Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Next-generation sequencing (NGS) has revolutionized genomic research by enabling high-throughput, cost-effective genome and transcriptome sequencing accelerating personalized medicine for complex diseases, including cancer. Whole genome/transcriptome sequencing (WGS/WTS) provides comprehensive insights, while targeted sequencing is more cost-effective and sensitive. In comparison to short-read sequencing, which still dominates the field due to high speed and cost-effectiveness, long-read sequencing can overcome alignment limitations and better discriminate similar sequences from alternative transcripts or repetitive regions. Hybrid sequencing combines the best strengths of different technologies for a more comprehensive view of genomic/transcriptomic variations. Understanding each technology's strengths and limitations is critical for translating cutting-edge technologies into clinical applications. In this study, we sequenced DNA and RNA libraries of reference samples using various targeted DNA and RNA panels and the whole transcriptome on both short-read and long-read platforms. This study design enables a comprehensive analysis of sequencing technologies, targeting protocols, and library preparation methods. Our expanded profiling landscape establishes a reference point for assessing current sequencing technologies, facilitating informed decision-making in genomic research and precision medicine.
Authors
- Rebecca Kusko (ORCID: https://orcid.org/0000-0001-6730-5990)
- Wenzhong Xiao (ORCID: https://orcid.org/0000-0003-4944-6380)
- Joshua Xu (ORCID: https://orcid.org/0000-0001-5313-5847)
- Scott Happe
- Carlos Pabón-Peña
- Paweł P. Łabaj (ORCID: https://orcid.org/0000-0002-4994-0234)
- Anne Bergstrom Lucas
- Jennifer S. LoCoco (ORCID: https://orcid.org/0000-0002-7437-5177)
- Michael Salmans
- Binsheng Gong (ORCID: https://orcid.org/0000-0002-8724-5435)
- Guangchun Chen
- Elizabeth Tseng (ORCID: https://orcid.org/0000-0002-1074-5095)
- Donald J. Johann
- Bohu Pan (ORCID: https://orcid.org/0000-0003-2812-3718)
- Wendell Jones (ORCID: https://orcid.org/0000-0002-9676-5387)
- Weida Tong (ORCID: https://orcid.org/0000-0003-3488-6148)
- Hagen Tilgner (ORCID: https://orcid.org/0000-0002-7058-3606)
- Todd Richmond (ORCID: https://orcid.org/0000-0003-1508-6540)
- Danielle Thierry‐Mieg (ORCID: https://orcid.org/0000-0001-9568-4211)
- Jean Thierry‐Mieg (ORCID: https://orcid.org/0000-0002-0396-6789)
- David P. Kreil (ORCID: https://orcid.org/0000-0001-7538-2056)
- Natalia Novoradovskaya
- Christopher E. Mason (ORCID: https://orcid.org/0000-0002-1850-1642)
- Tim R. Mercer (ORCID: https://orcid.org/0000-0001-8780-894X)
- Dan Li (ORCID: https://orcid.org/0000-0001-8675-2139)
Institutions
- Institute of Molecular Biotechnology (AT)
- Jagiellonian University (PL)
- National Institutes of Health (US)
- National Center for Toxicological Research (US)
- United States Food and Drug Administration (US)
- Harvard University (US)
- Agilent Technologies (United States) (US)
- The University of Queensland (AU)
- Illumina (United States) (US)
- Cornell University (US)
- Massachusetts General Hospital (US)
- MIND Research Institute (US)
- Center for Neuro-Oncology (US)
- National Center for Biotechnology Information (US)
- Winthrop Rockefeller Foundation (US)
- Weill Cornell Medicine (US)
- Pacific Biosciences (United States) (US)
- University of Arkansas for Medical Sciences (US)
- The University of Texas Southwestern Medical Center (US)
- BOKU University (AT)
- Stanford University (US)
Publication Details
- Journal
- Scientific Data
- Published
- 2024-08-16
- DOI
- https://doi.org/10.1038/s41597-024-03741-y
- Citations
- 7
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.64
Funders
- National Institutes of Health
- U.S. Food and Drug Administration
- U.S. National Library of Medicine