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Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR

BCOR is an epigenetic regulator altered by various mechanisms including BCOR-internal tandem duplication (BCOR-ITD) in a wide range of cancers. Six different BCOR-ITD in the 3’-part of the coding sequence of exon 15 have been reported ranging from 89 to 114 bp in length. BCOR-ITD is a common genetic...

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Autores principales: Barets, Doriane, Appay, Romain, Heinisch, Marie, Battistella, Maxime, Bouvier, Corinne, Chotard, Guillaume, Le Loarer, François, Macagno, Nicolas, Perbet, Romain, Pissaloux, Daniel, Rousseau, Audrey, Tauziède-Espariat, Arnaud, Varlet, Pascale, Vasiljevic, Alexandre, Colin, Carole, Fina, Frédéric, Figarella-Branger, Dominique
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948083/
https://www.ncbi.nlm.nih.gov/pubmed/33718245
http://dx.doi.org/10.3389/fonc.2021.645512
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author Barets, Doriane
Appay, Romain
Heinisch, Marie
Battistella, Maxime
Bouvier, Corinne
Chotard, Guillaume
Le Loarer, François
Macagno, Nicolas
Perbet, Romain
Pissaloux, Daniel
Rousseau, Audrey
Tauziède-Espariat, Arnaud
Varlet, Pascale
Vasiljevic, Alexandre
Colin, Carole
Fina, Frédéric
Figarella-Branger, Dominique
author_facet Barets, Doriane
Appay, Romain
Heinisch, Marie
Battistella, Maxime
Bouvier, Corinne
Chotard, Guillaume
Le Loarer, François
Macagno, Nicolas
Perbet, Romain
Pissaloux, Daniel
Rousseau, Audrey
Tauziède-Espariat, Arnaud
Varlet, Pascale
Vasiljevic, Alexandre
Colin, Carole
Fina, Frédéric
Figarella-Branger, Dominique
author_sort Barets, Doriane
collection PubMed
description BCOR is an epigenetic regulator altered by various mechanisms including BCOR-internal tandem duplication (BCOR-ITD) in a wide range of cancers. Six different BCOR-ITD in the 3’-part of the coding sequence of exon 15 have been reported ranging from 89 to 114 bp in length. BCOR-ITD is a common genetic alteration found in clear cell sarcoma of the kidney and primitive myxoid mesenchymal tumor of infancy (PMMTI) and it characterizes a new type of central nervous system tumor: “CNS tumor with BCOR-ITD”. It can also be detected in undifferentiated round cell sarcoma (URCS) and in high-grade endometrial stromal sarcoma (HGESS). Therefore, it is of utmost importance to search for this genetic alteration in these cancers with the most frequent technique being RNA-sequencing. Here, we developed a new droplet PCR assay (dPCR) to detect the six sequences characterizing BCOR-ITD. To achieve this goal, we used a single colored probe to detect both the duplicated region and the normal sequence that acts as a reference. We first generated seven synthetic DNA sequences: ITD0 (the normal sequence) and ITD1 to ITD6 (the duplicated sequences described in the literature) and then we set up the optima dPCR conditions. We validated our assay on 19 samples from a representative panel of human tumors (9 HGNET-BCOR, 5 URCS, 3 HGESS, and 2 PMMTI) in which BCOR-ITD status was known using at least one other method including RNA sequencing, RT-PCR or DNA-methylation profiling for CNS tumors. Our results showed that our technique was 100% sensitive and specific. DPCR detected BCOR-ITD in 13/19 of the cases; in the remaining 6 cases additional RNA-sequencing revealed BCOR gene fusions. To conclude, in the era of histomolecular classification of human tumors, our modified dPCR assay is of particular interest to detect BCOR-ITD since it is a robust and less expensive test that can be applied to a broad spectrum of cancers that share this alteration.
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spelling pubmed-79480832021-03-12 Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR Barets, Doriane Appay, Romain Heinisch, Marie Battistella, Maxime Bouvier, Corinne Chotard, Guillaume Le Loarer, François Macagno, Nicolas Perbet, Romain Pissaloux, Daniel Rousseau, Audrey Tauziède-Espariat, Arnaud Varlet, Pascale Vasiljevic, Alexandre Colin, Carole Fina, Frédéric Figarella-Branger, Dominique Front Oncol Oncology BCOR is an epigenetic regulator altered by various mechanisms including BCOR-internal tandem duplication (BCOR-ITD) in a wide range of cancers. Six different BCOR-ITD in the 3’-part of the coding sequence of exon 15 have been reported ranging from 89 to 114 bp in length. BCOR-ITD is a common genetic alteration found in clear cell sarcoma of the kidney and primitive myxoid mesenchymal tumor of infancy (PMMTI) and it characterizes a new type of central nervous system tumor: “CNS tumor with BCOR-ITD”. It can also be detected in undifferentiated round cell sarcoma (URCS) and in high-grade endometrial stromal sarcoma (HGESS). Therefore, it is of utmost importance to search for this genetic alteration in these cancers with the most frequent technique being RNA-sequencing. Here, we developed a new droplet PCR assay (dPCR) to detect the six sequences characterizing BCOR-ITD. To achieve this goal, we used a single colored probe to detect both the duplicated region and the normal sequence that acts as a reference. We first generated seven synthetic DNA sequences: ITD0 (the normal sequence) and ITD1 to ITD6 (the duplicated sequences described in the literature) and then we set up the optima dPCR conditions. We validated our assay on 19 samples from a representative panel of human tumors (9 HGNET-BCOR, 5 URCS, 3 HGESS, and 2 PMMTI) in which BCOR-ITD status was known using at least one other method including RNA sequencing, RT-PCR or DNA-methylation profiling for CNS tumors. Our results showed that our technique was 100% sensitive and specific. DPCR detected BCOR-ITD in 13/19 of the cases; in the remaining 6 cases additional RNA-sequencing revealed BCOR gene fusions. To conclude, in the era of histomolecular classification of human tumors, our modified dPCR assay is of particular interest to detect BCOR-ITD since it is a robust and less expensive test that can be applied to a broad spectrum of cancers that share this alteration. Frontiers Media S.A. 2021-02-25 /pmc/articles/PMC7948083/ /pubmed/33718245 http://dx.doi.org/10.3389/fonc.2021.645512 Text en Copyright © 2021 Barets, Appay, Heinisch, Battistella, Bouvier, Chotard, Le Loarer, Macagno, Perbet, Pissaloux, Rousseau, Tauziède-Espariat, Varlet, Vasiljevic, Colin, Fina and Figarella-Branger http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Oncology
Barets, Doriane
Appay, Romain
Heinisch, Marie
Battistella, Maxime
Bouvier, Corinne
Chotard, Guillaume
Le Loarer, François
Macagno, Nicolas
Perbet, Romain
Pissaloux, Daniel
Rousseau, Audrey
Tauziède-Espariat, Arnaud
Varlet, Pascale
Vasiljevic, Alexandre
Colin, Carole
Fina, Frédéric
Figarella-Branger, Dominique
Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title_full Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title_fullStr Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title_full_unstemmed Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title_short Specific and Sensitive Diagnosis of BCOR-ITD in Various Cancers by Digital PCR
title_sort specific and sensitive diagnosis of bcor-itd in various cancers by digital pcr
topic Oncology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948083/
https://www.ncbi.nlm.nih.gov/pubmed/33718245
http://dx.doi.org/10.3389/fonc.2021.645512
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