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16 results on '"Bystry V"'

1. STAT3 and TP53 mutations associate with poor prognosis in anaplastic large cell lymphoma

Author

Lobello, C, Tichy, B, Bystry, V, Radova, L, Filip, D, Mraz, M, Montes-Mojarro, I, Prokoph, N, Larose, H, Liang, H, Sharma, G, Mologni, L, Belada, D, Kamaradova, K, Fend, F, Gambacorti Passerini, C, Merkel, O, Turner, S, Janikova, A, Pospisilova, S, Lobello C., Tichy B., Bystry V., Radova L., Filip D., Mraz M., Montes-Mojarro I. -A., Prokoph N., Larose H., Liang H. -C., Sharma G. G., Mologni L., Belada D., Kamaradova K., Fend F., Gambacorti Passerini C., Merkel O., Turner S. D., Janikova A., Pospisilova S., Lobello, C, Tichy, B, Bystry, V, Radova, L, Filip, D, Mraz, M, Montes-Mojarro, I, Prokoph, N, Larose, H, Liang, H, Sharma, G, Mologni, L, Belada, D, Kamaradova, K, Fend, F, Gambacorti Passerini, C, Merkel, O, Turner, S, Janikova, A, Pospisilova, S, Lobello C., Tichy B., Bystry V., Radova L., Filip D., Mraz M., Montes-Mojarro I. -A., Prokoph N., Larose H., Liang H. -C., Sharma G. G., Mologni L., Belada D., Kamaradova K., Fend F., Gambacorti Passerini C., Merkel O., Turner S. D., Janikova A., and Pospisilova S.

Published
2021

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

Author

Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, J, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Trka, J, Langerak, A, Gonzalez, D, Pott, C, Bruggemann, M, Darzentas, N, Knecht H., Reigl T., Kotrova M., Appelt F., Stewart P., Bystry V., Krejci A., Grioni A., Pal K., Stranska K., Plevova K., 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 N., Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, J, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Trka, J, Langerak, A, Gonzalez, D, Pott, C, Bruggemann, M, Darzentas, N, Knecht H., Reigl T., Kotrova M., Appelt F., Stewart P., Bystry V., Krejci A., Grioni A., Pal K., Stranska K., Plevova K., 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., and Darzentas N.

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.

Published
2019

3. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Author

Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, J, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, A, Bruggemann M., Kotrova M., Knecht H., Bartram J., Boudjogrha M., Bystry V., Fazio G., Fronkova E., Giraud M., Grioni A., Hancock J., Herrmann D., Jimenez C., Krejci A., Moppett J., Reigl T., Salson M., Scheijen B., Schwarz M., Songia S., Svaton M., van Dongen J. J. M., Villarese P., Wakeman S., Wright G., Cazzaniga G., Davi F., Garcia-Sanz R., Gonzalez D., Groenen P. J. T. A., Hummel M., Macintyre E. A., Stamatopoulos K., Pott C., Trka J., Darzentas N., Langerak A. W., Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, J, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, A, Bruggemann M., Kotrova M., Knecht H., Bartram J., Boudjogrha M., Bystry V., Fazio G., Fronkova E., Giraud M., Grioni A., Hancock J., Herrmann D., Jimenez C., Krejci A., Moppett J., Reigl T., Salson M., Scheijen B., Schwarz M., Songia S., Svaton M., van Dongen J. J. M., Villarese P., Wakeman S., Wright G., Cazzaniga G., Davi F., Garcia-Sanz R., Gonzalez D., Groenen P. J. T. A., Hummel M., Macintyre E. A., Stamatopoulos K., Pott C., Trka J., Darzentas N., and Langerak A. W.

Abstract

Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0–14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0–14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.

Published
2019

4. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Author

Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, J, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, A, Bruggemann M., Kotrova M., Knecht H., Bartram J., Boudjogrha M., Bystry V., Fazio G., Fronkova E., Giraud M., Grioni A., Hancock J., Herrmann D., Jimenez C., Krejci A., Moppett J., Reigl T., Salson M., Scheijen B., Schwarz M., Songia S., Svaton M., van Dongen J. J. M., Villarese P., Wakeman S., Wright G., Cazzaniga G., Davi F., Garcia-Sanz R., Gonzalez D., Groenen P. J. T. A., Hummel M., Macintyre E. A., Stamatopoulos K., Pott C., Trka J., Darzentas N., Langerak A. W., Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, J, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, A, Bruggemann M., Kotrova M., Knecht H., Bartram J., Boudjogrha M., Bystry V., Fazio G., Fronkova E., Giraud M., Grioni A., Hancock J., Herrmann D., Jimenez C., Krejci A., Moppett J., Reigl T., Salson M., Scheijen B., Schwarz M., Songia S., Svaton M., van Dongen J. J. M., Villarese P., Wakeman S., Wright G., Cazzaniga G., Davi F., Garcia-Sanz R., Gonzalez D., Groenen P. J. T. A., Hummel M., Macintyre E. A., Stamatopoulos K., Pott C., Trka J., Darzentas N., and Langerak A. W.

