Use of next-generation sequencing and candidate gene analysis to identify underlying defects in patients with inherited platelet function disorders

Journal of Thrombosis and Haemostasis

Volumn 13, Issue 4, 2015, Pages 643-650

  Leo, V C ^a   Morgan, N V ^b   Bem, D ^b   Jones, M L ^c   Lowe, G C ^b   Lordkipanidze M ^b   Drake, S ^b   Simpson, M A ^d   Gissen, P ^e   Mumford, A ^c   Watson, S P ^b   Daly, M E ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

^d GUY S HOSPITAL   (United Kingdom)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bioinformatics; Bleeding; Blood platelet disorders; High throughput DNA sequencing; Platelets

Indexed keywords

DNA; GUANINE NUCLEOTIDE BINDING PROTEIN; PROTEINASE ACTIVATED RECEPTOR 1; GENETIC MARKER; INHIBITORY GUANINE NUCLEOTIDE BINDING PROTEIN;

ADOLESCENT; ADULT; AGED; ALGORITHM; ARTICLE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; EXOME; FEMALE; GENE CLUSTER; GENE IDENTIFICATION; GENE ONTOLOGY; GENETIC ANALYSIS; GENOTYPE; HOMOZYGOTE; HUMAN; INDEL MUTATION; INHERITED PLATELET FUNCTION DISORDER; MALE; MISSENSE MUTATION; NEXT GENERATION SEQUENCING; PATHOGENICITY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SIGNAL TRANSDUCTION; SPLICING DEFECT; THROMBOCYTE AGGREGATION; THROMBOCYTE DISORDER; THROMBOCYTE FUNCTION; BIOLOGY; BLOOD; BLOOD PLATELET DISORDERS; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; GENETIC ASSOCIATION STUDY; GENETIC MARKER; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; HEREDITY; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; METABOLISM; MIDDLE AGED; MUTATION; PREDICTIVE VALUE; PROCEDURES; SECRETION (PROCESS); SINGLE NUCLEOTIDE POLYMORPHISM; THROMBOCYTE; UNITED KINGDOM; VERY ELDERLY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; ALGORITHMS; BLOOD PLATELET DISORDERS; BLOOD PLATELETS; CHILD; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; EXOME; FEMALE; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GTP-BINDING PROTEIN ALPHA SUBUNITS, GI-GO; HEREDITY; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMOZYGOTE; HUMANS; MALE; MIDDLE AGED; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PREDICTIVE VALUE OF TESTS; SIGNAL TRANSDUCTION; UNITED KINGDOM; YOUNG ADULT;

EID: 84926128783     PISSN: 15387933     EISSN: 15387836     Source Type: Journal    
DOI: 10.1111/jth.12836     Document Type: Article

References (28)

