| Literature DB >> 31344359 |
Galen F Gao1, Joel S Parker2, Sheila M Reynolds3, Tiago C Silva4, Liang-Bo Wang5, Wanding Zhou6, Rehan Akbani7, Matthew Bailey5, Saianand Balu8, Benjamin P Berman9, Denise Brooks10, Hu Chen11, Andrew D Cherniack12, John A Demchok13, Li Ding5, Ina Felau13, Sharon Gaheen14, Daniela S Gerhard13, David I Heiman15, Kyle M Hernandez16, Katherine A Hoadley2, Reyka Jayasinghe17, Anab Kemal13, Theo A Knijnenburg3, Peter W Laird6, Michael K A Mensah13, Andrew J Mungall10, A Gordon Robertson10, Hui Shen6, Roy Tarnuzzer13, Zhining Wang13, Matthew Wyczalkowski5, Liming Yang13, Jean C Zenklusen13, Zhenyu Zhang18, Han Liang19, Michael S Noble20.
Abstract
We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.Entities:
Keywords: DNA methylation; The Cancer Genome Atlas; human reference genome; mRNA expression; microRNA expression; quality control; somatic copy number alteration; somatic mutation
Mesh：
Substances：
Year: 2019 PMID： 31344359 PMCID： PMC6707074 DOI： 10.1016/j.cels.2019.06.006
Source DB: PubMed Journal: Cell Syst ISSN： 2405-4712 Impact factor: 11.091