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A comprehensive high-throughput sequencing test for the diagnosis of inherited bleeding, thrombotic and platelet disorders

Ilenia Simeoni, Jonathan C. Stephens, Fengyuan Hu, Sri V.V. Deevi, Karyn Megy, Tadbir K. Bariana, Claire Lentaigne, Sol Schulman, Suthesh Sivapalaratnam, Minka J.A. Vries, Sarah K. Westbury, Daniel Greene, Sofia Papadia, Marie-Christine Alessi, Antony P. Attwood, Matthias Ballmaier, Gareth Baynam, Emilse Bermejo, Marta Bertoli, Paul F. Bray, Loredana Bury, Marco Cattaneo, Peter Collins, Louise C. Daugherty, Rémi Favier, Deborah L. French, Bruce Furie, Michael Gattens, Manuela Germeshausen, Cedric Ghevaert, Anne Goodeve, Jose Guerrero, Daniel J. Hampshire, Daniel P. Hart, Johan W.M. Heemskerk, Yvonne M.C. Henskens, Marian Hill, Nancy Hogg, Jennifer D. Jolley, Walter H. Kahr, Anne M. Kelly, Ron Kerr, Myrto Kostadima, Shinji Kunishima, Michele P. Lambert, Ri Liesner, Jose Lopez, Rutendo P. Mapeta, Mary Mathias, Carolyn M. Millar, Amit Nathwani, Marguerite Neerman-Arbez, Alan T. Nurden, Paquita Nurden, Maha Othman, Kathelijne Peerlinck, David J. Perry, Pawan Poudel, Pieter Reitsma, Matthew Rondina, Peter A. Smethurst, William Stevenson, Artur Szkotak, Salih Tuna, Christel van Geet, Deborah Whitehorn, David A. Wilcox, Bin Zhang, Shoshana Revel-Vilk, Paolo Gresele, Daniel Bellissimo, Christopher J. Penkett, Michael A. Laffan, Andrew D. Mumford, Augusto Rendon, Keith Gomez, Kathleen Freson, Willem H. Ouwehand and Ernest Turro

Key points

  • We have developed a targeted sequencing platform covering 63 genes linked to heritable bleeding, thrombotic and platelet disorders.

  • The ThromboGenomics platform provides a sensitive genetic test to obtain molecular diagnoses in patients with a suspected etiology.

Abstract

Inherited bleeding, thrombotic and platelet disorders (BPDs) are diseases affecting approximately 300 individuals per million births. With the exception of haemophilia and von Willebrand disease patients, a molecular analysis for patients with a BPD is often unavailable. Many specialised 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 (HTS) platform targeting 63 genes relevant for BPDs. The platform can call single nucleotide variants (SNVs), short insertions/deletions (indels) and large copy number variants (CNVs), 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 while 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 eight 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.

  • Submitted December 28, 2015.
  • Accepted April 7, 2016.