Fig. 2: BcR representation and SHM fate tree. | npj Systems Biology and Applications

Fig. 2: BcR representation and SHM fate tree.

From: Understanding repertoire sequencing data through a multiscale computational model of the germinal center

Fig. 2

a BcR sequence reconstruction and representation. From a IgH Fab repertoire sequence from dataset viii, whose FWR1 and FWR4 are partially missing, we infer its V and J genes and the corresponding partially reconstructed germline using IMGT High-VQuest. Red vertical bars represent mutations. The colors on each sequence represent the unknown (gray) and known (turquoise and dark blue) IgH genes. The CDRs appear are marked with black borders. Due to the highly variable nature of the D gene and the junctional diversity, only part of the CDR3 can be assigned to its corresponding germline sequence (i.e., small part corresponding to the V and J germline sequence). The remaining part is taken as is from the repertoire sequence. b SHM fate tree. After each cell division, m mutations occur in a daughter cell. This tree shows the probabilities of affecting the different FWR and CDR regions, and the probabilities for making a specific type of mutation (replacement or silent) and its effect (changing affinity, lethal, neutral).

Back to article page