TCGA Tissue Sample Requirements: High Quality Requirements Yield High Quality Data
The Cancer Genome Atlas’s (TCGA) strict sample criteria yielded high data quality. These are some of the standards that TCGA followed in acquiring and working with tissue samples.
- TCGA followed the principle of ‘no platform left behind’
- TCGA worked to ensure all research groups would have equal access to TCGA data, and so adopted the principle that no platform will be left behind. This means that every sample needed be analyzed through each platform. Therefore, a sufficient sized sample was crucial to the TCGA pipeline.
- For that reason, a resection sample was required as opposed to a biopsy sample. Biopsies could have not provided enough material (tissue) for the extracted RNA and DNA to be studied across all platforms.
- Second-generation sequencing platforms facilitated use of more heterogeneous samples
- Previously, tumor samples needed to be composed of at least 80 percent tumor nuclei. In other words, 80 percent of the cells in the sample were required to be cancer cells. However, with the advent of more powerful sequencing technology, termed second-generation sequencing platforms, TCGA became able to investigate samples with only 60 percent tumor nuclei. By decreasing the lower boundary, more samples qualified for the TCGA program, including higher numbers of samples from heterogeneous tumors such as pancreatic adenocarcinoma and diffuse gastric cancer. TCGA found that 60 percent was sufficient to generate high quality data in which the tumor’s signal could be distinguished from other cells’ signals.
- Neoadjuvant treatment was not allowable
- TCGA's goal was to accelerate the understanding of the underlying genomics of primary, untreated tumors. Cancer treatment can involve mutagens or carcinogens which could cloud the origin of the cancer.
- Sample from primary tumor was necessary
- A primary tumor is the tumor at the initial site of cancer, not where the cancer may have spread or metastasized, called the secondary tumor. TCGA only studied secondary tumors if they matched to a primary as part of a series (germline, primary and metastasis), or in tumor types for which the primary tumor is rarely diagnosed (such as in melanoma).
- Tumor samples were paired with a source of germline DNA
- TCGA required a second sample, discrete from the primary tumor, from the same patient. Most often, this sample came from blood to avoid any potential field effects in solid tumors, though some solid tumor normal samples were characterized. The matched sample allows researchers to compare the tumor sample to the germline DNA. In other words, the blood or germline sample serves as a normal comparison of the tumor’s genome.
- Biospecimens were frozen
- TCGA only characterized samples that were frozen soon after surgery to prevent degradation of the RNA and DNA. FFPE (formalin fixed paraffin embedded) samples were not used because of potential changes to the RNA and DNA that may arise from the fixation process.