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A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.

ABSTRACT: Inherited bleeding, thrombotic, and platelet disorders (BPDs) are diseases that affect ∼300 individuals per million births. With the exception of hemophilia and von Willebrand disease patients, a molecular analysis for patients with a BPD is often unavailable. Many specialized tests are usually required to reach a putative diagnosis and they are typically performed in a step-wise manner to control costs. This approach causes delays and a conclusive molecular diagnosis is often never reached, which can compromise treatment and impede rapid identification of affected relatives. To address this unmet diagnostic need, we designed a high-throughput sequencing platform targeting 63 genes relevant for BPDs. The platform can call single nucleotide variants, short insertions/deletions, and large copy number variants (though not inversions) which are subjected to automated filtering for diagnostic prioritization, resulting in an average of 5.34 candidate variants per individual. We sequenced 159 and 137 samples, respectively, from cases with and without previously known causal variants. Among the latter group, 61 cases had clinical and laboratory phenotypes indicative of a particular molecular etiology, whereas the remainder had an a priori highly uncertain etiology. All previously detected variants were recapitulated and, when the etiology was suspected but unknown or uncertain, a molecular diagnosis was reached in 56 of 61 and only 8 of 76 cases, respectively. The latter category highlights the need for further research into novel causes of BPDs. The ThromboGenomics platform thus provides an affordable DNA-based test to diagnose patients suspected of having a known inherited BPD.

SUBMITTER: Simeoni I

PROVIDER: S-EPMC5016734 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.

Simeoni Ilenia I Stephens Jonathan C JC Hu Fengyuan F Deevi Sri V V SV Megy Karyn K Bariana Tadbir K TK Lentaigne Claire C Schulman Sol S Sivapalaratnam Suthesh S Vries Minka J A MJ Westbury Sarah K SK Greene Daniel D Papadia Sofia S Alessi Marie-Christine MC Attwood Antony P AP Ballmaier Matthias M Baynam Gareth G Bermejo Emilse E Bertoli Marta M Bray Paul F PF Bury Loredana L Cattaneo Marco M Collins Peter P Daugherty Louise C LC Favier Rémi R French Deborah L DL Furie Bruce B Gattens Michael M Germeshausen Manuela M Ghevaert Cedric C Goodeve Anne C AC Guerrero Jose A JA Hampshire Daniel J DJ Hart Daniel P DP Heemskerk Johan W M JW Henskens Yvonne M C YM Hill Marian M Hogg Nancy N Jolley Jennifer D JD Kahr Walter H WH Kelly Anne M AM Kerr Ron R Kostadima Myrto M Kunishima Shinji S Lambert Michele P MP Liesner Ri R López José A JA Mapeta Rutendo P RP Mathias Mary M Millar Carolyn M CM Nathwani Amit A Neerman-Arbez Marguerite M Nurden Alan T AT Nurden Paquita P Othman Maha M Peerlinck Kathelijne K Perry David J DJ Poudel Pawan P Reitsma Pieter P Rondina Matthew T MT Smethurst Peter A PA Stevenson William W Szkotak Artur A Tuna Salih S van Geet Christel C Whitehorn Deborah D Wilcox David A DA Zhang Bin B Revel-Vilk Shoshana S Gresele Paolo P Bellissimo Daniel B DB Penkett Christopher J CJ Laffan Michael A MA Mumford Andrew D AD Rendon Augusto A Gomez Keith K Freson Kathleen K Ouwehand Willem H WH Turro Ernest E

Blood 20160415 23

Inherited bleeding, thrombotic, and platelet disorders (BPDs) are diseases that affect ∼300 individuals per million births. With the exception of hemophilia and von Willebrand disease patients, a molecular analysis for patients with a BPD is often unavailable. Many specialized tests are usually required to reach a putative diagnosis and they are typically performed in a step-wise manner to control costs. This approach causes delays and a conclusive molecular diagnosis is often never reached, whi ...[more]

