Mikocziova Ivana, Peres Ayelet, Gidoni Moriah, Greiff Victor, Yaari Gur, Sollid Ludvig M
K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway.
Department of Immunology, Oslo University Hospital, 0372 Oslo, Norway.
iScience. 2021 Sep 29;24(10):103192. doi: 10.1016/j.isci.2021.103192. eCollection 2021 Oct 22.
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.
从B细胞受体库推断免疫球蛋白基因中的种系多态性会受到体细胞超突变、测序/PCR错误以及参考等位基因长度变化的影响。由于存在大量基因重复且缺乏D基因，轻链推断尤其具有挑战性。我们分析了来自100名个体的幼稚B细胞受体库中的轻链cDNA序列。我们通过调整TIgGER功能的参数、扩展种系参考序列以及在多态性位置建立错配频率模式来优化轻链等位基因推断，以筛选出假阳性候选序列。我们鉴定出48个先前未报道的轻链可变基因变体。我们选择了14个变体进行验证，并通过桑格测序成功验证了其中11个。轻链5'UTR、L-PART1和L-PART2的聚类分析显示，在11个κ和9个λV等位基因中存在部分内含子保留。我们的结果为人类轻链免疫球蛋白基因座的种系变异提供了见解。
