Semin Thromb Hemost 2019; 45(07): 685-694
DOI: 10.1055/s-0039-1687888
Review Article
Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Genetic Techniques Used in the Diagnosis of Inherited Platelet Disorders

Andrew D. Mumford
1   School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
,
Sarah K. Westbury
1   School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
› Author Affiliations
Further Information

Publication History

Publication Date:
30 April 2019 (online)

Abstract

Recent advances in genetic analysis are bringing huge benefits to patients with rare genetic disorders, including those with inherited disorders of platelet number and function. Modern clinical hematological practice now has a range of genetic techniques available to enable the precision diagnosis of inherited platelet disorders (IPDs). There are some features of this disparate group of inherited disorders that present specific challenges to establishing an accurate genetic diagnosis. This review aims to introduce the techniques that are relevant for the genetic diagnosis of IPDs and will discuss the key considerations necessary for their application to the clinic.

 
  • References

  • 1 Morison IM, Cramer Bordé EM, Cheesman EJ. , et al. A mutation of human cytochrome c enhances the intrinsic apoptotic pathway but causes only thrombocytopenia. Nat Genet 2008; 40 (04) 387-389
  • 2 Daly ME. Transcription factor defects causing platelet disorders. Blood Rev 2017; 31 (01) 1-10
  • 3 Pecci A, Gresele P, Klersy C. , et al. Eltrombopag for the treatment of the inherited thrombocytopenia deriving from MYH9 mutations. Blood 2010; 116 (26) 5832-5837
  • 4 Rabbolini DJ, Chun Y, Latimer M. , et al. Diagnosis and treatment of MYH9-RD in an Australasian cohort with thrombocytopenia. Platelets 2017; 1: 1-8
  • 5 Westbury SK, Downes K, Burney C. , et al; NIHR BioResource–Rare Diseases. Phenotype description and response to thrombopoietin receptor agonist in DIAPH1-related disorder. Blood Adv 2018; 2 (18) 2341-2346
  • 6 Harrison P, Mackie I, Mumford A. , et al; British Committee for Standards in Haematology. Guidelines for the laboratory investigation of heritable disorders of platelet function. Br J Haematol 2011; 155 (01) 30-44
  • 7 Hayward CP, Pai M, Liu Y. , et al. Diagnostic utility of light transmission platelet aggregometry: results from a prospective study of individuals referred for bleeding disorder assessments. J Thromb Haemost 2009; 7 (04) 676-684
  • 8 Quiroga T, Goycoolea M, Panes O. , et al. High prevalence of bleeders of unknown cause among patients with inherited mucocutaneous bleeding. A prospective study of 280 patients and 299 controls. Haematologica 2007; 92 (03) 357-365
  • 9 Neuhaus C, Lang-Roth R, Zimmermann U. , et al. Extension of the clinical and molecular phenotype of DIAPH1-associated autosomal dominant hearing loss (DFNA1). Clin Genet 2017; 91 (06) 892-901
  • 10 Stritt S, Nurden P, Turro E. , et al; BRIDGE-BPD Consortium. A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss. Blood 2016; 127 (23) 2903-2914
  • 11 Ueyama T, Ninoyu Y, Nishio SY. , et al. Constitutive activation of DIA1 (DIAPH1) via C-terminal truncation causes human sensorineural hearing loss. EMBO Mol Med 2016; 8 (11) 1310-1324
  • 12 Canault M, Ghalloussi D, Grosdidier C. , et al. Human CalDAG-GEFI gene (RASGRP2) mutation affects platelet function and causes severe bleeding. J Exp Med 2014; 211 (07) 1349-1362
  • 13 Muller WA. Identification of a severe bleeding disorder in humans caused by a mutation in CalDAG-GEFI. J Exp Med 2014; 211 (07) 1271
  • 14 Pecci A, Panza E, Pujol-Moix N. , et al. Position of nonmuscle myosin heavy chain IIA (NMMHC-IIA) mutations predicts the natural history of MYH9-related disease. Hum Mutat 2008; 29 (03) 409-417
  • 15 Pecci A, Klersy C, Gresele P. , et al. MYH9-related disease: a novel prognostic model to predict the clinical evolution of the disease based on genotype-phenotype correlations. Hum Mutat 2014; 35 (02) 236-247
  • 16 Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 1986; 51 (Pt 1): 263-273
