Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening
Objective: The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia. Materials and Methods: Processes were established for registering and transferring samples fro...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2022-07-01
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| Series: | Cancer Informatics |
| Online Access: | https://doi.org/10.1177/11769351221110872 |
| _version_ | 1818197583912239104 |
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| author | Wesley Schaal Adam Ameur Ulla Olsson-Strömberg Monica Hermanson Lucia Cavelier Ola Spjuth |
| author_facet | Wesley Schaal Adam Ameur Ulla Olsson-Strömberg Monica Hermanson Lucia Cavelier Ola Spjuth |
| author_sort | Wesley Schaal |
| collection | DOAJ |
| description | Objective: The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia. Materials and Methods: Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp Results: The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application. Conclusions: Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications. |
| first_indexed | 2024-12-12T01:52:17Z |
| format | Article |
| id | doaj.art-4534f517db04444a98665e00a96b28af |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-12-12T01:52:17Z |
| publishDate | 2022-07-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-4534f517db04444a98665e00a96b28af2022-12-22T00:42:27ZengSAGE PublishingCancer Informatics1176-93512022-07-012110.1177/11769351221110872Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation ScreeningWesley Schaal0Adam Ameur1Ulla Olsson-Strömberg2Monica Hermanson3Lucia Cavelier4Ola Spjuth5Pincer Bio AB, Uppsala, SwedenDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SwedenDepartment of Medical Sciences, Uppsala University Hospital, Uppsala, SwedenDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SwedenDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SwedenPincer Bio AB, Uppsala, SwedenObjective: The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia. Materials and Methods: Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp Results: The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application. Conclusions: Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.https://doi.org/10.1177/11769351221110872 |
| spellingShingle | Wesley Schaal Adam Ameur Ulla Olsson-Strömberg Monica Hermanson Lucia Cavelier Ola Spjuth Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening Cancer Informatics |
| title | Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening |
| title_full | Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening |
| title_fullStr | Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening |
| title_full_unstemmed | Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening |
| title_short | Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening |
| title_sort | migrating to long read sequencing for clinical routine tki resistance mutation screening |
| url | https://doi.org/10.1177/11769351221110872 |
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