Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome.

Autor: Reis ALM; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia., Deveson IW; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia., Madala BS; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia., Wong T; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia., Barker C; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia., Xu J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Lennon N; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Mercer TR; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.; Australian Institute for Biotechnology and Nanoengineering, University of Queensland, Brisbane, QLD, Australia.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2022 Jan 12; Vol. 23 (1), pp. 19. Date of Electronic Publication: 2022 Jan 12.
DOI: 10.1186/s13059-021-02579-6
Abstrakt: Background: Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-complexity, and repetitive regions that are difficult to sequence and analyze. Despite their difficulty, these regions include many clinically important sequences that can inform the treatment of human diseases and improve the diagnostic yield of NGS.
Results: To evaluate the accuracy by which these difficult regions are analyzed with NGS, we built an in silico decoy chromosome, along with corresponding synthetic DNA reference controls, that encode difficult and clinically important human genome regions, including repeats, microsatellites, HLA genes, and immune receptors. These controls provide a known ground-truth reference against which to measure the performance of diverse sequencing technologies, reagents, and bioinformatic tools. Using this approach, we provide a comprehensive evaluation of short- and long-read sequencing instruments, library preparation methods, and software tools and identify the errors and systematic bias that confound our resolution of these remaining difficult regions.
Conclusions: This study provides an analytical validation of diagnosis using NGS in difficult regions of the human genome and highlights the challenges that remain to resolve these difficult regions.
(© 2022. The Author(s).)
Databáze: MEDLINE
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