Antibody categorization based on binding characteristics
AssigneeAmgen Fremont Inc.
InventorsWynn L. Walker, Michael L. Gallo, Xiao-Chi Jia, Keith Joho, Jaspal Singh Kang
Life of this patent
Estimating the term…
Abstract
Methods for categorizing antibodies based on their epitope binding characteristics are described. Methods and systems for determining the epitope recognition properties of different antibodies are provided. Also provided are data analysis processes for clustering antibodies on the basis of their epitope recognition properties and for identifying antibodies having distinct epitope binding characteristics.
Claims52
An antibody competition assay method for determining antibodies that bind to an epitope on an antigen, comprising:
- providing a set of antibodies that bind to an antigen;
- labelling each antibody of said set to form a labelled reference antibody set such that each labelled reference antibody is distinguishable from every other labelled reference antibody in said labelled reference antibody set;
- selecting a probe antibody from said set of antibodies that bind to the antigen;
- contacting said probe antibody with said labelled reference antibody set in the presence of said antigen;
- detecting said probe antibody in a complex comprising said antigen, one labelled reference antibody bound to said antigen, and said labelled probe antibody bound to said antigen;
- identifying each said labelled reference antibody bound to said antigen in each said complex;
- determining whether said probe antibody competes with any reference antibody in said labelled reference antibody set, wherein competition indicates that said probe antibody binds to the same epitope as another antibody in said set of antibodies that bind to an antigen.
The method of claim 49, comprising generating an individual normalized intensity matrix for each said individual experiment and further comprising generating a single normalized intensity matrix by computing the average intensity value of each antibody pair represented in each individual normalized intensity matrix.
A method for characterizing antibodies based on binding characteristics, comprising:
- providing a labelled reference antibody set such that each labelled reference antibody in said set is distinguishable from every other labelled reference antibody in said labelled reference antibody set, and wherein each antibody binds to an antigen;
- selecting a probe antibody from said set of antibodies that binds to the antigen;
- contacting said probe antibody with said labelled reference antibody set in the presence of said antigen;
- detecting said probe antibody in a complex comprising said antigen, one labelled reference antibody bound to said antigen, and said labelled probe antibody bound to said antigen;
- identifying each said labelled reference antibody bound to said antigen in each said complex;
- determining whether said probe antibody competes with any reference antibody in said labelled reference antibody set, wherein competition indicates that said probe antibody binds to the same epitope as another antibody in said set of antibodies that bind to an antigen;
- providing input data representing the outcomes of at least one antibody competition assay using a set of antibodies that bind to an antigen, further wherein wherein said input data comprises signal intensity values representing the outcomes of at least one antibody competition assay using a set of antibodies that bind to an antigen;
- storing said input data in matrix format;
- subtracting a first matrix comprising signal intensity values from a first antibody competition assay in which antigen was not added, from a second matrix comprising signal intensity values from a second antibody competition assay in which antigen was added, to form a background normalized intensity matrix;
- calculating the value in each diagonal cell of said background normalized intensity matrix;
- determining cells in each column of said background normalized intensity matrix having values significantly higher than the value in each diagonal cell of said column;
- and
- grouping columns having similar binding patterns as a bin.
Dependencies are inferred from the claim text.