Whole exome sequencing identifies genetic variants in inherited thrombocytopenia with secondary qualitative function defects

Abstract

Inherited thrombocytopenias are a heterogeneous group of disorders characterized by abnormally low platelet counts which can be associated with abnormal bleeding. Next-generation sequencing has previously been employed in these disorders for the confirmation of suspected genetic abnormalities, and more recently in the discovery of novel disease-causing genes. However its full potential has not yet been exploited. Over the past 6 years we have sequenced the exomes from 55 patients, including 37 index cases and 18 additional family members, all of whom were recruited to the UK Genotyping and Phenotyping of Platelets study. All patients had inherited or sustained thrombocytopenia of unknown etiology with platelet counts varying from 11×10⁹/L to 186×10⁹/L. Of the 51 patients phenotypically tested, 37 (73%), had an additional secondary qualitative platelet defect. Using whole exome sequencing analysis we have identified "pathogenic" or "likely pathogenic" variants in 46% (17/37) of our index patients with thrombocytopenia. In addition, we report variants of uncertain significance in 12 index cases, including novel candidate genetic variants in previously unreported genes in four index cases. These results demonstrate that whole exome sequencing is an efficient method for elucidating potential pathogenic genetic variants in inherited thrombocytopenia. Whole exome sequencing also has the added benefit of discovering potentially pathogenic genetic variants for further study in novel genes not previously implicated in inherited thrombocytopenia.

Figure 1.

Bioinformatics pipeline analysis of whole exome sequencing data. Initial WES analysis focused on comparison with a panel of 358 genes (Online Supplementary Table S1), after which screening of exome variants focused on novel variants. Variants were classified using the ACMG consensus guidelines.

Figure 2.

Spatial amino acid locations of all thrombocytopenia-causing variants present within RUNT transcription factor 1 (RUNX1) (RefSeq NP_001001890). Previously disease-causing variants found the HGMD (www.hgmd.cf.ac.uk) and ClinVar (www.ncbi.nlm.nih.gov/clinvar/) databases are denoted above. The eight variants found within RUNX1 in the GAPP cohort of 54 patients who have undergone whole exome sequencing are denoted below and the effect on the protein or predicted splice-site is shown.