The goals of the ABRF-NGS Study are to evaluate the performance of NGS platforms and to identify optimal methods and best practices. The study is a coordinated effort of five ABRF Research Groups (RG’s), involving over 20 core facility laboratories. The long-term goals of the ABRF-NGS study are to help optimize the detection of genetic variation with the latest sequencing tools and to establish a community resource for self-evaluation and self-improvement that will allow users of NGS technologies to readily compare and improve their own performance data and to evaluate existing and emerging protocols and platforms.
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
Nature Biotechnology 32(9):915-925
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
The ABRF-NGS Study is a collaboration between the DNA Sequencing Research Group (DSRG), Genomics Research Group (GRG), Nucleic Acid Research Group (NARG), Biomedical ‘Omics Research Group (BORG), and Genomics Bioinformatics Research Group (GBIRG).
The ABRF-NGS leadership group consists of scientific leads, project coordinators, and the chairs of all the RG’s that are involved in the study. Chris Mason (Weill Cornell Medical College; GBIRG) and Don Baldwin (Pathonomics LLC; GRG) are the scientific leads for the study. George Grills (Cornell University; EB), Charles Nicolet (University of Southern California; DSRG) and Scott Tighe (University of Vermont; NARG) are the project coordinators. Platform working groups focus on platform-specific protocols and generate data at core laboratory sites. A bioinformatics/bio-IT working group is focused on the analytical tools and approaches for each phase of the study and on the challenges of building a web-based community database resource.
Phase 1 of the ABRF-NGS Study focused on RNA sequencing (RNA-seq), using standard Microarray Quality Control Consortium (MAQC) total RNA samples combined with External RNA Controls Consortium (ERCC) synthetic spike-in RNA. This RNA profiling phase of the ABRF-NGS Study included the Illumina HiSeq 2000/2500 and MiSeq, Roche 454 GS FLX+, Life Technologies Ion Torrent PGM and Proton, and Pacific Biosciences PacBio RS platforms. The study assessed sequencing accuracy, absolute and relative expression levels, RNA splice junction detection, and differential expression detection between samples. In a similar fashion, the currently ongoing Phase 2 of the ABRF-NGS Study is collaborating with the NIST Genome in a Bottle Consortium and other sequencing community stakeholders to utilize standardized reference genomic DNA samples.
Phase 1 participants included Christopher Mason (Weill Cornell Medical College), Don Baldwin (Pathonomics, LLC), Scott Tighe (University of Vermont), Charles Nicolet (University of Southern California), George Grills (Cornell University), Kip Bodi (Tufts University), Joe Boland (NIH/NCI/SAIC-Frederick), William Farmerie (University of Florida), Yuan (Gary) Gao (Lieber Institute for Brain Development), Deb Grove (Penn State University), Belynda Hicks (NCI/SAIC-Frederick), Amy Hutchinson (NIH/NCI/SAIC-Frederick), Nadereh Jafari (Northwestern University), Dewey Kim (Johns Hopkins University), Ryan Kim (UC Davis), Shawn Levy (HudsonAlpha Institute), Sheng Li (Weill Cornell Medical College), Dawei Lin (University of California at Davis), Dayna Oschwald (New York Genome Center), Anoja Perera (Stowers Institute for Medical Research), Jaroslaw Pillardy (Cornell University), Nalini Raghavachari (NIH/NHLBI), Jeffrey Rosenfeld (University of Medicine and Dentistry of New Jersey), Peter Schweitzer (Cornell University), Todd Smith (Perkin Elmer/Geospiza), Agnes Viale (Memorial Sloan-Kettering Cancer Institute), and Chris Wright (University of Illinois).