Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Name
nihms-1775951.pdf
Description
Accepted version
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1.33 MB
Format
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Checksum (MD5)
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Author(s)
Gydush, Gregory
Nguyen, Erica
Bae, Jin H
Blewett, Timothy
Rhoades, Justin
Reed, Sarah C
Shea, Douglas
Xiong, Kan
Liu, Ruolin
Yu, Fangyan
Date Issued
March 17, 2022
Journal
Nature Biomedical Engineering
Publisher
Springer Science and Business Media LLC
Citation
Gydush, G., Nguyen, E., Bae, J.H. et al. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nat. Biomed. Eng 6, 257–266 (2022).
Version
Author's final manuscript
Abstract
Assaying for large numbers of low-frequency mutations requires sequencing at extremely high depth and accuracy. Increasing sequencing depth aids the detection of low-frequency mutations yet limits the number of loci that can be simultaneously probed. Here we report a method for the accurate tracking of thousands of distinct mutations that requires substantially fewer reads per locus than conventional hybrid-capture duplex sequencing. The method, which we named MAESTRO (for minor-allele-enriched sequencing through recognition oligonucleotides), combines massively parallel mutation enrichment with duplex sequencing to track up to 10,000 low-frequency mutations, with up to 100-fold fewer reads per locus. We show that MAESTRO can be used to test for chimaerism by tracking donor-exclusive single-nucleotide polymorphisms in sheared genomic DNA from human cell lines, to validate whole-exome sequencing and whole-genome sequencing for the detection of mutations in breast-tumour samples from 16 patients, and to monitor the patients for minimal residual disease via the analysis of cell-free DNA from liquid biopsies. MAESTRO improves the breadth, depth, accuracy and efficiency of mutation testing by sequencing.
MIT Department
Broad Institute of MIT and Harvard
Koch Institute for Integrative Cancer Research at MIT
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Creative Commons Attribution-Noncommercial-ShareAlike
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DOI of Published Version
https://doi.org/10.1038/s41551-022-00855-9
