Journal: medRxiv
Article Title: Calling for diversity: improving transfusion safety through high-throughput blood group microarray genotyping
doi: 10.1101/2023.12.15.23299980
Figure Lengend Snippet: ( A ), Dot plot of RHD (NG_007494.1, x-axis) and RHCE (NG_009208.3, y-axis) ISBT genomic reference sequences created with the YASS genomic similarity search tool. The diagonal line indicates the successful forward alignment and hence the sequence similarity of the two genes over almost their entire sequence. ( B ) Schematic approach of microarray genotyping. An immobilized probe on a bead chip designed against a specific genomic locus is hybridized with a target fragment. A polymerase extends the 3’ end of the probe by one base according to the template sequence that represents the desired SNP position. dNTPs are labeled with a specific hapten for subsequent fluorescent staining. Depending on the respective extended base and the wavelength of the fluorescent signal detected, the genotype for the desired SNP position can be determined for homozygous A or B, as well as heterozygous AB individuals. ( C ) Due to sequence paralogies, such as in RHD and RHCE , the 50 bp probes are not unique enough in the genomic context to exclusively bind their desired genomic fragments. As a result, signals detected by the camera constitute complex mixed signals from both paralogous loci as well as from different alleles present that cannot be easily interpreted.
Article Snippet: To decrease the complexity of our model and ensure convergence of the neural network given our sample size, we determined the allele discriminating SNPs out of the 1,500 SNPs typed on the array for the paralogous loci and evaluated if the B-allele frequency (BAF) in the Illumina raw genotyping data and genotypes of RhCDE- and MNS-SNPs correlated with the frequency of the reference antigen of our reference data.
Techniques: Sequencing, Microarray, Labeling, Staining
