Antigenic Cartography

Concept of Shape space

• Basic of antigenic cartography tracks back the concept of "shape space" first propound by Perelson and Oster back in 1979.
• In this concept, antigen and antibody are considered as 'points in an abstract shape space' with their own coordinates which consist of abstract parameters. Distances between those points denote affinity with each other.

Perelson, A. S., & Oster, G. F. (1979). Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination. Journal of Theoretical Biology, 81(4), 645–670. https://doi.org/10.1016/0022-5193(79)90275-3

Multidimensional scaling (MDS) algorithm

• 多次元尺度構成法 in Japanese

k-Means clustering

k-means法とは？可視化してわかりやすく解説 https://hogetech.info/algorithm/kmeans

Antigenic distance

Cai, Z., Zhang, T., & Wan, X. F. (2012). Antigenic distance measurements for seasonal influenza vaccine selection. Vaccine, 30(2), 448–453. https://doi.org/10.1016/j.vaccine.2011.10.051

Antigenic cartography

• The first propounders of Antigenic Cartography were Smith DJ et al. in 2004 by using hemagluttinin inhibition (HI) assay of influenza AH3N2 viruses.

Smith, D. J., Lapedes, A. S., de Jong, J. C., Bestebroer, T. M., Rimmelzwaan, G. F., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2004). Mapping the Antigenic and Genetic Evolution of Influenza Virus. Science, 305(5682), 371–376. https://doi.org/10.1126/science.1097211

• The following is a well documented review of antigenic cartography.

Sitaras, I. (2020). Antigenic cartography: Overview and current developments. In Methods in Molecular Biology (Vol. 2123, pp. 61–68). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0346-8_5