case_images: PMC11090686_01
case_images: Genotyping of DPYD SNPs associated with toxicity and enzymatic activity reduction in the patient diagnosed with adenocarcinoma. The figure schematically presents the outcomes of SS for exon 11, 13, 14 (including a portion of intron 14-15), 18, 22, and intron 10. The yellow arrows indicate the forward primers used for PCR and sequencing, while the green arrows represent the reverse primers. Below the schematic representation, are reported the GRCh37/hg19 reference genome, the patient's sequence, and the electropherograms obtained through SS using the forward primer. The investigated SNPs are highlighted in red
case_images: etat-05-1002223-g001.jpg
case_images: PMC11090686_01_etat-05-1002223-g001.jpg
case_images: fig1
case_images: Using already reported primers pair, PCR-SS revealed that the patient carried the most common genotypes for rs56038477, rs1801160, rs67376798, rs3918290, and rs75017182 (Figure 1). Concerning the SNP rs55886062, a reading frameshift was observed in the electropherogram using both the forward and reverse primers (Figure 1).
case_images: WGS data visualization. The upper part of image shows the schematic representation of WGS results about the genomic region (chr1: 97981161-97981656) containing rs55886062 (chr1: 97981343). Chromosome short and long arms are reported as "p" and "q" letter in the scheme, respectively. WGS identified the presence of T/T genotype for rs55886062 (depicted in green) and an A insertion downstream the primer of the forward primer (rs145228578 or 1-97981199-T-TA, shown in purple) and upstream of the annealing region of reverse primer (rs141050810 or 1-97981622-G-GA, shown in orange). The primers used for PCR are represented in blue. In the lower part of figure, binary alignment and map (BAM) files containing WGS data from the proband are loaded into the Integrative Genomics Viewer (IGV). Noteworthy findings are highlighted in red boxes, including rs55886062 (in a green box), rs145228578 or 1-97981199-T-TA (in a purple box) and rs141050810 or 1-97981622-G-GA (in an orange box)
case_images: etat-05-1002223-g002.jpg
case_images: PMC11090686_01_etat-05-1002223-g002.jpg
case_images: fig2
case_images: Therefore, WGS results confirmed that the patient carried the homozygous T allele for rs55886062 (Figure 2, in green) and highlighted presence of one-base insertion A located downstream the forward primer (Figure 2, in violet) and another insertion upstream the annealing region of the reverse primer (Figure 2, in orange).
case_images: Frequencies of 1-97981199-T-TA and 1-97981622-G-GA across various ethnic populations. (A) Histogram displays the population frequencies of 1-97981199-T-TA obtained from the gnomAD v2.1.1 database; (B) the population frequencies of 1-97981622-G-GA taken from the same database are reported
case_images: etat-05-1002223-g003.jpg
case_images: PMC11090686_01_etat-05-1002223-g003.jpg
case_images: fig3
case_images: It is worth noting that these genetic variants were found to be quite rare among non-Finnish Europeans (0.05%) but more prevalent in Africans (16%; Figure 3).
case_images: Genotyping of rs55886062 using primer pairs designed in close proximity to the SNP site. The schematic representation displays the results of SS, employing a primer pair positioned within the region flanked by the primers previously used to amplify exon 13 of the DPYD gene. In the figure, the yellow arrow represents the forward primer used for PCR and sequencing, while the green arrow represents the reverse primer. Below the representation, the GRCh37/hg19 reference genome, the patient's sequence, and the electropherogram obtained via SS with the forward primer are reported. The investigated SNPs are highlighted in red
case_images: etat-05-1002223-g004.jpg
case_images: PMC11090686_01_etat-05-1002223-g004.jpg
case_images: fig4
case_images: Subsequent sequencing of this amplified region successfully verified the patient's genotype for rs55886062, as shown in Figure 4.