The ABRF NGS Study: a multi-platform Assessment of Transcriptome Profiling by RNA-Seq

September 2021 - ABRF NGS Study featured in Nature Biotechnology 
See related story in GenomeWeb.

This online ABRF seminar, produced in collaboration with GenomeWeb, details the results of the first phase of an ongoing study being conducted by ABRF Research Groups that aims to evaluate the performance of six next-generation sequencing platforms: Illumina HiSeq 2000/2500, Illumina MiSeq, Roche 454 GS FLX, Life Technologies Ion Torrent PGM, Life Technologies Ion Torrent Proton, and Pacific Biosciences PacBio RS.





The first phase of the study focused on transcriptome analysis and involved more than 20 core facility laboratories who used standard reference samples from the Microarray Quality Control Consortium to perform replicate RNA‐seq experiments on these platforms. A paper describing the study was recently published in Nature Biotechnology.

This webinar will discuss the findings from this phase, which showed high intra‐platform consistency and inter‐platform concordance for expression measures, but also demonstrated highly variable rates of efficiency and costs for splice isoform detection between platforms. The speakers will also describe a comparison of alternative aligners for each platform, which showed that algorithm choice affects mapping rates and transcript coverage more than gene quantification.

The speakers will also provide an overview of the next phase of the study, which is focused on DNA reference standards, and will discuss the study's goal of establishing a community resource that will allow users of sequencing technologies to easily compare performance data as instruments and protocols change.


  • George Grills, Cornell University, ABRF Executive Board
  • Scott Tighe, University of Vermont, ABRF Nucleic Acid Research Group
  • Christopher Mason, Weill Cornell Medical College, ABRF Genomics Bioinformatics Research Group
  • Don Baldwin, Pathonomics LLC, ABRF Genomics Research Group
  • Marc Salit, National Institute of Standards and Technology

Read the manuscript here!

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.  

Sheng Li, Scott W Tighe, Charles M Nicolet, Deborah Grove, Shawn Levy, William Farmerie, Agnes Viale, Chris Wright, Peter A Schweitzer, Yuan Gao, Dewey Kim, Joe Boland, Belynda Hicks, Ryan Kim, Sagar Chhangawala, Nadereh Jafari, Nalini Raghavachari, Jorge Gandara, Natàlia Garcia-Reyero, Cynthia Hendrickson, David Roberson, Jeffrey A Rosenfeld, Todd Smith, Jason G Underwood, May Wang, Paul Zumbo, Don A Baldwin, George S Grills & Christopher E Mason