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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/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).

SUBMITTER: Giusti GNN

PROVIDER: S-EPMC10435716 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Giusti Guilherme Navarro Nilo GNN Ribeiro Antonio Vítor AV Jotta Patrícia Yoshioka PY Thonier Florian F Yunes José Andrés JA Meidanis João J

EJHaem 20230710 3

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, w ...[more]

PMID: 37601854

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