Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing
Abstract 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 FusionPle...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2021-08-01
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| Series: | Cancer Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/cam4.4101 |
| _version_ | 1818889025653571584 |
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| author | Cecilia Yeung Xiaoyu Qu Olga Sala‐Torra David Woolston Jerry Radich Min Fang |
| author_facet | Cecilia Yeung Xiaoyu Qu Olga Sala‐Torra David Woolston Jerry Radich Min Fang |
| author_sort | Cecilia Yeung |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-19T17:02:28Z |
| format | Article |
| id | doaj.art-d669c35621ee4ac09f5fb7c1aef47e29 |
| institution | Directory Open Access Journal |
| issn | 2045-7634 |
| language | English |
| last_indexed | 2024-12-19T17:02:28Z |
| publishDate | 2021-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Medicine |
| spelling | doaj.art-d669c35621ee4ac09f5fb7c1aef47e292022-12-21T20:13:17ZengWileyCancer Medicine2045-76342021-08-0110165629564210.1002/cam4.4101Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testingCecilia Yeung0Xiaoyu Qu1Olga Sala‐Torra2David Woolston3Jerry Radich4Min Fang5Fred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USASeattle Cancer Care Alliance Seattle WA USAFred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USAFred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USAFred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USAFred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USAAbstract 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.https://doi.org/10.1002/cam4.4101leukemiamolecular pathologynext‐generation sequencingRT‐qPCR |
| spellingShingle | Cecilia Yeung Xiaoyu Qu Olga Sala‐Torra David Woolston Jerry Radich Min Fang Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing Cancer Medicine leukemia molecular pathology next‐generation sequencing RT‐qPCR |
| title | Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing |
| title_full | Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing |
| title_fullStr | Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing |
| title_full_unstemmed | Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing |
| title_short | Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing |
| title_sort | mutational profiling in acute lymphoblastic leukemia by rna sequencing and chromosomal genomic array testing |
| topic | leukemia molecular pathology next‐generation sequencing RT‐qPCR |
| url | https://doi.org/10.1002/cam4.4101 |
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