Abstract

Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0–14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0–14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.

Published
2019

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

Author

Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, J, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Trka, J, Langerak, A, Gonzalez, D, Pott, C, Bruggemann, M, Darzentas, N, Knecht H., Reigl T., Kotrova M., Appelt F., Stewart P., Bystry V., Krejci A., Grioni A., Pal K., Stranska K., Plevova K., 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 N., Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, J, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Trka, J, Langerak, A, Gonzalez, D, Pott, C, Bruggemann, M, Darzentas, N, Knecht H., Reigl T., Kotrova M., Appelt F., Stewart P., Bystry V., Krejci A., Grioni A., Pal K., Stranska K., Plevova K., 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., and Darzentas N.

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.

Published
2019

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

Author

Knecht, H., Reigl, T., Kotrova, M, Appelt, F., Stewart, P., Bystry, V., Krejčí, A. (Alena), Grioni, A., Pal, K. (Karin) van der, Stranska, K., Plevova, K. (K.), Rijntjes, J., Songia, S., Svaton, M., Fronkova, E., Bartram, J., Scheijen, B. (Blanca), Herrmann, D., Garcia-Sanz, R. (Ramon), Hancock, J., Moppett, J. (John), van Dongen, JJM, Cazzaniga, G. (Gianni), Davi, F. (Frédéric), Groenen, P., Hummel, M. (Michael), Macintyre, E.A. (Elizabeth), Stamatopoulos, K. (Kostas), Trka, J. (Jan), Langerak, A.W. (Anton), Gonzalez, D., Pott, C. (Christiane), Bruggemann, M, Darzentas, N. (Nikos), Knecht, H., Reigl, T., Kotrova, M, Appelt, F., Stewart, P., Bystry, V., Krejčí, A. (Alena), Grioni, A., Pal, K. (Karin) van der, Stranska, K., Plevova, K. (K.), Rijntjes, J., Songia, S., Svaton, M., Fronkova, E., Bartram, J., Scheijen, B. (Blanca), Herrmann, D., Garcia-Sanz, R. (Ramon), Hancock, J., Moppett, J. (John), van Dongen, JJM, Cazzaniga, G. (Gianni), Davi, F. (Frédéric), Groenen, P., Hummel, M. (Michael), Macintyre, E.A. (Elizabeth), Stamatopoulos, K. (Kostas), Trka, J. (Jan), Langerak, A.W. (Anton), Gonzalez, D., Pott, C. (Christiane), Bruggemann, M, and Darzentas, N. (Nikos)

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.

Published
2019
Full Text
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7. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Author

Bruggemann, M, Kotrova, M, Knecht, H., Bartram, J., Boudjogrha, M., Bystry, V., Fazio, G., Fronkova, E., Giraud, M., Grioni, A., Hancock, J., Herrmann, D., Jimenez, C. (Cecilia), Krejčí, A. (Alena), Moppett, J. (John), Reigl, T., Salson, M., Scheijen, B. (Blanca), Schwarz, M. (Michael), Songia, S., Svaton, M., van Dongen, JJM, Villarese, P. (Patrick), Wakeman, S., Wright, G, Cazzaniga, G. (Gianni), Davi, F. (Frédéric), Garcia-Sanz, R. (Ramon), Gonzalez, D., Groenen, P., Hummel, M. (Michael), Macintyre, E.A. (Elizabeth), Stamatopoulos, K. (Kostas), Pott, C. (Christiane), Trka, J. (Jan), Darzentas, N. (Nikos), Langerak, A.W. (Anton), Bruggemann, M, Kotrova, M, Knecht, H., Bartram, J., Boudjogrha, M., Bystry, V., Fazio, G., Fronkova, E., Giraud, M., Grioni, A., Hancock, J., Herrmann, D., Jimenez, C. (Cecilia), Krejčí, A. (Alena), Moppett, J. (John), Reigl, T., Salson, M., Scheijen, B. (Blanca), Schwarz, M. (Michael), Songia, S., Svaton, M., van Dongen, JJM, Villarese, P. (Patrick), Wakeman, S., Wright, G, Cazzaniga, G. (Gianni), Davi, F. (Frédéric), Garcia-Sanz, R. (Ramon), Gonzalez, D., Groenen, P., Hummel, M. (Michael), Macintyre, E.A. (Elizabeth), Stamatopoulos, K. (Kostas), Pott, C. (Christiane), Trka, J. (Jan), Darzentas, N. (Nikos), and Langerak, A.W. (Anton)

