VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.

Background T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants. Methods To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors’ variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences. Results From the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5 ′ UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire. Conclusions We reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.

597 unrelated persons, comprising of 401 males and 196 females, were investigated for glucose-6-phosphate dehydrogenase (G6PD) and haemoglobin phenotypes by starch gel electrophoresis. The levels of G6PD activity were assayed in order to study the quantitative expression of G6PD phenotypes and the influence of haemoglobin phenotypes on such expression. There was no significant difference in the levels of G6PD activity in subjects with GdA or GdB. The mean levels of the enzyme activity were 165.5 ± 33.7 and 164.8 ± 33.8 1U/10¹² red cells in males and 159.3 ± 27.8 and 163.4 ± 33.5 IU/10¹² red cells in females, respectively. 14 subjects with Gd(+) ‘Khartoum’ had significantly (p < 0.001) higher level of enzyme activity with a mean above 200 IU/10¹² red cells. On the other hand, 20 subjects with GdB(int) (demonstrated by visual comparison of starch gel) showed significantly (p < 0.001) lower levels of enzyme activity (107.6 ± 23.5 IU/10¹² red cells). The heterozygotes GdAB also had slightly, but not significantly lower levels of enzyme activity than either GdA or GdB. The mean level of activity for GdAB was 140.1 ± 29.4 IU/10¹² red cells.

1,416 males and 564 female subjects from four Negroid and five Arab tribes and a group of mixed tribes of the Sudan were investigated for the phenotypic distribution of red cell glucose-6-phosphate dehydrogenase by starch gel electrophoresis. In general, the tribes of Negroid origin had higher frequency of Gd^A compared to the tribes of Arab ancestry. However, the Nilotes showed a lower frequency of Gd^A allele and the Mahass tribe claiming an Arab origin had a higher frequency of Gd^A. The immigrant groups from the neighbouring African countries also had a higher frequency of Gd^A. Gd^B (Khartoum) was present in low frequencies in both the Arab and Negroid tribes. A great deal of intratribal variation in the phenotypic distribution of G6PD was observed in the Nuba and Gáali tribes from different localities

T and B cell repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of T and B cell receptors (TCRs and BCRs, respectively) are challenging to decipher due to repetitive elements and undocumented structural variants. To confront this challenge, AIRR-seq-based methods have been developed recently for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. Applying these methods to AIRR-seq data reveals a plethora of undocumented genomic variations. However, this approach relies on complete coverage of the receptors' variable regions, and most T cell studies sequence only a small fraction of the variable region. Here, we adapted BCR inference methods to full and partial TCR sequences, and identified 38 undocumented polymorphisms in TRBV, 15 of them were also observed in genomic data assemblies. Further, we identified 31 undocumented 5' UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found the two documented TRBD2 alleles to be equally abundant in the population, and show that the single nucleotide that differentiates them is strongly associated with dramatic changes in the expressed repertoire. Our findings expand the knowledge of genomic variation in the TRB (T Cell Receptor Beta) locus and provide a basis for annotation of TCR repertoires for future basic and clinical studies.