Structurally Mapping Antibody Repertoires
Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this pap...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2018.01698/full |
| _version_ | 1811314972409462784 |
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| author | Konrad Krawczyk Sebastian Kelm Aleksandr Kovaltsuk Jacob D. Galson Dominic Kelly Johannes Trück Johannes Trück Cristian Regep Jinwoo Leem Wing K. Wong Jaroslaw Nowak James Snowden Michael Wright Laura Starkie Anthony Scott-Tucker Jiye Shi Charlotte M. Deane |
| author_facet | Konrad Krawczyk Sebastian Kelm Aleksandr Kovaltsuk Jacob D. Galson Dominic Kelly Johannes Trück Johannes Trück Cristian Regep Jinwoo Leem Wing K. Wong Jaroslaw Nowak James Snowden Michael Wright Laura Starkie Anthony Scott-Tucker Jiye Shi Charlotte M. Deane |
| author_sort | Konrad Krawczyk |
| collection | DOAJ |
| description | Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this paper, we enrich these large-scale sequence datasets with structural information. Enriching a sequence with its structural data allows better approximation of many vital features, such as its binding site and specificity. Here, we describe the structural annotation of antibodies pipeline that maps the outputs of large Ig-seq experiments to known antibody structures. We demonstrate the viability of our protocol on five separate Ig-seq datasets covering ca. 35 m unique amino acid sequences from ca. 600 individuals. Despite the great theoretical diversity of antibodies, we find that the majority of sequences coming from such studies can be reliably mapped to an existing structure. |
| first_indexed | 2024-04-13T11:22:02Z |
| format | Article |
| id | doaj.art-47fb86b0ffff496db413cd8995409a66 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T11:22:02Z |
| publishDate | 2018-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-47fb86b0ffff496db413cd8995409a662022-12-22T02:48:48ZengFrontiers Media S.A.Frontiers in Immunology1664-32242018-07-01910.3389/fimmu.2018.01698387101Structurally Mapping Antibody RepertoiresKonrad Krawczyk0Sebastian Kelm1Aleksandr Kovaltsuk2Jacob D. Galson3Dominic Kelly4Johannes Trück5Johannes Trück6Cristian Regep7Jinwoo Leem8Wing K. Wong9Jaroslaw Nowak10James Snowden11Michael Wright12Laura Starkie13Anthony Scott-Tucker14Jiye Shi15Charlotte M. Deane16Department of Statistics, Oxford University, Oxford, United KingdomUCB Pharma, Slough, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomDivision of Immunology, Children’s Research Center, University Children’s Hospital, Zurich, SwitzerlandDivision of Immunology, Children’s Research Center, University Children’s Hospital, Zurich, SwitzerlandDivision of Immunology, Children’s Research Center, University Children’s Hospital, Zurich, SwitzerlandOxford Vaccine Group, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomUCB Pharma, Slough, United KingdomUCB Pharma, Slough, United KingdomUCB Pharma, Slough, United KingdomUCB Pharma, Slough, United KingdomUCB Pharma, Slough, United KingdomDepartment of Statistics, Oxford University, Oxford, United KingdomEvery human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this paper, we enrich these large-scale sequence datasets with structural information. Enriching a sequence with its structural data allows better approximation of many vital features, such as its binding site and specificity. Here, we describe the structural annotation of antibodies pipeline that maps the outputs of large Ig-seq experiments to known antibody structures. We demonstrate the viability of our protocol on five separate Ig-seq datasets covering ca. 35 m unique amino acid sequences from ca. 600 individuals. Despite the great theoretical diversity of antibodies, we find that the majority of sequences coming from such studies can be reliably mapped to an existing structure.https://www.frontiersin.org/article/10.3389/fimmu.2018.01698/fullantibody specificityB-cell receptornext-generation sequencingstructural homologyproteinbioinformatics tools |
| spellingShingle | Konrad Krawczyk Sebastian Kelm Aleksandr Kovaltsuk Jacob D. Galson Dominic Kelly Johannes Trück Johannes Trück Cristian Regep Jinwoo Leem Wing K. Wong Jaroslaw Nowak James Snowden Michael Wright Laura Starkie Anthony Scott-Tucker Jiye Shi Charlotte M. Deane Structurally Mapping Antibody Repertoires Frontiers in Immunology antibody specificity B-cell receptor next-generation sequencing structural homology protein bioinformatics tools |
| title | Structurally Mapping Antibody Repertoires |
| title_full | Structurally Mapping Antibody Repertoires |
| title_fullStr | Structurally Mapping Antibody Repertoires |
| title_full_unstemmed | Structurally Mapping Antibody Repertoires |
| title_short | Structurally Mapping Antibody Repertoires |
| title_sort | structurally mapping antibody repertoires |
| topic | antibody specificity B-cell receptor next-generation sequencing structural homology protein bioinformatics tools |
| url | https://www.frontiersin.org/article/10.3389/fimmu.2018.01698/full |
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