  • 17 Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74 (12) 5463-5467
  • 18 Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A 1977; 74 (02) 560-564
  • 19 Bentley DR, Balasubramanian S, Swerdlow HP. , et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008; 456 (7218): 53-59
  • 20 Shendure J, Porreca GJ, Reppas NB. , et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309 (5741): 1728-1732
  • 21 Rothberg JM, Hinz W, Rearick TM. , et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475 (7356): 348-352
  • 22 Kunishima S, Kitamura K, Yasutomi M, Kobayashi R. Diagnostic biomarker for ACTN1 macrothrombocytopenia. Blood 2015; 126 (22) 2525-2526
  • 23 Kunishima S, Nishimura S, Suzuki H, Imaizumi M, Saito H. TUBB1 mutation disrupting microtubule assembly impairs proplatelet formation and results in congenital macrothrombocytopenia. Eur J Haematol 2014; 92 (04) 276-282
  • 24 Sadananda SN, Foo JN, Toh MT. , et al. Targeted next-generation sequencing to diagnose disorders of HDL cholesterol. J Lipid Res 2015; 56 (10) 1993-2001
  • 25 Millat G, Chanavat V, Rousson R. Evaluation of a new high-throughput next-generation sequencing method based on a custom AmpliSeq™ library and ion torrent PGM™ sequencing for the rapid detection of genetic variations in long QT syndrome. Mol Diagn Ther 2014; 18 (05) 533-539
  • 26 Roy NB, Wilson EA, Henderson S. , et al. A novel 33-Gene targeted resequencing panel provides accurate, clinical-grade diagnosis and improves patient management for rare inherited anaemias. Br J Haematol 2016; 175 (02) 318-330
  • 27 Simeoni I, Stephens JC, Hu F. , et al. A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders. Blood 2016; 127 (23) 2791-2803
  • 28 Richards S, Aziz N, Bale S. , et al; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17 (05) 405-424
  • 29 Jones ML, Murden SL, Bem D. , et al; UK GAPP study group. Rapid genetic diagnosis of heritable platelet function disorders with next-generation sequencing: proof-of-principle with Hermansky-Pudlak syndrome. J Thromb Haemost 2012; 10 (02) 306-309
  • 30 Bastida JM, Lozano ML, Benito R. , et al. Introducing high-throughput sequencing into mainstream genetic diagnosis practice in inherited platelet disorders. Haematologica 2018; 103 (01) 148-162
  • 31 Sulonen AM, Ellonen P, Almusa H. , et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol 2011; 12 (09) R94
  • 32 Auton A, Brooks LD, Durbin RM. , et al; 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 2015; 526 (7571): 68-74
  • 33 Johnson B, Lowe GC, Futterer J. , et al; UK GAPP Study Group. Whole exome sequencing identifies genetic variants in inherited thrombocytopenia with secondary qualitative function defects. Haematologica 2016; 101 (10) 1170-1179
  • 34 Leo VC, Morgan NV, Bem D. , et al; UK GAPP Study Group. Use of next-generation sequencing and candidate gene analysis to identify underlying defects in patients with inherited platelet function disorders. J Thromb Haemost 2015; 13 (04) 643-650
  • 35 Westbury SK, Turro E, Greene D. , et al; BRIDGE-BPD Consortium. Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. Genome Med 2015; 7 (01) 36
  • 36 Fletcher SJ, Johnson B, Lowe GC. , et al; UK Genotyping and Phenotyping of Platelets study group. SLFN14 mutations underlie thrombocytopenia with excessive bleeding and platelet secretion defects. J Clin Invest 2015; 125 (09) 3600-3605
  • 37 Leinøe E, Zetterberg E, Kinalis S. , et al. 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. Br J Haematol 2017; 179 (02) 308-322
  • 38 Spielmann M, Mundlos S. Looking beyond the genes: the role of non-coding variants in human disease. Hum Mol Genet 2016; 25 (R2): R157-R165
  • 39 Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nat Rev Genet 2010; 11 (08) 559-571
  • 40 Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). Available at: www.genome.gov/sequencingcostsdata . Accessed June 2018
  • 41 Pleines I, Woods J, Chappaz S. , et al. Mutations in tropomyosin 4 underlie a rare form of human macrothrombocytopenia. J Clin Invest 2017; 127 (03) 814-829
