NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program
Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/12/11/3180 |
| _version_ | 1797549430869590016 |
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| author | Thomas Delcourt Kevin Vanneste Mohamed Rida Soumali Wim Coucke Vanessa Ghislain Aline Hebrant Els Van Valckenborgh Sigrid C. J. De Keersmaecker Nancy H. Roosens Philippe Van De Walle Marc Van Den Bulcke Aline Antoniou |
| author_facet | Thomas Delcourt Kevin Vanneste Mohamed Rida Soumali Wim Coucke Vanessa Ghislain Aline Hebrant Els Van Valckenborgh Sigrid C. J. De Keersmaecker Nancy H. Roosens Philippe Van De Walle Marc Van Den Bulcke Aline Antoniou |
| author_sort | Thomas Delcourt |
| collection | DOAJ |
| description | Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017–2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and <i>BRCA1/BRCA2</i> genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced. |
| first_indexed | 2024-03-10T15:14:36Z |
| format | Article |
| id | doaj.art-25d2c12a98ba47f78d1b42b235b2a84e |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T15:14:36Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-25d2c12a98ba47f78d1b42b235b2a84e2023-11-20T18:59:15ZengMDPI AGCancers2072-66942020-10-011211318010.3390/cancers12113180NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment ProgramThomas Delcourt0Kevin Vanneste1Mohamed Rida Soumali2Wim Coucke3Vanessa Ghislain4Aline Hebrant5Els Van Valckenborgh6Sigrid C. J. De Keersmaecker7Nancy H. Roosens8Philippe Van De Walle9Marc Van Den Bulcke10Aline Antoniou11Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, 1050 Brussels, BelgiumQuality of Laboratories, Sciensano, 1050 Brussels, BelgiumQuality of Laboratories, Sciensano, 1050 Brussels, BelgiumQuality of Laboratories, Sciensano, 1050 Brussels, BelgiumCancer Centre, Sciensano, 1050 Brussels, BelgiumCancer Centre, Sciensano, 1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, 1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, 1050 Brussels, BelgiumQuality of Laboratories, Sciensano, 1050 Brussels, BelgiumCancer Centre, Sciensano, 1050 Brussels, BelgiumQuality of Laboratories, Sciensano, 1050 Brussels, BelgiumNext-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017–2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and <i>BRCA1/BRCA2</i> genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced.https://www.mdpi.com/2072-6694/12/11/3180next-generation sequencinghemato-oncologyoncologyexternal quality assessmentcancer |
| spellingShingle | Thomas Delcourt Kevin Vanneste Mohamed Rida Soumali Wim Coucke Vanessa Ghislain Aline Hebrant Els Van Valckenborgh Sigrid C. J. De Keersmaecker Nancy H. Roosens Philippe Van De Walle Marc Van Den Bulcke Aline Antoniou NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program Cancers next-generation sequencing hemato-oncology oncology external quality assessment cancer |
| title | NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program |
| title_full | NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program |
| title_fullStr | NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program |
| title_full_unstemmed | NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program |
| title_short | NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program |
| title_sort | ngs for hemato oncology in belgium evaluation of laboratory performance and feasibility of a national external quality assessment program |
| topic | next-generation sequencing hemato-oncology oncology external quality assessment cancer |
| url | https://www.mdpi.com/2072-6694/12/11/3180 |
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