Numbering Schemes

December 12, 2023 00:33
Updated

This article describes what numbering schemes are and how to annotate your sequences using the different numbering schemes supported in Geneious Biologics. To find out more about using your own offsets to adjust CDR and FR definitions, see our article here. If you would like to know how to create liabilities based on specific numbered positions, see this article: Positional Liabilities based on Antibody Numbering.

What are Antibody Numbering Schemes?

Various antibody numbering schemes have been defined over the years by different academic groups. These numbering schemes allow scientists to compare and analyze both novel and existing antibody sequences using a standardized framework; informing and aiding in humanization as well as antibody engineering.

Broadly, the various antibody numbering schemes have been developed using one of two approaches: Sequence-based or Structure-based. Both numbering scheme approaches attempt to define CDR and FR boundaries, and to explain the differences in length across antibodies by placing insertion/deletion sites (indels) at specific conserved points in their numbering sequences.

Sequence-based numbering schemes, such as IMGT and Kabat, were developed by analyzing alignments of known antibody sequences (Kabat) or alignments of the germline genes (IMGT). The indel positions in these schemes represent areas of high sequence variability at those points, in addition to variations in length.
Structure-based numbering schemes, such as Chothia and Martin, were developed by analyzing the experimentally determined 3D structures of antibodies. The indel positions in these schemes represent areas of greater conformational flexibility.

What Numbering Schemes are available in Biologics?

Kabat

The Kabat CDR definitions and numbering used in Biologics are based on those described in the following publication:

Kabat EA, Te Wu T, Foeller C, Perry HM, Gottesman KS. Sequences of Proteins of Immunological Interest. (1991). U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health.

IMGT

The IMGT CDR definitions and numbering used in Biologics are based on those described in the following publication:

Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V., & Lefranc, G. (2003). IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Developmental & Comparative Immunology, 27(1), 55–77. https://doi.org/10.1016/S0145-305X(02)00039-3

Chothia

The Chothia CDR definitions and numbering are known to vary from publication to publication, and to also vary within the figures of papers themselves. For the sake of consistency, Geneious Biologics uses the definitions described in the 1997 publication:

Al-Lazikani, B., Lesk, A. M., & Chothia, C. (1997). Standard conformations for the canonical structures of immunoglobulins. Journal of Molecular Biology, 273(4), 927–948. https://doi.org/10.1006/jmbi.1997.1354

Martin

The Martin CDR definitions and numbering used in Biologics are based on those described in the following publication:

Abhinandan, K. R., & Martin, A. C. R. (2008). Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Molecular Immunology, 45(14), 3832–3839. https://doi.org/10.1016/j.molimm.2008.05.022

How to specify a Numbering Scheme in Biologics

When using Antibody Annotator or Single Clone Analysis, the numbering options can be found under Analysis Options:

Screenshot_2022-10-27_at_5.05.08_PM.png

The dropdown allows you to select either IMGT, Kabat, Chothia, Martin, AHo or From Database. You can then tick the checkbox next to the dropdown if you would like to have your sequences annotated with numbers.

Our default liabilities will check numbered sequences for highly conserved residues. If you'd like to learn more about these default positional liabilities or how to specify your own, please see our main article: Positional Liabilities based on Antibody Numbering.

Using Numbering with a Custom Reference Database

If you are using your own Custom Reference Database, then you can either:

Use the From Database option if you have added numbering annotations to your reference sequences. Please contact us if you would like to know how to correctly format the numbers on your reference sequences.
Use any of the above Numbering Schemes excluding IMGT. This is because the IMGT numbering is derived from the annotated germline sequences themselves.