Abstract
Unlabelled Box AbstractBackgroundThe UK Genotyping and Phenotyping of Platelets study has recruited and analyzed 129 patients with suspected heritable bleeding. Previously, 55 individuals had a definitive genetic diagnosis based on whole exome sequencing (WES) and platelet morphological and functional testing. A significant challenge in this field is defining filtering criteria to identify the most likely candidate mutations for diagnosis and further study. ObjectiveIdentify candidate gene mutations for the remaining 74 patients with platelet‐based bleeding with unknown genetic cause, forming the basis of future re‐recruitment and further functional testing and assessment. MethodsUsing python‐based data frame indexing, we first identify and filter all novel and rare variants using a panel of 116 genes known to cause bleeding across the full cohort of WES data. This identified new variants not previously reported in this cohort. We then index the remaining patients, with rare or novel variants in known bleeding genes against a murine RNA sequencing dataset that models proplatelet‐forming megakaryocytes. ResultsFiltering against known genes identified candidate variants in 59 individuals, including novel variants in several known genes. In the remaining cohort of “unknown” patients, indexing against differentially expressed genes revealed candidate gene variants in several novel unreported genes, focusing on 14 patients with a severe clinical presentation. ConclusionsWe identified candidate mutations in a cohort of patients with no previous genetic diagnosis. This work involves innovative coupling of RNA sequencing and WES to identify candidate variants forming the basis of future study in a significant number of undiagnosed patients.
Highlights
The UK Genotyping and Phenotyping of Platelets (GAPP)[1] study previously reported a cohort of 55 patients with whole exome sequencing (WES) recruited from hemophilia centers nationwide with a significant clinical history of bleeding.[2]
Of the 129 patients recruited in this study and assessed by the GAPP study, 55 have been reported in previous work and are classified as having known causes of bleeding (Figure 1B)
We reasoned that an automated approach that uses an up-to-date list of clinically relevant platelet-based bleeding genes would better identify candidate mutations in the full GAPP cohort
Summary
The UK Genotyping and Phenotyping of Platelets (GAPP)[1] study previously reported a cohort of 55 patients with whole exome sequencing (WES) recruited from hemophilia centers nationwide with a significant clinical history of bleeding.[2]. 55 individuals have had a definitive genetic diagnosis to identify novel disease-causing genes (eg, SLFN14)[3] or new pathogenic variants in known genes (eg, GP1BA/B, WAS) yielding an overall detection rate of 42.63% (Figure 1B).[4,5] Through an extensive panel of platelet function testing[6] and morphological assessment,[7] these genetic findings have been correlated to the physiological and clinical effects of these rare genetic variants. The genetic causes of bleeding in a significant number of GAPP-recruited patients remain unknown, despite an established clinical and family history. We assess these individuals through a series of iterative bioinformatic filtering approaches to identify novel and “known” candidate disease-causing variants. The mean platelet volume in patients tested ranged between 8.3 fL and 15.1 fL
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