{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Luo J"],"funding":["Shenzhen Science and Technology Program"],"pagination":["btaf346"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12282942"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["41(7)"],"pubmed_abstract":["<h4>Motivation</h4>B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumulation of advantageous mutations under successive rounds of somatic hypermutation (SHM) and selection, and are often incompatible with repertoire input.<h4>Results</h4>To address previous limitations, we developed AffMB (Affinity Maturation of B-cell receptor), a comprehensive toolkit for tracking affinity maturation through the generation and visualization of SHM-ordered, inheritance-based B-cell lineage trees from single-cell or bulk B-cell receptor sequencing data. The SHM-ordered inheritance tree algorithm outperformed state-of-the-art benchmarks in simulations. When applied to single-cell data from BNT162b2 vaccination (n = 42), AffMB demonstrated the ability to infer immunization responses and showed the feasibility of identifying potential high-affinity antibody sequences.<h4>Availability and implementation</h4>AffMB is an open-source Python package that supports contig FASTA or AIRR rearrangement TSV inputs. The source code for AffMB is freely available at https://github.com/deepomicslab/AffMB."],"journal":["Bioinformatics (Oxford, England)"],"pubmed_title":["AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees."],"pmcid":["PMC12282942"],"funding_grant_id":["JCYJ20200109143216036"],"pubmed_authors":["Zou Y","Luo J","Li SC"],"additional_accession":[]},"is_claimable":false,"name":"AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.","description":"<h4>Motivation</h4>B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumulation of advantageous mutations under successive rounds of somatic hypermutation (SHM) and selection, and are often incompatible with repertoire input.<h4>Results</h4>To address previous limitations, we developed AffMB (Affinity Maturation of B-cell receptor), a comprehensive toolkit for tracking affinity maturation through the generation and visualization of SHM-ordered, inheritance-based B-cell lineage trees from single-cell or bulk B-cell receptor sequencing data. The SHM-ordered inheritance tree algorithm outperformed state-of-the-art benchmarks in simulations. When applied to single-cell data from BNT162b2 vaccination (n = 42), AffMB demonstrated the ability to infer immunization responses and showed the feasibility of identifying potential high-affinity antibody sequences.<h4>Availability and implementation</h4>AffMB is an open-source Python package that supports contig FASTA or AIRR rearrangement TSV inputs. The source code for AffMB is freely available at https://github.com/deepomicslab/AffMB.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jul","modification":"2026-03-27T16:21:14.467Z","creation":"2025-08-30T03:05:57.728Z"},"accession":"S-EPMC12282942","cross_references":{"pubmed":["40674579"],"doi":["10.1093/bioinformatics/btaf346"]}}