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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data
Galen F Gao1, Joel S Parker2, Sheila M Reynolds3
1Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; The University of Texas Southwestern Medical School, Dallas, TX 75390, USA.
Cell Systems
|July 26, 2019
Summary
This study compares The Cancer Genome Atlas (TCGA) multi-omic data between human reference genomes GRCh37 (hg19) and GRCh38 (hg38). Results show high concordance, guiding optimal use of cancer genomics data.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- The Cancer Genome Atlas (TCGA) is a crucial resource for cancer genomics.
- Updating TCGA data to the latest human reference genome (GRCh38/hg38) is essential for current research.
- Differences between GRCh37 (hg19) and GRCh38 (hg38) can impact biological interpretation.
Purpose of the Study:
- To systematically analyze the impact of synchronizing TCGA multi-omic data to the GRCh38 human reference genome.
- To quantify the concordance between legacy GRCh37 (hg19) and harmonized GRCh38 (hg38) TCGA datasets.
- To provide strategies for mitigating differences and informing the use of TCGA data.
Main Methods:
- Analysis of five TCGA molecular data platforms: mRNA, miRNA, single nucleotide variants, DNA methylation, and copy number alterations.
- Comparison of sample, gene, and probe-level data between GRCh37 (hg19) and GRCh38 (hg38) versions.
- Utilized updated software, pipelines, and annotations for data harmonization.
Main Results:
- Demonstrated high concordance between the GRCh37 (hg19) and GRCh38 (hg38) TCGA datasets.
- Identified specific gene lists highlighting differences post-harmonization.
- Developed strategies to address and mitigate the impact of remaining discrepancies on biological interpretation.
Conclusions:
- The GRCh37 (hg19) and GRCh38 (hg38) TCGA datasets are highly concordant.
- Informed use of both legacy and harmonized TCGA omics data is promoted.
- A framework is provided for future comparisons as new data and reference genomes emerge.
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