Abstract
Inference of germline polymorphisms in immunoglobulin genes from B cell receptor repertoires is complicated by somatic hypermutations, sequencing/PCR errors, and by varying length of reference alleles. The light chain inference is particularly challenging owing to large gene duplications and absence of D genes. We analyzed the light chain cDNA sequences from naïve B cell receptor repertoires from 100 individuals. We optimized light chain allele inference by tweaking parameters of the TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false-positive candidates. We identified 48 previously unreported variants of light chain variable genes. We selected 14 variants for validation and successfully validated 11 by Sanger sequencing. Clustering of light chain 5′UTR, L-PART1, and L-PART2 revealed partial intron retention in 11 kappa and 9 lambda V alleles. Our results provide insight into germline variation in human light chain immunoglobulin loci.
| Original language | English |
|---|---|
| Article number | 103192 |
| Journal | iScience |
| Volume | 24 |
| Issue number | 10 |
| DOIs | |
| State | Published - 22 Oct 2021 |
Bibliographical note
Publisher Copyright:© 2021 The Authors
Funding
We would like to thank Knut E.A. Lundin for coordinating collection of blood samples of participating subjects and for being responsible for the ethical approval for the project. We would also like to thank Omri Snir and Ida Lindeman for providing gDNA samples for validation, Marie K. Johannesen and Bjørg Simonsen for technical assistance, and Aviv Omer for the helpful discussions. The authors are grateful to all study participants. This research was supported by Research Council of Norway through its Center of Excellence funding scheme [179573/V40]; South-Eastern Norway Regional Health Authority [2016113]; Stiftelsen KG Jebsen [SKGJ-MED-017 to L.M.S.]; ISF [832/16 to G.Y. M.G. and A.P.]; European Union's Horizon 2020 research and innovation program [825821]. The contents of this document are the sole responsibility of the iReceptor Plus Consortium and can under no circumstances be regarded as reflecting the position of the European Union. L.M.S. and G.Y. conceived and designed the research; L.M.S. G.Y. and V.G. supervised the project; I.M. performed the experimental work; A.P. I.M. M.G. and G.Y. analyzed the data; I.M. A.P. L.M.S. G.Y. and V.G. wrote the paper. All authors edited the manuscript. V.G. declares advisory board positions in aiNET GmbH and Enpicom B.V. V.G. is also a consultant for Roche/Genentech. All remaining authors declare no conflict of interests. We would like to thank Knut E.A. Lundin for coordinating collection of blood samples of participating subjects and for being responsible for the ethical approval for the project. We would also like to thank Omri Snir and Ida Lindeman for providing gDNA samples for validation, Marie K. Johannesen and Bjørg Simonsen for technical assistance, and Aviv Omer for the helpful discussions. The authors are grateful to all study participants. This research was supported by Research Council of Norway through its Center of Excellence funding scheme [ 179573/V40 ]; South-Eastern Norway Regional Health Authority [ 2016113 ]; Stiftelsen KG Jebsen [ SKGJ-MED-017 to L.M.S.]; ISF [ 832/16 to G.Y., M.G., and A.P.]; European Union's Horizon 2020 research and innovation program [ 825821 ]. The contents of this document are the sole responsibility of the iReceptor Plus Consortium and can under no circumstances be regarded as reflecting the position of the European Union.
| Funders | Funder number |
|---|---|
| Horizon 2020 Framework Programme | |
| European Commission | |
| Israel Science Foundation | 832/16 |
| Norges Forskningsråd | 179573/V40 |
| Helse Sør-Øst RHF | SKGJ-MED-017, 2016113 |
| Horizon 2020 | 825821 |
Keywords
- Genetics
- Genomics
- Immunology
- Molecular genetics