Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

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Authors	KNECHT H. REIGL Tomáš KOTROVA M. APPELT F. STEWART P. BYSTRÝ Vojtěch KREJČÍ Adam GRIONI A. PÁL Karol STRÁNSKÁ Kamila PLEVOVÁ Karla RIJNTJES J. SONGIA S. SVATON M. FRONKOVA E. BARTRAM J. SCHEIJEN B. HERRMANN D. GARCIA-SANZ R. HANCOCK J. MOPPETT J. VAN DONGEN J.J.M. CAZZANIGA G. DAVI F. GROENEN P.J.T.A. HUMMEL M. MACINTYRE E.A. STAMATOPOULOS K. TRKA J. LANGERAK A.W. GONZALEZ D. POTT C. BRUGGEMANN M. DARZENTAS Nikos
Year of publication	2019
Type	Article in Periodical
Magazine / Source	Leukemia
MU Faculty or unit	Central European Institute of Technology
Citation
Web	https://www.nature.com/articles/s41375-019-0499-4.pdf
Doi	http://dx.doi.org/10.1038/s41375-019-0499-4
Keywords	MINIMAL RESIDUAL DISEASE; ACUTE LYMPHOBLASTIC-LEUKEMIA; CELL LYMPHOMA; IMMUNOGLOBULIN; PCR; STANDARDIZATION; PRIMERS; RELAPSE; RISK
Description	Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.
Related projects:	CERIT Scientific Cloud Encyklopedie CLL podskupin: unikátní znalostní databáze vybavená bioinformatickými nástroji použitelná v personalizované biomedicíně a klinické praxi