The role of genetic sequencing in the diagnostic workup for chronic immune thrombocytopenia

Abstract

Immune thrombocytopenia (ITP) is a heterogenous autoimmune disorder diagnosed by excluding other conditions. Misdiagnosis of primary ITP occurs in patients with inherited thrombocytopenia and primary immunodeficiency syndromes. This study investigates whether genetic testing for inherited thrombocytopenia or primary immunodeficiency can enhance diagnostic accuracy in ITP, and guide treatment strategies. We performed whole genome sequencing or targeted panel sequencing on peripheral blood samples in a cohort of 80 participants with chronic ITP, utilizing the ThromboGenomics panel (n = 72) and the Genomics of Rare Immune Disorders panel (n = 50) consisting of genes known to cause bleeding and platelet disorders (BPDG) or primary immuodeficiency genes (PIDG) respectively. A replication cohort of 73 patients underwent clinical genomics testing with either the R90 (BPDG, n = 35) or R15 (PIDG, n = 50) National Health Service Genomics panels. Known pathogenic or likely pathogenic, disease-causing, variants were identified in 9 patients in the first cohort (11%, 95% confidence interval [CI]: 5-20); 7 patients (10%, 95% CI: 4-19) in BPDG and 2 patients (4% CI,1-14) in PIDG. In addition, 26 patients (32.5%) carried variants of uncertain significance. In the replication cohort, 8% (95% CI, 2-20) and 9% (95% CI, 2-23) of patients had a pathogenic variant identified on the R15 (PIDG) or R90 panel (BPDG), respectively. The findings impacted clinical management such as avoidance of immunosuppression (ANKRD26, GP1BB, ETV6, TUBB1, and ITGB3) and eligibility for allogeneic stem cell transplantation (UNC13D). Our findings demonstrate that genomic sequencing identifies diagnostically relevant variants in patients with chronic ITP. Identification of these variants can guide treatment decisions and improve patient outcomes.

Graphical abstract

Figure 1.

Study participants and genomic sequencing method. 100kGP, 100,000 Genomes Project; NIHR RDC, National Institute of Health Research Rare Diseases Consortium.

Figure 2.

Patients with identified variants, stratified by sequencing method. 100kGP, 100,000 Genomes Project; NIHR RDC, National Institute of Health Research Rare Diseases Consortium; P, pathogenic.

Figure 3.

Variant association with clinical and demographic variables. (A) Clinical characteristics separated by cohort of those with a variant identified and those without. Clinical characteristics include P values for χ² test of association. (B) Variant detection stratified by demographic variables.

Figure 4.

Proportion of patients (%) with pathogenic or LP variants identified with binomial CIs in the test and replication cohorts.

Figure 5.

Distribution of variants identified by gene and ACMG classification. ACMG, American College of Medical Genetics.

Figure 6.

Number of patients (correlates to size of segment) with variants identified per gene and mode of inheritance in test and replication cohorts. Any genes with pathogenic or LP variants are in red font.