Nature Reviews Genetics 12, 87-98 (February 2011) | doi:10.1038/nrg2934

Article series: Applications of next-generation sequencing

RNA sequencing: advances, challenges and opportunities

Fatih Ozsolak1 & Patrice M. Milos1  About the authors


In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.

Author affiliations

  1. Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA.

Correspondence to: Fatih Ozsolak1 Email:

Correspondence to: Patrice M. Milos1 Email:

Published online 30 December 2010