Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing
Background: The detection of <i>CEBPA</i> and <i>FLT3</i> mutations by next generation sequencing (NGS) is challenging due to high GC content and Internal Tandem Duplications (ITDs). Recent advances have been made to surmount these challenges. In this study, we compare three...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/4/630 |
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| author | Ratilal Akabari Dahui Qin Mohammad Hussaini |
| author_facet | Ratilal Akabari Dahui Qin Mohammad Hussaini |
| author_sort | Ratilal Akabari |
| collection | DOAJ |
| description | Background: The detection of <i>CEBPA</i> and <i>FLT3</i> mutations by next generation sequencing (NGS) is challenging due to high GC content and Internal Tandem Duplications (ITDs). Recent advances have been made to surmount these challenges. In this study, we compare three commercial kits and evaluate the performance of these more advanced hybrid-capture and AMP-chemistry based methods. Methods: Amplicon-based TSM 54-Gene Panel (Illumina) was evaluated against hybridization-capture SOPHiA Genetics MSP, OGT SureSeq, and AMP chemistry-based VariantPlex (Archer) for wet-lab workflow and data-analysis pipelines. Standard kit directions and commercial analysis pipelines were followed. Seven <i>CEBPA</i> and 10 <i>FLT3</i>-positive cases were identified that previously were missed on an amplicon NGS assay. The average reads, coverage uniformity, and the detection of <i>CEBPA</i> or <i>FLT3</i> mutations were compared. Results: All three panels detected all 10 <i>CEBPA</i> mutations and all 10 <i>FLT3</i> ITDs with 100% sensitivity. In addition, there was high concordance (100%) between all three panels detecting 47/47 confirmed variants in a set of core myeloid genes. Conclusions: The results show that the NGS assays are now able to reliably detect <i>CEBPA</i> mutations and <i>FLT3</i> ITDs. These assays may allow foregoing additional orthogonal testing for <i>CEBPA</i> and <i>FLT3</i>. |
| first_indexed | 2024-03-09T10:36:32Z |
| format | Article |
| id | doaj.art-b94096b073f945c1b2d3cc47b00fcce9 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T10:36:32Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-b94096b073f945c1b2d3cc47b00fcce92023-12-01T20:57:03ZengMDPI AGGenes2073-44252022-04-0113463010.3390/genes13040630Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation SequencingRatilal Akabari0Dahui Qin1Mohammad Hussaini2Department of Pathology, Molecular Oncology and Genetics Diagnostics, SUNY Upstate Medical University, Syracuse, NY 13210, USADepartment of Pathology, Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Pathology, Moffitt Cancer Center, Tampa, FL 33612, USABackground: The detection of <i>CEBPA</i> and <i>FLT3</i> mutations by next generation sequencing (NGS) is challenging due to high GC content and Internal Tandem Duplications (ITDs). Recent advances have been made to surmount these challenges. In this study, we compare three commercial kits and evaluate the performance of these more advanced hybrid-capture and AMP-chemistry based methods. Methods: Amplicon-based TSM 54-Gene Panel (Illumina) was evaluated against hybridization-capture SOPHiA Genetics MSP, OGT SureSeq, and AMP chemistry-based VariantPlex (Archer) for wet-lab workflow and data-analysis pipelines. Standard kit directions and commercial analysis pipelines were followed. Seven <i>CEBPA</i> and 10 <i>FLT3</i>-positive cases were identified that previously were missed on an amplicon NGS assay. The average reads, coverage uniformity, and the detection of <i>CEBPA</i> or <i>FLT3</i> mutations were compared. Results: All three panels detected all 10 <i>CEBPA</i> mutations and all 10 <i>FLT3</i> ITDs with 100% sensitivity. In addition, there was high concordance (100%) between all three panels detecting 47/47 confirmed variants in a set of core myeloid genes. Conclusions: The results show that the NGS assays are now able to reliably detect <i>CEBPA</i> mutations and <i>FLT3</i> ITDs. These assays may allow foregoing additional orthogonal testing for <i>CEBPA</i> and <i>FLT3</i>.https://www.mdpi.com/2073-4425/13/4/630<i>CEBPA</i><i>FLT3</i>AMLnext generation sequencing (NGS)Internal Tandem Duplication (ITD) |
| spellingShingle | Ratilal Akabari Dahui Qin Mohammad Hussaini Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing Genes <i>CEBPA</i> <i>FLT3</i> AML next generation sequencing (NGS) Internal Tandem Duplication (ITD) |
| title | Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing |
| title_full | Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing |
| title_fullStr | Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing |
| title_full_unstemmed | Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing |
| title_short | Technological Advances: <i>CEBPA</i> and <i>FLT3</i> Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing |
| title_sort | technological advances i cebpa i and i flt3 i internal tandem duplication mutations can be reliably detected by next generation sequencing |
| topic | <i>CEBPA</i> <i>FLT3</i> AML next generation sequencing (NGS) Internal Tandem Duplication (ITD) |
| url | https://www.mdpi.com/2073-4425/13/4/630 |
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