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

Johnson, Benjamin C.; Lowe, Gillian; Fütterer, Jane Wong; Lordkipanidzé, Marie; MacDonald, Deborah J.; Simpson, Michael A.; Sánchez-Guiu, Isabel; Drake, Sian; Bem, Danai; Leo, Vincenzo C.; Fletcher, Sarah J.; Dawood, B; Rivera, José; Allsup, David; Biss, Tina; Bolton-Maggs, Phb; Collins, Peter William; Curry, Nicola; Grimley, Charlotte; James, Beki; Makris, Mike; Jayashree, Muralidharan; Pavord, Sue; Talks, Katherine; Thachil, Jecko; Wilde, J. T.; Williams, M.; Harrison, Paul; Gissen, Paul; Mundell, Stuart J.; Mumford, Andrew D; Daly, Mary E.; Watson, Steve P.; Morgan, Neil V.

doi:10.3324/haematol.2016.146316

Cited by 121 publications

(154 citation statements)

References 38 publications

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“…This approach was made possible due to a pre ‐ established in‐house genomic centre and an existing close collaboration between the two coagulation units localized in the Öresund Region. To date, in the diagnostic work‐up of rare IBD, NGS‐based gene panels have been implemented by two large research collaborations: the ThromboGenomics platform (Simeoni et al , 2016) and the GAPP study group (Johnson et al , 2016). We implemented WES in our clinics, allowing consecutive expansion of the number of genes analysed.…”

Section: Discussionmentioning

confidence: 99%

“…We included both platelet‐ and non‐platelet‐related genes in the IBD gene panel and report a higher number of class 4 and 5 variants in patients with thrombocytopenia compared to those with normal platelet counts. The genetic diagnosis of rare IBD with normal platelet counts is hampered by a knowledge gap, while it is estimated that the genetic causes of thrombocytopenia have been identified in approximately 50% of patients (Johnson et al , 2016). One of the greater challenges we encountered in the process was the classification of VUS in the many relatively new genes and their subsequent translation into clinical practice.…”

Section: Discussionmentioning

confidence: 99%

“…Of particular interest, only one of our patients had a (benign) variant in the gene ( P4HB ) encoding PDI, indicating that PDI variants were not a common cause of bleeding disorders in our patient cohort. We anticipate that an additional number of our patients will be diagnosed by WES, especially those patients with a normal platelet count, given the considerable efforts that are currently being directed towards the discovery of new causal variants in IBD patients (Bariana et al , 2017; Johnson et al , 2016; Simeoni et al , 2016). …”

Section: Discussionmentioning

confidence: 99%

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Application of whole‐exome sequencing to direct the specific functional testing and diagnosis of rare inherited bleeding disorders in patients from the Öresund Region, Scandinavia

et al. 2017

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SummaryRare inherited bleeding disorders (IBD) are a common cause of bleeding tendency. To ensure a correct diagnosis, specialized laboratory analyses are necessary. This study reports the results of an upfront diagnostic strategy using targeted whole exome sequencing. In total, 156 patients with a significant bleeding assessment tool score participated in the study, of which a third had thrombocytopenia. Eighty‐seven genes specifically associated with genetic predisposition to bleeding were analysed by whole exome sequencing. Variants were classified according to the five‐tier scheme. We identified 353 germline variants. Eight patients (5%) harboured a known pathogenic variant. Of the 345 previously unknown variants, computational analyses predicted 99 to be significant. Further filtration according to the Mendelian inheritance pattern, resulted in 59 variants being predicted to be clinically significant. Moreover, 34% (20/59) were assigned as novel class 4 or 5 variants upon targeted functional testing. A class 4 or 5 variant was identified in 30% of patients with thrombocytopenia (14/47) versus 11% of patients with a normal platelet count (12/109) (P < 0·01). An IBD diagnosis has a major clinical impact. The genetic investigations detailed here extricated our patients from a diagnostic conundrum, thus demonstrating that continuous optimization of the diagnostic work‐up of IBD is of great benefit.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Application of whole‐exome sequencing to direct the specific functional testing and diagnosis of rare inherited bleeding disorders in patients from the Öresund Region, Scandinavia

et al. 2017

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“…Previous studies by the UK‐GAPP study group have demonstrated the applicability of using light transmission aggregometry (LTA), including lumiaggregometry, for investigation of PRP samples having platelet counts exceeding 1 × 10 8 /mL 13 and an in‐house flow‐cytometry assay to assess platelet function in patients having platelet counts in PRP of less than 1 × 10 8 /mL 12 …”

