Large-scale profiling of microRNAs for The Cancer Genome Atlas

Nucleic Acids Res. 2016 Jan 8;44(1):e3. doi: 10.1093/nar/gkv808. Epub 2015 Aug 13.


The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Datasets as Topic
  • Gene Expression Profiling / methods*
  • Genomics / methods*
  • Humans
  • MicroRNAs / genetics*
  • Neoplasms / genetics*


  • MicroRNAs