SHUGAY, Mikhail, A.R. ZARETSKY, D.A. SHAGIN, I.A. SHAGINA, I.A. VOLCHENKOV, A.A. SHELENKOV, Mikhail LEBEDIN, D.V. BAGAEV, S. LUKYANOV a Dmitriy CHUDAKOV. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Computational Biology. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2017, roč. 13, č. 5, s. nestránkováno, 17 s. ISSN 1553-734X. Dostupné z: https://dx.doi.org/10.1371/journal.pcbi.1005480. |
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@article{1411034, author = {Shugay, Mikhail and Zaretsky, A.R. and Shagin, D.A. and Shagina, I.A. and Volchenkov, I.A. and Shelenkov, A.A. and Lebedin, Mikhail and Bagaev, D.V. and Lukyanov, S. and Chudakov, Dmitriy}, article_location = {SAN FRANCISCO}, article_number = {5}, doi = {http://dx.doi.org/10.1371/journal.pcbi.1005480}, keywords = {CIRCULATING TUMOR DNA; THERAPEUTIC RESPONSE; IMMUNE REPERTOIRES; COLORECTAL-CANCER; SOMATIC MUTATION; SEQUENCING ERROR; RARE MUTATIONS; SOLID TUMORS; GENOME; PLASMA}, language = {eng}, issn = {1553-734X}, journal = {PLoS Computational Biology}, title = {MAGERI: Computational pipeline for molecular-barcoded targeted resequencing}, url = {http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&type=printable}, volume = {13}, year = {2017} }
TY - JOUR ID - 1411034 AU - Shugay, Mikhail - Zaretsky, A.R. - Shagin, D.A. - Shagina, I.A. - Volchenkov, I.A. - Shelenkov, A.A. - Lebedin, Mikhail - Bagaev, D.V. - Lukyanov, S. - Chudakov, Dmitriy PY - 2017 TI - MAGERI: Computational pipeline for molecular-barcoded targeted resequencing JF - PLoS Computational Biology VL - 13 IS - 5 SP - nestránkováno EP - nestránkováno PB - PUBLIC LIBRARY SCIENCE SN - 1553734X KW - CIRCULATING TUMOR DNA KW - THERAPEUTIC RESPONSE KW - IMMUNE REPERTOIRES KW - COLORECTAL-CANCER KW - SOMATIC MUTATION KW - SEQUENCING ERROR KW - RARE MUTATIONS KW - SOLID TUMORS KW - GENOME KW - PLASMA UR - http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&type=printable L2 - http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&type=printable N2 - Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols. ER -
SHUGAY, Mikhail, A.R. ZARETSKY, D.A. SHAGIN, I.A. SHAGINA, I.A. VOLCHENKOV, A.A. SHELENKOV, Mikhail LEBEDIN, D.V. BAGAEV, S. LUKYANOV a Dmitriy CHUDAKOV. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. \textit{PLoS Computational Biology}. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2017, roč.~13, č.~5, s.~nestránkováno, 17 s. ISSN~1553-734X. Dostupné z: https://dx.doi.org/10.1371/journal.pcbi.1005480.
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