September 29, 2014

The ABRF NGS Study: A Multi-Platform Assessment of Transcriptome Profiling by RNA-Seq


This online seminar details the results of the first phase of an ongoing study being conducted by the Association of Biomolecular Resource Facilities' 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

Jay Shendure and his colleagues have developed a new method to more comprehensively identify human cell types, the NY Times reports.

Researchers in the UK and Japan have shown that infertility in mice with three sex chromosomes can be overcome, according to the Guardian.

China is embracing preimplantation genetic diagnosis, Nature News reports. 

In PLOS this week: host genetic factors associated with cervical neoplasia progression, population patterns for an ancient flowering rainforest plant, and more.

Sponsored by
Ion Torrent

This webinar will discuss how next-generation sequencing (NGS) can help clinical research labs and pathologists save time, money, and samples compared to single-analyte oncology research assays.