Extended Data Fig. 10: Thrombocytopenia due to compound regulatory and coding rare variants in MPL.
From: Whole-genome sequencing of patients with rare diseases in a national health system
a, Top, smoothed covariance between H3K27ac ChIP–seq and ATAC-seq (as in Fig. 4a) and coverage tracks generated by RedPop for activated CD4+ T cells (aCD4), B cells, erythroblasts, megakaryocytes, monocytes and resting CD4+ T cells (rCD4). Middle, MPL gene with exons in yellow. Bottom, positions of the deletion (blue bar) and SNV (blue dot) in the proband. b, Pedigree for the proband with thrombocytopenia owing to a 454-bp deletion encompassing exon 10 of MPL, which was inherited from the mother, and an SNV just upstream of the 5′ untranslated region of MPL. c, Sanger sequencing traces confirming the presence of the heterozygous SNV in the proband and its absence in the mother. d, Gel electrophoresis of PCR amplicons covering the deletion confirming presence of the deletion in the proband and the mother. The PCR was conducted on two independent samples in the proband and once in the mother and the control (wt). e, MFI on the y-axis obtained by the flow cytometry measurement of MPL abundance (CD110) on the membrane of platelets from five unrelated healthy controls, the mother and the proband. The MFI was normalized to unstained platelets. We fitted a linear regression model with an intercept term representing the mean in the control, a coefficient representing the difference in means between the mother and control (P = 0.1828) and a coefficient representing the difference in means between the proband and control (P = 0.0086). Distribution summaries show mean ± s.e.m. where multiple observations are available. f, Results of luciferase reporter assays in K562 cells expressing empty pGL3 vector or after cloning with an MPL promoter fragment containing the wild-type G allele (MPL-SNV-G) or the variant A allele (MPL-SNV-A). The measurements were derived from n = 4 independent transfection experiments. The P values were obtained by one-way ANOVA and adjusted for multiple comparisons using Tukey’s method. Distribution summaries show mean ± s.e.m.