Section: Methodsmentioning

confidence: 99%

“…Due to the high percentage of variants within known IT genes as identified by whole exome sequencing (WES) in a previous study, 12 and the increasing advances in custom panel next generation sequencing, an IT‐specific next‐generation sequencing (NGS) panel was designed and included within the UK‐GAPP patient workflow. Incorporating a small custom panel prior to WES has the potential to filter out variants with a genetic etiology of disease within known IT‐causing genes.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive targeted next‐generation sequencing panel for genetic diagnosis of patients with suspected inherited thrombocytopenia

Johnson

Doak

Allsup

et al. 2018

Research and Practice in Thrombosis and Haemostasis

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BackgroundInherited thrombocytopenias (ITs) are a heterogeneous group of disorders characterized by low platelet counts and often disproportionate bleeding with over 30 genes currently implicated. Previously the UK‐GAPP study using whole exome sequencing (WES) identified a pathogenic variant in 19 of 47 (40%) patients of which 71% had variants in genes known to cause IT.AimsTo employ a targeted next‐generation sequencing platform to improve efficiency of diagnostic testing and reduce overall costs.MethodsWe have developed an IT‐specific gene panel as a pre‐screen for patients prior to WES using the Agilent SureSelectQXT transposon‐based enrichment system.ResultsThirty‐one patients were analyzed using the panel‐based sequencing, of which; 10% (3/31) were identified with a classified pathogenic variant, 16% (5/31) were identified with a likely pathogenic variant, 51% (16/31) were identified with variants of unknown significance, and 23% (7/31) were identified with either no variant or a benign variant.Discussion and ConclusionAlthough requiring further clarification of the impact of the genetic variations, the application of an IT‐specific next generation sequencing panel is an viable method of pre‐screening patients for variants in known IT‐causing genes prior to WES. With an added benefit of distinguishing IT from idiopathic thrombocytopenic purpura (ITP) and the potential to identify variants in genes known to have a predisposition to hematological malignancies, it could become a critical step in improving patient clinical management.

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Investigation of calmodulin‐like and rod domain mutations suggests common molecular mechanism for α‐actinin‐1‐linked congenital macrothrombocytopenia

et al. 2019

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Actinin-1 mutations cause dominantly inherited congenital macrothrombocytopenia (CMTP), with mutations in the actin-binding domain increasing actinin's affinity for F-actin. In this study, we examined nine CMTP-causing mutations in the calmodulin-like and rod domains of actinin-1. These mutations increase, to varying degrees, actinin's ability to bundle actin filaments in vitro. Mutations within the calmodulin-like domain decrease its thermal stability slightly but do not dramatically affect calcium binding, with mutant proteins retaining calcium-dependent regulation of filament bundling in vitro. The G764S and E769K mutations increase cytoskeletal association of actinin in cells, and all mutant proteins colocalize with F-actin in cultured HeLa cells. Thus, CMTP-causing actinin-1 mutations outside the actin-binding domain also increase actin association, suggesting a common molecular mechanism underlying actinin-1 related CMTP.

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

Cited by 121 publications

References 38 publications

Application of whole‐exome sequencing to direct the specific functional testing and diagnosis of rare inherited bleeding disorders in patients from the Öresund Region, Scandinavia

Application of whole‐exome sequencing to direct the specific functional testing and diagnosis of rare inherited bleeding disorders in patients from the Öresund Region, Scandinavia

A comprehensive targeted next‐generation sequencing panel for genetic diagnosis of patients with suspected inherited thrombocytopenia

Investigation of calmodulin‐like and rod domain mutations suggests common molecular mechanism for α‐actinin‐1‐linked congenital macrothrombocytopenia

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