Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing.
RT-qPCR
leukemia
molecular pathology
next-generation sequencing
Journal
Cancer medicine
ISSN: 2045-7634
Titre abrégé: Cancer Med
Pays: United States
ID NLM: 101595310
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
revised:
29
04
2021
received:
24
07
2020
accepted:
02
05
2021
pubmed:
22
7
2021
medline:
19
2
2022
entrez:
21
7
2021
Statut:
ppublish
Résumé
Comprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B-acute lymphoblastic leukemia (B-ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next-generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B-ALL. We performed RNA NGS and CGAT on 28 B-ALL samples and, in four patients, compared fixed cell pellets to paired cryo-preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis. Among the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT-qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well-known drug resistance implications. We conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.
Sections du résumé
BACKGROUND
Comprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B-acute lymphoblastic leukemia (B-ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next-generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B-ALL.
METHODS
We performed RNA NGS and CGAT on 28 B-ALL samples and, in four patients, compared fixed cell pellets to paired cryo-preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis.
RESULTS
Among the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT-qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well-known drug resistance implications.
CONCLUSIONS
We conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.
Identifiants
pubmed: 34288525
doi: 10.1002/cam4.4101
pmc: PMC8366081
doi:
Substances chimiques
Antineoplastic Agents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5629-5642Subventions
Organisme : Archer Challenge Grant
Informations de copyright
© 2021 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.
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