Genome Characterization Pipeline

Tissue Source Sites (TSS): 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:

• Formalin-fixed paraffin-embedded (FFPE) tissues
• Frozen tissue

Biospecimen Core Resource (BCR): Responsible for collecting and processing samples.

The BCR has two components:

• The Biospecimen Processing Center at Nationwide Children’s Hospital processes all tissues to ensure that they meet rigorous quality standards and isolates DNA, RNA, proteins, and other analytes to send to Genome Characterization Centers (GCCs).

Clinical Data Center (CDC): Responsible for collecting and and curating clinical data. 

• The CDC at Information Management Services, Inc. works with collection sites to ensure that clinical data is properly collected and in the correct format. It also helps identify standardized clinical data points. Importantly, the CDC oversees informed consent to protect patients’ rights and de-identifies all clinical data about patients to safeguard their privacy.

Genome Characterization Centers (GCCs): Generate data from samples received from the Biospecimen Core Resource (BCR).

Each GCC provides support for distinct genomic or epigenomic pipelines:

• Broad Institute performs whole genome sequencing and whole exome sequencing.
• University of North Carolina performs total RNA and microRNA sequencing.
• New York Genome Center performs methylation arrays and single-cell sequencing.
• Azenta Life Science performs whole exome sequencing.

Additional GCCs with other specialities may be utilized as new molecular technologies become available.

The GCCs send raw sequencing data, associated metadata, and other characterization data generated to the Genomic Data Commons (GDC), where it is shared with the research community.

Genomic Data Commons (GDC): Harmonizes genomic data by applying a standardized set of data processing protocols and bioinformatic pipelines. Resulting data may be utilized by researchers in many ways.

Data generated by the Genome Characterization Pipeline are made available to the public via the GDC for use by researchers worldwide. Some data are released open access while others are controlled access and require users to apply for authentication. 

By bringing harmonized data to one location and increasing accessibility, the GDC aims to accelerate the rate of cancer discoveries and facilitate precision oncology.