardized workflow called the Genome Characterization Pipeline. Learn more about how it works below.

Tissue Collection and Processing

  • CCG partners with clinical trials and community oncology groups that collect tumor tissue samples and normal tissue, usually blood, from patients who choose to participate. Tumor tissues are preserved in one of two ways: the majority of the samples that CCG studies are formalin-fixed paraffin-embedded (FFPE) tissues and some are frozen tissue.
  • CCG’s Biospecimen Core Resource (BCR) at Nationwide Children’s Hospital processes all tissues to ensure that they meet rigorous quality standards, oversees informed consent to protect patients’ rights, and de-identifies all clinical data about patients to safeguard their privacy.
  • The BCR also isolates DNA, RNA, and proteins from qualifying tissues and sends these analytes to CCG’s Genome Characterization Centers (GCC)s.

Genome Characterization

  • The Genome Characterization Centers (GCC)s generate data from the DNA, RNA, and proteins that they receive from the Biospecimen Core Resource (BCR).
  • CCG has three GCCs that each specialize in a different modality of genomic interrogation:
  • The GCCs send the information that they generate to CCG’s Genomic Data Analysis Network (GDAN) and share it through the Genomic Data Commons (GDC).

Genomic Data Analysis

  • The CCG Genomic Data Analysis Network (GDAN) is a diverse team of scientists from 13 institutions across the United States and Canada that takes the raw output of genomic characterization techniques from CCG’s Genome Characterization Centers (GCCs) and performs analyses that transform these big data into biological insight.
  • The GDAN has a wide range of expertise, from identifying DNA mutation drivers to integrating and visualizing multi-omics data.
  • The GDAN shares the results of their analyses with CCG’s Analysis Working Groups (AWG)s and deposits their data in the Genomic Data Commons (GDC).

Data Sharing and Discovery

  • CCG’s Analysis Working Groups (AWG)s, collaborative teams of scientists and clinicians, analyze data from the Genomic Data Analysis Network (GDAN) and produce novel analyses, resulting in peer-reviewed publications that advance their fields and spur future research.
  • The rich data generated by the CCG pipeline are made publicly available in the NCI Genomic Data Commons (GDC) for use by researchers across the world. Some data are released as open access and are available to anyone; others are controlled access and require users to apply for authentication. See Data Access Processes and Tools for details.
  • By bringing data to one location and increasing accessibility, the GDC aims to accelerate the rate of discovery about cancer and facilitate precision oncology. Learn more about how the Genomic Data Commons is providing an expandable data sharing platform.
  • Posted: August 4, 2017

Most text on the National Cancer Institute website may be reproduced or reused freely. The National Cancer Institute should be credited as the source and a link to this page included, e.g., “NCI's Genome Characterization Pipeline was originally published by the National Cancer Institute.”

Please note that blog posts that are written by individuals from outside the government may be owned by the writer, and graphics may be owned by their creator. In such cases, it is necessary to contact the writer, artists, or publisher to obtain permission for reuse.

We welcome your comments on this post. All comments must follow our comment policy.