Indel-correcting DNA barcodes for high-throughput sequencing.

Autor:	Hawkins JA; Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712.; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712., Jones SK Jr; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712., Finkelstein IJ; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712., Press WH; Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.; Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712.
Jazyk:	angličtina
Zdroj:	Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2018 Jul 03; Vol. 115 (27), pp. E6217-E6226. Date of Electronic Publication: 2018 Jun 20.
DOI:	10.1073/pnas.1802640115
Abstrakt:	Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate filled/truncated right end edit (FREE) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced guanine-cytosine (GC) content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error correction levels that may be useful in diverse high-throughput applications, including >10 6 single-error-correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with >10 15 error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community. Competing Interests: The authors declare no conflict of interest. (Copyright © 2018 the Author(s). Published by PNAS.)
Databáze:	MEDLINE
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