PMID: 27084890

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Project description:Excessive bleeding at surgery is a feared complication in patients with inherited platelet disorders. However, very few studies have evaluated the frequency of surgical bleeding in these hemorrhagic disorders. We performed a worldwide, multicentric, retrospective study to assess the bleeding complications of surgery, the preventive and therapeutic approaches adopted, and their efficacy in patients with inherited platelet disorders: the Surgery in Platelet disorders And Therapeutic Approach (SPATA) study. We rated the outcome of 829 surgical procedures carried out in 423 patients with well-defined forms of inherited platelet disorders: 238 inherited platelet function disorders and 185 inherited platelet number disorders. Frequency of surgical bleeding was high in patients with inherited platelet disorders (19.7%), with a significantly higher bleeding incidence in inherited platelet function disorders (24.8%) than in inherited platelet number disorders (13.4%). The frequency of bleeding varied according to the type of inherited platelet disorder, with biallelic Bernard Soulier syndrome having the highest occurrence (44.4%). Frequency of bleeding was predicted by a pre-operative World Health Organization bleeding score of 2 or higher. Some types of surgery were associated with a higher bleeding incidence, like cardiovascular and urological surgery. The use of pre-operative pro-hemostatic treatments was associated with a lower bleeding frequency in patients with inherited platelet function disorders but not in inherited platelet number disorders. Desmopressin, alone or with antifibrinolytic agents, was the preventive treatment associated with the lowest bleedings. Platelet transfusions were used more frequently in patients at higher bleeding risk. Surgical bleeding risk in inherited platelet disorders is substantial, especially in inherited platelet function disorders, and bleeding history, type of disorder, type of surgery and female sex are associated with higher bleeding frequency. Prophylactic pre-operative pro-hemostatic treatments appear to be required and are associated with a lower bleeding incidence.

Project description:IntroductionBreast cancer is the most diagnosed and second leading cause of cancer deaths in the U.S. female population. An estimated 5 to 10 percent of all breast cancers are inherited, caused by mutations in the breast cancer susceptibility genes (BRCA1/2). As many as 90% of all mutations are nonsense mutations, causing a truncated polypeptide product. A popular and low cost method of mutation detection has been the protein truncation test (PTT), where target regions of BRCA1/2 are PCR amplified, transcribed/translated in a cell-free protein synthesis system and analyzed for truncated polypeptides by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and autoradiography. We previously reported a novel High Throughput Solid-Phase PTT (HTS-PTT) based on an enzyme-linked immunosorbent assay (ELISA) format that eliminates the need for radioactivity, SDS-PAGE and subjective interpretation of the results. Here, we report the next generation HTS-PTT using triple-epitope-tagged proteins and demonstrate, for the first time, its efficacy on clinical genomic DNA samples for BRCA1/2 analysis.MethodsSegments of exons 11 of BRCA1/2 open reading frames were PCR amplified from either blood derived genomic DNA or cell line mRNA. PCR primers incorporate elements for cell-free transcription/translation and epitope tagging. Cell-free expressed nascent proteins are then antibody-captured onto the wells of a microtiter plate and the relative amount of truncated polypeptide measured using antibodies against the N- and C-terminal epitope tags in an ELISA format.Results100% diagnostic sensitivity and 96% specificity for truncating mutations in exons 11 of BRCA1/2 was achieved on one hundred blood-derived clinical genomic DNA samples which were previously assayed using the conventional gel based PTT. Feasibility of full gene coverage for BRCA1/2 using mRNA source material is also demonstrated.ConclusionsOverall, the HTS-PTT provides a simple, quantitative, objective, low cost and high throughput method for analysis of truncating mutations as an alternative to gel based PTT for BRCA analysis. The technology is readily accessible to virtually any laboratory, with the only major instrumentation required being a PCR thermocycler and a basic micro-well plate reader. When compared to conventional gel based PTT, the HTS-PTT provides excellent concordance.

Dataset Information

A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.

Publications

A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.

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