Abstract

Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was

Published
2019
Full Text
View/download PDF

8. A simple RNA target capture NGS strategy for fusion genes assessment in the diagnostics of pediatric B-cell acute lymphoblastic leukemia

Author

Grioni, A, Fazio, G, Rigamonti, S, Bystry, V, Daniele, G, Dostalova, Z, Quadri, M, Saitta, C, Silvestri, D, Songia, S, Storlazzi, C, Biondi, A, Darzentas, N, Cazzaniga, G, Grioni, Andrea, Fazio, Grazia, Rigamonti, Silvia, Bystry, Vojtech, Daniele, Giulia, Dostalova, Zuzana, Quadri, Manuel, Saitta, Claudia, Silvestri, Daniela, Songia, Simona, Storlazzi, Clelia T., Biondi, Andrea, Darzentas, Nikos, Cazzaniga, Giovanni, Grioni, A, Fazio, G, Rigamonti, S, Bystry, V, Daniele, G, Dostalova, Z, Quadri, M, Saitta, C, Silvestri, D, Songia, S, Storlazzi, C, Biondi, A, Darzentas, N, Cazzaniga, G, Grioni, Andrea, Fazio, Grazia, Rigamonti, Silvia, Bystry, Vojtech, Daniele, Giulia, Dostalova, Zuzana, Quadri, Manuel, Saitta, Claudia, Silvestri, Daniela, Songia, Simona, Storlazzi, Clelia T., Biondi, Andrea, Darzentas, Nikos, and Cazzaniga, Giovanni

Abstract

Acute lymphoblastic leukemia (ALL) is the most frequent pediatric cancer. Fusion genes are hallmarks of ALL, and they are used as biomarkers for risk stratification as well as targets for precision medicine. Hence, clinical diagnostics pursues broad and comprehensive strategies for accurate discovery of fusion genes. Currently, the gold standard methodologies for fusion gene detection are fluorescence in situ hybridization and polymerase chain reaction; these, however, lack sensitivity for the identification of new fusion genes and breakpoints. In this study, we implemented a simple operating procedure (OP) for detecting fusion genes. The OP employs RNA CaptureSeq, a versatile and effortless next-generation sequencing assay, and an in-house as well as a purpose-built bioinformatics pipeline for the subsequent data analysis. The OP was evaluated on a cohort of 89 B-cell precursor ALL (BCP-ALL) pediatric samples annotated as negative for fusion genes by the standard techniques. The OP confirmed 51 samples as negative for fusion genes, and, more importantly, it identified known (KMT2A rearrangements) as well as new fusion events (JAK2 rearrangements) in the remaining 38 investigated samples, of which 16 fusion genes had prognostic significance. Herein, we describe the OP and its deployment into routine ALL diagnostics, which will allow substantial improvements in both patient risk stratification and precision medicine.

Published
2019

9. First evidence of a paediatric patient with Cornelia de Lange syndrome with acute lymphoblastic leukaemia

Author

Fazio, G, Massa, V, Grioni, A, Bystry, V, Rigamonti, S, Saitta, C, Galbiati, M, Rizzari, C, Consarino, C, Biondi, A, Selicorni, A, Cazzaniga, G, Fazio, Grazia, Massa, Valentina, GRIONI, ANDREA, Bystry, Vojtech, Rigamonti, Silvia, Saitta, Claudia, Galbiati, Marta, Rizzari, Carmelo, Consarino, Caterina, Biondi, Andrea, Selicorni, Angelo, Cazzaniga, Giovanni, Fazio, G, Massa, V, Grioni, A, Bystry, V, Rigamonti, S, Saitta, C, Galbiati, M, Rizzari, C, Consarino, C, Biondi, A, Selicorni, A, Cazzaniga, G, Fazio, Grazia, Massa, Valentina, GRIONI, ANDREA, Bystry, Vojtech, Rigamonti, Silvia, Saitta, Claudia, Galbiati, Marta, Rizzari, Carmelo, Consarino, Caterina, Biondi, Andrea, Selicorni, Angelo, and Cazzaniga, Giovanni

