Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio
Abstract Whole exome sequencing (WES) is essential for identifying genetic variants linked to diseases. This study compares available to date four exome enrichment kits: Agilent SureSelect Human All Exon v8, Roche KAPA HyperExome, Vazyme VAHTS Target Capture Core Exome Panel, and Nanodigmbio NEXome...
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11196-z |
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| author | Vera Belova Iuliia Vasiliadis Zhanna Repinskaia Alina Samitova Anna Shmitko Natalya Ponikarovskaya Oleg Suchalko Valery Cheranev Shatalov Peter Shegai Peter Kaprin Andrey Denis Rebrikov Dmitriy Korostin |
| author_facet | Vera Belova Iuliia Vasiliadis Zhanna Repinskaia Alina Samitova Anna Shmitko Natalya Ponikarovskaya Oleg Suchalko Valery Cheranev Shatalov Peter Shegai Peter Kaprin Andrey Denis Rebrikov Dmitriy Korostin |
| author_sort | Vera Belova |
| collection | DOAJ |
| description | Abstract Whole exome sequencing (WES) is essential for identifying genetic variants linked to diseases. This study compares available to date four exome enrichment kits: Agilent SureSelect Human All Exon v8, Roche KAPA HyperExome, Vazyme VAHTS Target Capture Core Exome Panel, and Nanodigmbio NEXome Plus Panel v1. We evaluated target design, coverage statistics, and variant calling accuracy across these four different exome capture products. All kits showed high target coverage, with 10x coverage exceeding 97.5% and 20x coverage above 95%. Roche exhibited the most uniform coverage, indicated by the lowest fold-80 scores, while Nanodigmbio had more on-target reads due to fewer off-target reads. Variant calling performance, evaluated using in-lab standard E701 DNA sample, showed high recall rates for all kits, especially Agilent v8. All kits achieved an F-measure above 95.87%. Nanodigmbio had the highest precision with the fewest false positives but a slightly lower F-measure than other kits. This study also highlights the performance of new solutions from Vazyme (China) and Nanodigmbio (China), which were comparable to Agilent v8 and Roche KAPA kits. These findings assist researchers and clinicians in selecting appropriate exome capture solutions. |
| format | Article |
| id | doaj-art-4831ed3789464c5e82217b003be9747d |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-4831ed3789464c5e82217b003be9747d2025-02-02T12:10:17ZengBMCBMC Genomics1471-21642025-01-0126111010.1186/s12864-024-11196-zComparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and NanodigmbioVera Belova0Iuliia Vasiliadis1Zhanna Repinskaia2Alina Samitova3Anna Shmitko4Natalya Ponikarovskaya5Oleg Suchalko6Valery Cheranev7Shatalov Peter8Shegai Peter9Kaprin Andrey10Denis Rebrikov11Dmitriy Korostin12Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityNational Medical Research Radiological Centre of the Ministry of Health of the Russian FederationNational Medical Research Radiological Centre of the Ministry of Health of the Russian FederationNational Medical Research Radiological Centre of the Ministry of Health of the Russian FederationCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityAbstract Whole exome sequencing (WES) is essential for identifying genetic variants linked to diseases. This study compares available to date four exome enrichment kits: Agilent SureSelect Human All Exon v8, Roche KAPA HyperExome, Vazyme VAHTS Target Capture Core Exome Panel, and Nanodigmbio NEXome Plus Panel v1. We evaluated target design, coverage statistics, and variant calling accuracy across these four different exome capture products. All kits showed high target coverage, with 10x coverage exceeding 97.5% and 20x coverage above 95%. Roche exhibited the most uniform coverage, indicated by the lowest fold-80 scores, while Nanodigmbio had more on-target reads due to fewer off-target reads. Variant calling performance, evaluated using in-lab standard E701 DNA sample, showed high recall rates for all kits, especially Agilent v8. All kits achieved an F-measure above 95.87%. Nanodigmbio had the highest precision with the fewest false positives but a slightly lower F-measure than other kits. This study also highlights the performance of new solutions from Vazyme (China) and Nanodigmbio (China), which were comparable to Agilent v8 and Roche KAPA kits. These findings assist researchers and clinicians in selecting appropriate exome capture solutions.https://doi.org/10.1186/s12864-024-11196-zWhole exome sequencingExome enrichment kitsAgilentRocheVazymeNanodigmbio |
| spellingShingle | Vera Belova Iuliia Vasiliadis Zhanna Repinskaia Alina Samitova Anna Shmitko Natalya Ponikarovskaya Oleg Suchalko Valery Cheranev Shatalov Peter Shegai Peter Kaprin Andrey Denis Rebrikov Dmitriy Korostin Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio BMC Genomics Whole exome sequencing Exome enrichment kits Agilent Roche Vazyme Nanodigmbio |
| title | Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio |
| title_full | Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio |
| title_fullStr | Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio |
| title_full_unstemmed | Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio |
| title_short | Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio |
| title_sort | comparative evaluation of four exome enrichment solutions in 2024 agilent roche vazyme and nanodigmbio |
| topic | Whole exome sequencing Exome enrichment kits Agilent Roche Vazyme Nanodigmbio |
| url | https://doi.org/10.1186/s12864-024-11196-z |
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