International Standards for Genomes, Transcriptomes, and Metagenomes.
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine.
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, USA;; Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA.
Christopher E
CE
Mason
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, USA;; School of Medicine, New York Medical College, Valhalla, New York 10595, USA.
Ebrahim
E
Afshinnekoo
Advanced Genomics Lab, University of Vermont Cancer Center, Burlington, Vermont 05405, USA.
Scott
S
Tighe
Hangzhou Cancer Institute in Hangzhou Cancer Hospital, Hangzhou, China; and.
Shixiu
S
Wu
HudsonAlpha Institute of Technology, Huntsville, Alabama 35806, USA.
Shawn
S
Levy
D000818:Animals; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D020869:Gene Expression Profiling / Q000592:standards*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards; D006801:Humans; D054892:Metagenome; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000592:standards; D012984:Software; D059467:Transcriptome
D004247:DNA
epigenomics; epitranscriptomics; genomics; metagenomics; transcriptomics