238: Germline polymorphisms shape antibody light chain repertoires

Engelbrecht E et al., Nat Commun - Long-read sequencing of IGK and IGL paired with AIRR-seq shows that common germline SNVs, SVs, and alleles drive inter-individual differences in light chain gene usage and CDR3 properties. Key terms: immunoglobulin-kappa, immunoglobulin-lambda, germline-variation, antibody-repertoire, long-read-sequencing. Study Highlights:The authors combined targeted long-read genomic sequencing of IGK and IGL in 177 donors with matched AIRR-seq (IGK n=164, IGL n=168) to generate phased SNV, SV, and allele callsets and personalized germline databases. Cis guQTL analysis identified 2,352 variants in the unmutated IGK repertoire linked to usage changes in 21 IGKV and 3 IGKJ genes, and 911 variants in IGL linked to 22 IGLV and 3 IGLJ genes, indicating germline variation affects >70% of light chain genes. Lead variants mapped to intergenic regions, RSSs, coding exons and structural variants, with examples including a premature stop in IGKV2-29, a K50D missense in IGKV1-5, RSS spacer changes in IGLV3-16, and copy-number SVs that alter gene usage. Genetic effects were stronger in the antigen-naïve repertoire, associated with shifts in encoded V/J alleles and CDR3 physicochemical properties, and IGK exhibited larger LD blocks and coordinated multi-gene usage compared with IGL. Conclusion:Germline polymorphisms across IGK and IGL establish reproducible baseline differences in light chain gene availability and amino acid composition that likely influence antibody-mediated responses. Music:Enjoy the music based on this article at the end of the episode. Article title:Germline polymorphisms in the immunoglobulin kappa and lambda loci underpinning antibody light chain repertoire variability First author:Engelbrecht E Journal:Nat Commun DOI:10.1038/s41467-025-66759-9 Reference:Engelbrecht E, Rodriguez OL, Lees W, Vanwinkle Z, Shields K, Schultze S, Gibson WS, Smith DR, Jana U, Saha S, Peres A, Yaari G, Smith ML, Watson CT. Germline polymorphisms in the immunoglobulin kappa and lambda loci underpinning antibody light chain repertoire variability. Nat Commun. 2025. https://doi.org/10.1038/s41467-025-66759-9 License:CC BY 4.0 International License Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/ig-light-chain-variation QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-24. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited the core scientific narrative describing targeted SMRT sequencing of IGK/IGL loci, creation of personalized germline references, guQTL mapping linking variants to gene usage, variant mechanisms (coding, RSS, CNV), LD architecture differences, CDR3 physicochemical properties, and naive vs. antigen-experienced re- transcript topics: IGK vs IGL locus architecture and diversity; SMRT long-read sequencing and personalized germline references; guQTL mapping and gene usage in IGK/IGL; Coding variants: IGKV2-29 stop codon; Coding variants: IGKV1-5 K50D; Regulatory variants: RSS spacers (IGLV3-16) QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- Long-read SMRT sequencing of IGK and IGL... Chapters (00:00:00) - How your genetic blueprint shapes your immunity(00:01:38) - Personal genetics of the human genome(00:05:13) - What Did Genomic Personalization Reveal About the Immunity(00:08:21) - How genetic variation affects the way your body recognizes molecules