Insights into next generation sequencing guided antibody selection strategies
Abstract Therapeutic antibody discovery often relies on in-vitro display methods to identify lead candidates. Assessing selected output diversity traditionally involves random colony picking and Sanger sequencing, which has limitations. Next-generation sequencing (NGS) offers a cost-effective soluti...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-45538-w |
| _version_ | 1797274523494514688 |
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| author | M. Frank Erasmus Fortunato Ferrara Sara D’Angelo Laura Spector Camila Leal-Lopes André A. Teixeira Jesper Sørensen Suhani Nagpal Kathryn Perea-Schmittle Alok Choudhary William Honnen David Calianese Luis Antonio Rodriguez Carnero Simon Cocklin Victor Greiff Abraham Pinter Andrew R. M. Bradbury |
| author_facet | M. Frank Erasmus Fortunato Ferrara Sara D’Angelo Laura Spector Camila Leal-Lopes André A. Teixeira Jesper Sørensen Suhani Nagpal Kathryn Perea-Schmittle Alok Choudhary William Honnen David Calianese Luis Antonio Rodriguez Carnero Simon Cocklin Victor Greiff Abraham Pinter Andrew R. M. Bradbury |
| author_sort | M. Frank Erasmus |
| collection | DOAJ |
| description | Abstract Therapeutic antibody discovery often relies on in-vitro display methods to identify lead candidates. Assessing selected output diversity traditionally involves random colony picking and Sanger sequencing, which has limitations. Next-generation sequencing (NGS) offers a cost-effective solution with increased read depth, allowing a comprehensive understanding of diversity. Our study establishes NGS guidelines for antibody drug discovery, demonstrating its advantages in expanding the number of unique HCDR3 clusters, broadening the number of high affinity antibodies, expanding the total number of antibodies recognizing different epitopes, and improving lead prioritization. Surprisingly, our investigation into the correlation between NGS-derived frequencies of CDRs and affinity revealed a lack of association, although this limitation could be moderately mitigated by leveraging NGS clustering, enrichment and/or relative abundance across different regions to enhance lead prioritization. This study highlights NGS benefits, offering insights, recommendations, and the most effective approach to leverage NGS in therapeutic antibody discovery. |
| first_indexed | 2024-03-07T14:59:37Z |
| format | Article |
| id | doaj.art-9f677d7c2e9c4172a391dac8c4424094 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T14:59:37Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9f677d7c2e9c4172a391dac8c44240942024-03-05T19:13:47ZengNature PortfolioScientific Reports2045-23222023-10-0113111610.1038/s41598-023-45538-wInsights into next generation sequencing guided antibody selection strategiesM. Frank Erasmus0Fortunato Ferrara1Sara D’Angelo2Laura Spector3Camila Leal-Lopes4André A. Teixeira5Jesper Sørensen6Suhani Nagpal7Kathryn Perea-Schmittle8Alok Choudhary9William Honnen10David Calianese11Luis Antonio Rodriguez Carnero12Simon Cocklin13Victor Greiff14Abraham Pinter15Andrew R. M. Bradbury16Specifica LLC, a Q2 Solutions CompanySpecifica LLC, a Q2 Solutions CompanySpecifica LLC, a Q2 Solutions CompanySpecifica LLC, a Q2 Solutions CompanyNew Mexico ConsortiumNew Mexico ConsortiumOpenEye, Cadence Molecular SciencesOpenEye, Cadence Molecular SciencesSpecifica LLC, a Q2 Solutions CompanyPublic Health Research Institute, New Jersey Medical School, Rutgers, The State University of New JerseyPublic Health Research Institute, New Jersey Medical School, Rutgers, The State University of New JerseyPublic Health Research Institute, New Jersey Medical School, Rutgers, The State University of New JerseyNew Mexico ConsortiumSpecifica LLC, a Q2 Solutions CompanyUniversity of OsloPublic Health Research Institute, New Jersey Medical School, Rutgers, The State University of New JerseySpecifica LLC, a Q2 Solutions CompanyAbstract Therapeutic antibody discovery often relies on in-vitro display methods to identify lead candidates. Assessing selected output diversity traditionally involves random colony picking and Sanger sequencing, which has limitations. Next-generation sequencing (NGS) offers a cost-effective solution with increased read depth, allowing a comprehensive understanding of diversity. Our study establishes NGS guidelines for antibody drug discovery, demonstrating its advantages in expanding the number of unique HCDR3 clusters, broadening the number of high affinity antibodies, expanding the total number of antibodies recognizing different epitopes, and improving lead prioritization. Surprisingly, our investigation into the correlation between NGS-derived frequencies of CDRs and affinity revealed a lack of association, although this limitation could be moderately mitigated by leveraging NGS clustering, enrichment and/or relative abundance across different regions to enhance lead prioritization. This study highlights NGS benefits, offering insights, recommendations, and the most effective approach to leverage NGS in therapeutic antibody discovery.https://doi.org/10.1038/s41598-023-45538-w |
| spellingShingle | M. Frank Erasmus Fortunato Ferrara Sara D’Angelo Laura Spector Camila Leal-Lopes André A. Teixeira Jesper Sørensen Suhani Nagpal Kathryn Perea-Schmittle Alok Choudhary William Honnen David Calianese Luis Antonio Rodriguez Carnero Simon Cocklin Victor Greiff Abraham Pinter Andrew R. M. Bradbury Insights into next generation sequencing guided antibody selection strategies Scientific Reports |
| title | Insights into next generation sequencing guided antibody selection strategies |
| title_full | Insights into next generation sequencing guided antibody selection strategies |
| title_fullStr | Insights into next generation sequencing guided antibody selection strategies |
| title_full_unstemmed | Insights into next generation sequencing guided antibody selection strategies |
| title_short | Insights into next generation sequencing guided antibody selection strategies |
| title_sort | insights into next generation sequencing guided antibody selection strategies |
| url | https://doi.org/10.1038/s41598-023-45538-w |
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