  • 42 Turro E, Greene D, Wijgaerts A. , et al; BRIDGE-BPD Consortium. A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies. Sci Transl Med 2016; 8 (328) 328ra30
  • 43 Sivapalaratnam S, Westbury SK, Stephens JC. , et al; NIHR BioResource. Rare variants in GP1BB are responsible for autosomal dominant macrothrombocytopenia. Blood 2017; 129 (04) 520-524
  • 44 Westbury SK, Canault M, Greene D. , et al; NIHR BioResource–Rare Diseases Consortium. Expanded repertoire of RASGRP2 variants responsible for platelet dysfunction and severe bleeding. Blood 2017; 130 (08) 1026-1030
  • 45 Albers CA, Paul DS, Schulze H. , et al. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat Genet 2012; 44 (04) 435-439 , S1–S2
  • 46 Hayward CP, Liang M, Tasneem S. , et al. The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes. PLoS One 2017; 12 (03) e0173991
  • 47 Nurden AT, Freson K, Seligsohn U. Inherited platelet disorders. Haemophilia 2012; 18 (Suppl. 04) 154-160
  • 48 Breton-Gorius J, Favier R, Guichard J. , et al. A new congenital dysmegakaryopoietic thrombocytopenia (Paris-Trousseau) associated with giant platelet alpha-granules and chromosome 11 deletion at 11q23. Blood 1995; 85 (07) 1805-1814
  • 49 Nakagawa M, Okuno M, Okamoto N, Fujino H, Kato H. Bernard-Soulier syndrome associated with 22q11.2 microdeletion. Am J Med Genet 2001; 99 (04) 286-288
  • 50 Ren H, Francis W, Boys A. , et al. BAC-based PCR fragment microarray: high-resolution detection of chromosomal deletion and duplication breakpoints. Hum Mutat 2005; 25 (05) 476-482
  • 51 Koboldt DC, Larson DE, Chen K, Ding L, Wilson RK. Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol 2012; 838: 369-384
  • 52 Hayes JL, Tzika A, Thygesen H. , et al. Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation. Genomics 2013; 102 (03) 174-181
  • 53 Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet 2008; 83 (05) 610-615
  • 54 Köhler S, Doelken SC, Mungall CJ. , et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 2014; 42 (Database issue): D966-D974
  • 55 Köhler S, Vasilevsky NA, Engelstad M. , et al. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2017; 45 (D1): D865-D876
  • 56 Greene D, Richardson S, Turro E. ; NIHR BioResource. Phenotype similarity regression for identifying the genetic determinants of rare diseases. Am J Hum Genet 2016; 98 (03) 490-499
  • 57 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215 (03) 403-410
  • 58 Rehm HL, Bale SJ, Bayrak-Toydemir P. , et al; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15 (09) 733-747
  • 59 Lek M, Karczewski KJ, Minikel EV. , et al; Exome Aggregation Consortium. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016; 536 (7616): 285-291
  • 60 McLaren W, Gil L, Hunt SE. , et al. The Ensembl variant effect predictor. Genome Biol 2016; 17 (01) 122
  • 61 Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009; 4 (07) 1073-1081
  • 62 Adzhubei IA, Schmidt S, Peshkin L. , et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 7 (04) 248-249
  • 63 Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014; 46 (03) 310-315
  • 64 Strande NT, Riggs ER, Buchanan AH. , et al. Evaluating the clinical validity of gene-disease associations: an evidence-based framework Developed by the Clinical Genome Resource. Am J Hum Genet 2017; 100 (06) 895-906
  • 65 Stenson PD, Mort M, Ball EV. , et al. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017; 136 (06) 665-677
  • 66 Landrum MJ, Lee JM, Benson M. , et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 2016; 44 (D1): D862-D868
  • 67 Landrum MJ, Lee JM, Benson M. , et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res 2018; 46 (D1): D1062-D1067
  • 68 Matthijs G, Souche E, Alders M. , et al. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet 2016; 24 (10) 1515
  • 69 Karbassi I, Maston GA, Love A. , et al. A standardized DNA variant scoring system for pathogenicity assessments in Mendelian disorders. Hum Mutat 2016; 37 (01) 127-134