Abstract

Cornelia de Lange syndrome (CdLS) is a rare autosomal-dominant genetic disorder characterised by prenatal and postnatal growth and mental retardation, facial dysmorphism and upper limb abnormalities. Germline mutations of cohesin complex genes SMC1A, SMC3, RAD21 or their regulators NIPBL and HDAC8 have been identified in CdLS as well as somatic mutations in myeloid disorders. We describe the first case of a paediatric patient with CdLS with B-cell precursor Acute Lymphoblastic Leukaemia (ALL). The patient did not show any unusual cytogenetic abnormality, and he was enrolled into the high risk arm of AIEOP-BFM ALL2009 protocol because of slow early response, but 3 years after discontinuation, he experienced an ALL relapse. We identified a heterozygous mutation in exon 46 of NIPBL, causing frameshift and a premature stop codon (RNA-Targeted Next generation Sequencing Analysis). The analysis of the family indicated a de novo origin of this previously not reported deleterious variant. As for somatic cohesin mutations in acute myeloid leukaemia, also this ALL case was not affected by aneuploidy, thus suggesting a major impact of the non-canonical role of NIPBL in gene regulation. A potential biological role of NIPBL in leukaemia has still to be dissected.

Published
2019

10. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Author

Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, JJM, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, EA, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, Ton, Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, JJM, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, EA, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, and Langerak, Ton

Published
2019

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

Author

Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, van der Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, JJM, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, EA, Stamatopoulos, K, Trka, J, Langerak, Ton, Gonzalez, D, Pott, C, Bruggemann, M, Darzentas, N, Knecht, H, Reigl, T, Kotrova, M, Appelt, F, Stewart, P, Bystry, V, Krejci, A, Grioni, A, van der Pal, K, Stranska, K, Plevova, K, Rijntjes, J, Songia, S, Svaton, M, Fronkova, E, Bartram, J, Scheijen, B, Herrmann, D, Garcia-Sanz, R, Hancock, J, Moppett, J, van Dongen, JJM, Cazzaniga, G, Davi, F, Groenen, P, Hummel, M, Macintyre, EA, Stamatopoulos, K, Trka, J, Langerak, Ton, Gonzalez, D, Pott, C, Bruggemann, M, and Darzentas, N

Published
2019

12. ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data

Author

Bystry, V., Reigl, T., Krejci, A., Demko, M., Hanakova, B., Grioni, A., Knecht, H., Schlitt, M., Dreger, P., Sellner, L., Herrmann, D., Pingeon, M., Boudjoghra, M., Rijntjes, J., Pott, C., Langerak, A.W., Groenen, P.J.T.A., Davi, F., Bruggemann, M., Darzentas, N., Bystry, V., Reigl, T., Krejci, A., Demko, M., Hanakova, B., Grioni, A., Knecht, H., Schlitt, M., Dreger, P., Sellner, L., Herrmann, D., Pingeon, M., Boudjoghra, M., Rijntjes, J., Pott, C., Langerak, A.W., Groenen, P.J.T.A., Davi, F., Bruggemann, M., and Darzentas, N.

Abstract

Item does not contain fulltext

Published
2017

13. ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data

Author

Bystry, V., Reigl, T., Krejci, A., Demko, M., Hanakova, B., Grioni, A., Knecht, H., Schlitt, M., Dreger, P., Sellner, L., Herrmann, D., Pingeon, M., Boudjoghra, M., Rijntjes, J., Pott, C., Langerak, A.W., Groenen, P.J.T.A., Davi, F., Bruggemann, M., Darzentas, N., Bystry, V., Reigl, T., Krejci, A., Demko, M., Hanakova, B., Grioni, A., Knecht, H., Schlitt, M., Dreger, P., Sellner, L., Herrmann, D., Pingeon, M., Boudjoghra, M., Rijntjes, J., Pott, C., Langerak, A.W., Groenen, P.J.T.A., Davi, F., Bruggemann, M., and Darzentas, N.

