Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol

Assessment of minimal residual disease in acute lymphoblastic leukemia by immune repertoire NGS requires spiking CDR3 sequences at known quantities into the patient's sample. Recently, the EuroClonality‐NGS group released one of the most comprehensive protocols for this purpose. ARResT/Interrog...

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Autores principales: Giusti, Guilherme Navarro Nilo, Ribeiro, Antonio Vítor, Jotta, Patrícia Yoshioka, Thonier, Florian, Yunes, José Andrés, Meidanis, João
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Short Reports
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435716/
https://www.ncbi.nlm.nih.gov/pubmed/37601854
http://dx.doi.org/10.1002/jha2.749
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author Giusti, Guilherme Navarro Nilo
Ribeiro, Antonio Vítor
Jotta, Patrícia Yoshioka
Thonier, Florian
Yunes, José Andrés
Meidanis, João
author_facet Giusti, Guilherme Navarro Nilo
Ribeiro, Antonio Vítor
Jotta, Patrícia Yoshioka
Thonier, Florian
Yunes, José Andrés
Meidanis, João
author_sort Giusti, Guilherme Navarro Nilo
collection PubMed
description Assessment of minimal residual disease in acute lymphoblastic leukemia by immune repertoire NGS requires spiking CDR3 sequences at known quantities into the patient's sample. Recently, the EuroClonality‐NGS group released one of the most comprehensive protocols for this purpose. ARResT/Interrogate is a closed‐source software for processing these NGS libraries, developed by this same group. Vidjil, an open‐source alternative, currently cannot handle libraries prepared using this protocol. Here, we present a Vidjil add‐on to solve this issue. EuroClonality‐NGS prepared samples analyzed with Vidjil and ARResT/Interrogate were highly concordant (r = 0.998) and presented low error (root‐mean‐square error, RMSE = 0.112).
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spelling pubmed-104357162023-08-19 Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol Giusti, Guilherme Navarro Nilo Ribeiro, Antonio Vítor Jotta, Patrícia Yoshioka Thonier, Florian Yunes, José Andrés Meidanis, João EJHaem Short Reports Assessment of minimal residual disease in acute lymphoblastic leukemia by immune repertoire NGS requires spiking CDR3 sequences at known quantities into the patient's sample. Recently, the EuroClonality‐NGS group released one of the most comprehensive protocols for this purpose. ARResT/Interrogate is a closed‐source software for processing these NGS libraries, developed by this same group. Vidjil, an open‐source alternative, currently cannot handle libraries prepared using this protocol. Here, we present a Vidjil add‐on to solve this issue. EuroClonality‐NGS prepared samples analyzed with Vidjil and ARResT/Interrogate were highly concordant (r = 0.998) and presented low error (root‐mean‐square error, RMSE = 0.112). John Wiley and Sons Inc. 2023-07-10 /pmc/articles/PMC10435716/ /pubmed/37601854 http://dx.doi.org/10.1002/jha2.749 Text en © 2023 The Authors. eJHaem published by British Society for Haematology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Short Reports
Giusti, Guilherme Navarro Nilo
Ribeiro, Antonio Vítor
Jotta, Patrícia Yoshioka
Thonier, Florian
Yunes, José Andrés
Meidanis, João
Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title_full Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title_fullStr Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title_full_unstemmed Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title_short Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
title_sort vidjil add‐on for mrd quantification of samples processed using the euroclonality‐ngs protocol
topic Short Reports
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435716/
https://www.ncbi.nlm.nih.gov/pubmed/37601854
http://dx.doi.org/10.1002/jha2.749
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