Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol
Abstract 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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-08-01
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| Series: | eJHaem |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/jha2.749 |
| _version_ | 1797685617503502336 |
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| author | Guilherme Navarro Nilo Giusti Antonio Vítor Ribeiro Patrícia Yoshioka Jotta Florian Thonier José Andrés Yunes João Meidanis |
| author_facet | Guilherme Navarro Nilo Giusti Antonio Vítor Ribeiro Patrícia Yoshioka Jotta Florian Thonier José Andrés Yunes João Meidanis |
| author_sort | Guilherme Navarro Nilo Giusti |
| collection | DOAJ |
| description | Abstract 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). |
| first_indexed | 2024-03-12T00:46:48Z |
| format | Article |
| id | doaj.art-235af646bb574808a9ffa39c408c8856 |
| institution | Directory Open Access Journal |
| issn | 2688-6146 |
| language | English |
| last_indexed | 2024-03-12T00:46:48Z |
| publishDate | 2023-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | eJHaem |
| spelling | doaj.art-235af646bb574808a9ffa39c408c88562023-09-14T15:30:47ZengWileyeJHaem2688-61462023-08-014377077410.1002/jha2.749Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocolGuilherme Navarro Nilo Giusti0Antonio Vítor Ribeiro1Patrícia Yoshioka Jotta2Florian Thonier3José Andrés Yunes4João Meidanis5Centro de Pesquisa Boldrini Centro Infantil Boldrini CampinasSão PauloBrazilInstituto de Matemática Estatística e Computação Científica Universidade Estadual de Campinas CampinasSão PauloBrazilCentro de Pesquisa Boldrini Centro Infantil Boldrini CampinasSão PauloBrazilCentre Inria Université de Rennes RennesFranceCentro de Pesquisa Boldrini Centro Infantil Boldrini CampinasSão PauloBrazilInstituto de Computação Universidade Estadual de Campinas CampinasSão PauloBrazilAbstract 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).https://doi.org/10.1002/jha2.749immune repertoireimmunoglobulin genesleukemiaminimal residual diseaseT‐cell receptorVidjil |
| spellingShingle | Guilherme Navarro Nilo Giusti Antonio Vítor Ribeiro Patrícia Yoshioka Jotta Florian Thonier José Andrés Yunes João Meidanis Vidjil add‐on for MRD quantification of samples processed using the EuroClonality‐NGS protocol eJHaem immune repertoire immunoglobulin genes leukemia minimal residual disease T‐cell receptor Vidjil |
| 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 | immune repertoire immunoglobulin genes leukemia minimal residual disease T‐cell receptor Vidjil |
| url | https://doi.org/10.1002/jha2.749 |
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