Abstract

Item does not contain fulltext

Published
2017

15. HIGHER-ORDER IMMUNOGLOBULIN SEQUENCE RELATIONS FOR MAJOR SUBSETS OF CHRONIC LYMPHOCYTIC LEUKEMIA : UNIQUENESS VERSUS EQUIVALENCE

Author

Agathangelidis, A., Bystry, V., Hadzidimitriou, A., Sutton, L. A., Minga, E., Kienle, D., Davis, Z., Yan, X. J., Shanafelt, T., Boudjogra, M., Plevova, K., Gounari, M., Xochelli, A., Navarro, A., Chatzouli, M., Pedersen, L. B., Baliakas, Panagiotis, Scarfo, L., Rossi, D., Veronese, S., Facco, M., Bikos, V., Karan-Djurasevic, T., Pavlovic, S., Mansouri, Larry, Poiron, C., Chu, C. C., Stalika, E., Giudicelli, V., Panagiotidis, P., Sudarikov, A., Anagnostopoulos, A., Trentin, L., Catherwood, M., Montillo, M., Gaidano, G., Campo, E., Geisler, C. H., Langerak, A. W., Pospisilova, S., Lefranc, M. P., Chiorazzi, N., Oscier, D., Jelinek, D. F., Stilgenbauer, S., Belessi, C., Davi, F., Rosenquist, Richard, Ghia, P., Darzentas, N., Stamatopoulos, Kostas, Agathangelidis, A., Bystry, V., Hadzidimitriou, A., Sutton, L. A., Minga, E., Kienle, D., Davis, Z., Yan, X. J., Shanafelt, T., Boudjogra, M., Plevova, K., Gounari, M., Xochelli, A., Navarro, A., Chatzouli, M., Pedersen, L. B., Baliakas, Panagiotis, Scarfo, L., Rossi, D., Veronese, S., Facco, M., Bikos, V., Karan-Djurasevic, T., Pavlovic, S., Mansouri, Larry, Poiron, C., Chu, C. C., Stalika, E., Giudicelli, V., Panagiotidis, P., Sudarikov, A., Anagnostopoulos, A., Trentin, L., Catherwood, M., Montillo, M., Gaidano, G., Campo, E., Geisler, C. H., Langerak, A. W., Pospisilova, S., Lefranc, M. P., Chiorazzi, N., Oscier, D., Jelinek, D. F., Stilgenbauer, S., Belessi, C., Davi, F., Rosenquist, Richard, Ghia, P., Darzentas, N., and Stamatopoulos, Kostas

Published
2015

16. Higher-order immunoglobulin sequence relations for major subsets of chronic lymphocytic leukemia: uniqueness versus equivalence

Author

Agathangelidis, Andreas, Bystry, V., Hadzidimitriou, A., Sutton, L. A., Minga, Eva, Kienle, D., Davis, Z., Yan, X. J., Shanafelt, T., Boudjogra, M., Plevova, K., Gounari, M., Xochelli, A., Navarro, A., Chatzouli, M., Pedersen, L. B., Baliakas, Panagiotis, Scarfo, L., Rossi, D., Veronese, S., Facco, M., Bikos, V., Karan-Đurašević, Teodora, Pavlović, S., Mansouri, L., Poiron, C., Chu, C. C., Stalika, E., Giudicelli, V., Panagiotidis, P., Sudarikov, A., Anagnostopoulos, Achilles, Trentin, L., Catherwood, M., Montillo, M., Gaidano, G., Campo, E., Geisler, C. H., Langerak, A. W., Pospisilova, S., Lefranc, M. P., Chiorazzi, N., Oscier, D., Jelinek, D. F., Stilgenbauer, S., Belessi, C., Davi, F., Rosenquist, R., Ghia, P., Darzentas, N., Stamatopoulos, K., Agathangelidis, Andreas, Bystry, V., Hadzidimitriou, A., Sutton, L. A., Minga, Eva, Kienle, D., Davis, Z., Yan, X. J., Shanafelt, T., Boudjogra, M., Plevova, K., Gounari, M., Xochelli, A., Navarro, A., Chatzouli, M., Pedersen, L. B., Baliakas, Panagiotis, Scarfo, L., Rossi, D., Veronese, S., Facco, M., Bikos, V., Karan-Đurašević, Teodora, Pavlović, S., Mansouri, L., Poiron, C., Chu, C. C., Stalika, E., Giudicelli, V., Panagiotidis, P., Sudarikov, A., Anagnostopoulos, Achilles, Trentin, L., Catherwood, M., Montillo, M., Gaidano, G., Campo, E., Geisler, C. H., Langerak, A. W., Pospisilova, S., Lefranc, M. P., Chiorazzi, N., Oscier, D., Jelinek, D. F., Stilgenbauer, S., Belessi, C., Davi, F., Rosenquist, R., Ghia, P., Darzentas, N., and Stamatopoulos, K.

Published
2015

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