Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection
The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performanc...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2015-03-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/000114264 |
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| author | Agnes Zopf Roman Raim Martin Danzer Norbert Niklas Rita Spilka Johannes Pröll Christian Gabriel Andreas Nechansky Markus Roucka |
| author_facet | Agnes Zopf Roman Raim Martin Danzer Norbert Niklas Rita Spilka Johannes Pröll Christian Gabriel Andreas Nechansky Markus Roucka |
| author_sort | Agnes Zopf |
| collection | DOAJ |
| description | The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations. |
| format | Article |
| id | doaj-art-48ce54324e2547dcbfd7102c04485ccc |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2015-03-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-48ce54324e2547dcbfd7102c04485ccc2025-08-20T02:25:50ZengTaylor & Francis GroupBioTechniques0736-62051940-98182015-03-0158312613410.2144/000114264Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detectionAgnes Zopf0Roman Raim1Martin Danzer2Norbert Niklas3Rita Spilka4Johannes Pröll5Christian Gabriel6Andreas Nechansky7Markus Roucka81Red Cross Transfusion Service for Upper Austria, Linz, Austria2VelaLabs, Vienna, Austria1Red Cross Transfusion Service for Upper Austria, Linz, Austria1Red Cross Transfusion Service for Upper Austria, Linz, Austria3Laboratory of Pathology Dr. Obrist & Dr. Brunnhuber OG, Zams, Austria1Red Cross Transfusion Service for Upper Austria, Linz, Austria1Red Cross Transfusion Service for Upper Austria, Linz, Austria2VelaLabs, Vienna, Austria2VelaLabs, Vienna, AustriaThe detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.https://www.future-science.com/doi/10.2144/000114264KRAScompact sequencingHyborghybcell technologynext-generation sequencing |
| spellingShingle | Agnes Zopf Roman Raim Martin Danzer Norbert Niklas Rita Spilka Johannes Pröll Christian Gabriel Andreas Nechansky Markus Roucka Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection BioTechniques KRAS compact sequencing Hyborg hybcell technology next-generation sequencing |
| title | Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection |
| title_full | Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection |
| title_fullStr | Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection |
| title_full_unstemmed | Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection |
| title_short | Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection |
| title_sort | introduction of the hybcell based compact sequencing technology and comparison to state of the art methodologies for kras mutation detection |
| topic | KRAS compact sequencing Hyborg hybcell technology next-generation sequencing |
| url | https://www.future-science.com/doi/10.2144/000114264 |
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