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Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS
- Source :
- Leukemia, Leukemia, 33, 9, pp. 2254-2265, Leukemia, 33(9), 2254-2265. Nature Publishing Group, Digital.CSIC. Repositorio Institucional del CSIC, instname, Leukemia, 33, 2254-2265, Leukemia, 33(9), 2254-2265. NATURE PUBLISHING GROUP, EuroClonality-NGS Working Group 2019, ' Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS ', Leukemia . https://doi.org/10.1038/s41375-019-0499-4
- Publication Year :
- 2019
- Publisher :
- NATURE PUBLISHING GROUP, 2019.
-
Abstract
- 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.<br />This work was supported by Ministry of Health of the Czech Republic, grant no. 16-34272A; computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures”. Analyses in Prague (JT, EF and MS) were supported by Ministry of Health, Czech Republic, grant no. 00064203, and by PRIMUS/17/MED/11. Analyses in the Monza (Centro Ricerca Tettamanti, SS, AG and GC) laboratory were supported by the Italian Association for Cancer Research (AIRC) and Comitato Maria Letizia Verga.
- Subjects :
- 0301 basic medicine
Genetic Markers
Quality Control
Cancer Research
Neoplasm, Residual
Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2]
Receptors, Antigen, T-Cell
Immunoglobulins
Human cell line
Computational biology
Biology
Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9]
DNA sequencing
Article
03 medical and health sciences
0302 clinical medicine
All institutes and research themes of the Radboud University Medical Center
SDG 3 - Good Health and Well-being
Genetic Marker
Genetics research
Immunoglobulin
Humans
Multiplex
Cancer genetics
Gene Rearrangement
Computational Biology
High-Throughput Nucleotide Sequencing
Reproducibility of Results
Hematology
Gene rearrangement
Minimal residual disease
3. Good health
Identification (information)
030104 developmental biology
Oncology
Genetic marker
030220 oncology & carcinogenesis
Primer (molecular biology)
Human
Subjects
Details
- Language :
- English
- ISSN :
- 00064203 and 08876924
- Database :
- OpenAIRE
- Journal :
- Leukemia, Leukemia, 33, 9, pp. 2254-2265, Leukemia, 33(9), 2254-2265. Nature Publishing Group, Digital.CSIC. Repositorio Institucional del CSIC, instname, Leukemia, 33, 2254-2265, Leukemia, 33(9), 2254-2265. NATURE PUBLISHING GROUP, EuroClonality-NGS Working Group 2019, ' Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS ', Leukemia . https://doi.org/10.1038/s41375-019-0499-4
- Accession number :
- edsair.doi.dedup.....de78cda79a5e6031838658ea5f867c70