Fig. 2

Association and validation of guanylate binding protein 5 (GBP5) differential splicing with rs80800372 genotype. a Schematic of the sequence level differences between the three alternate transcripts of GBP5, including the position of the putative causal variant (rs340943904, bracketed). The schematic displays how the rs340943904 G allele creates a new splice acceptor site in intron 9 (underlined blue text) while the T allele destroys the splice site. The wild-type splicing transcript includes only the sequence in black, while the +5bp insert transcript includes the extra five nucleotides shown in blue. The retained intron transcript includes the entire 281 nucleotide intron. The rs340943904 G allele is in perfect linkage disequilibrium (LD) with the unfavorable rs80800372 “A” allele while the rs340943904 T allele is in perfect LD with the favorable rs80800372 “B” allele. b Differential splicing of GBP5 by rs80800372 genotype across all days post infection (dpi) time points. Splicing was measured as the percentage of read counts from each alternate transcript standardized for all read counts from the PHGC trial 3 RNA-seq data. This figure demonstrates that very little wild-type splicing transcript is produced by the AA (red) genotype compared to the AB (blue) rs80800372 genotype (p<0.0001; Bonferonni adjusted p<0.001). In contrast, considerably more of the alternate transcript (+5bps insertion) is produced in the AA compared to the AB rs80800372 genotyped individuals. c Confirmation of GBP5 differential splicing due to rs80800372 genotype across all dpi following infection using quantitative capillary electrophoresis. This analysis validates that very little or no wild-type splicing transcript is produced by AA (red) vs. AB (blue) SSC4 rs80800372 genotyped individuals (p<0.01; Bonferonni adjusted p<0.05). Consistent with the RNA-seq results, more of the alternate transcript with five extra nucleotides is quantified in blood RNA from AA vs. AB rs80800372 genotyped individuals. Expression values are presented as transcript molarity