1. Bolton-Maggs PH, Chalmers EA, Collins PW, Harrison P, Kitchen S, Liesner RJ, Minford A, Mumford AD, Parapia LA, Perry DJ, Watson SP, Wilde JT, Williams MD, Ukhcdo. A review of inherited platelet disorders with guidelines for their management on behalf of the UKHCDO. Br J Haematol 2006; 135: 603-33.
2. Miller JL. Platelet function testing: an improved approach utilizing lumi-aggregation and an interactive computer system. Am J Clin Pathol 1984; 81: 471-6.
3. Dawood BB, Lowe GC, Lordkipanidze M, Bem D, Daly ME, Makris M, Mumford A, Wilde JT, Watson SP. Evaluation of participants with suspected heritable platelet function disorders including recommendation and validation of a streamlined agonist panel. Blood 2012; 120: 5041-9.
4. Dawood BB, Wilde J, Watson SP. Reference curves for aggregation and ATP secretion to aid diagnose of platelet-based bleeding disorders: effect of inhibition of ADP and thromboxane A(2) pathways. Platelets 2007; 18: 329-45.
5. Mumford AD, Dawood BB, Daly ME. A novel thromboxane A(2) receptor D304N variant that abrogates ligand binding in a patient with a bleeding diathesis. Blood 2010; 115: 363-9.
6. Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, Bertone P, Jordan G, Kettleborough RN, Kiddle G, Kostadima M, Read RJ, Sipos B, Sivapalaratnam S, Smethurst PA, Stephens J, Voss K, Nurden A, Rendon A, Nurden P, Ouwehand WH. Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet 2011; 43: 735-7.
7. Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P, Breuning MH, Debili N, Deloukas P, Favier R, Fiedler J, Hobbs CM, Huang N, Hurles ME, Kiddle G, Krapels I, 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: 435-9.
8. Gunay-Aygun M, Falik-Zaccai TC, Vilboux T, Zivony-Elboum Y, Gumruk F, Cetin M, Khayat M, Boerkoel CF, Kfir N, Huang Y, Maynard D, Dorward H, Berger K, Kleta R, Anikster Y, Arat M, Freiberg AS, Kehrel BE, Jurk K, Cruz P, et al. NBEAL2 is mutated in gray platelet syndrome and is required for biogenesis of platelet alpha-granules. Nat Genet 2011; 43: 732-4.
9. Jones ML, Murden SL, Bem D, Mundell SJ, Gissen P, Daly ME, Watson SP, Mumford AD, group UGs. Rapid genetic diagnosis of heritable platelet function disorders with next-generation sequencing: proof-of-principle with Hermansky-Pudlak syndrome. J Thromb Haemost 2012; 10: 306-9.
10. Kahr WH, Hinckley J, Li L, Schwertz H, Christensen H, Rowley JW, Pluthero FG, Urban D, Fabbro S, Nixon B, Gadzinski R, Storck M, Wang K, Ryu GY, Jobe SM, Schutte BC, Moseley J, Loughran NB, Parkinson J, Weyrich AS, et al. Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome. Nat Genet 2011; 43: 738-40.
11. Kunishima S, Okuno Y, Yoshida K, Shiraishi Y, Sanada M, Muramatsu H, Chiba K, Tanaka H, Miyazaki K, Sakai M, Ohtake M, Kobayashi R, Iguchi A, Niimi G, Otsu M, Takahashi Y, Miyano S, Saito H, Kojima S, Ogawa S. ACTN1 mutations cause congenital macrothrombocytopenia. Am J Hum Genet 2013; 92: 431-8.
12. Stevenson WS, Morel-Kopp MC, Chen Q, Liang HP, Bromhead CJ, Wright S, Turakulov R, Ng AP, Roberts AW, Bahlo M, Ward CM. GFI1B mutation causes a bleeding disorder with abnormal platelet function. J Thromb Haemost 2013; 11: 2039-47.
13. Stockley J, Morgan NV, Bem D, Lowe GC, Lordkipanidze M, Dawood B, Simpson MA, Macfarlane K, Horner K, Leo VC, Talks K, Motwani J, Wilde JT, Collins PW, Makris M, Watson SP, Daly ME. Enrichment of FLI1 and RUNX1 mutations in families with excessive bleeding and platelet dense granule secretion defects. Blood 2013; 122: 4090-3.
14. Watson SP, Lowe GC, Lordkipanidze M, Morgan NV, consortium G. Genotyping and phenotyping of platelet function disorders. J Thromb Haemost 2013; 11: 351-63.
15. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26: 841-2.
16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and 1000 Genome Project Data Processing Subgroup. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009; 25: 2078-9.
17. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Res 2010; 38: W3-6.
18. Lowe GC, Lordkipanidze M, Watson SP. Utility of the ISTH bleeding assessment tool in predicting platelet defects in participants with suspected inherited platelet function disorders. J Thromb Haemost 2013; 11: 1663-8.
19. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4: 44-57.
20. Daly ME, Dawood BB, Lester WA, Peake IR, Rodeghiero F, Goodeve AC, Makris M, Wilde JT, Mumford AD, Watson SP, Mundell SJ. Identification and characterization of a novel P2Y 12 variant in a patient diagnosed with type 1 von Willebrand disease in the European MCMDM-1VWD study. Blood 2009; 113: 4110.
21. Nisar S, Daly ME, Federici AB, Artoni A, Mumford AD, Watson SP, Mundell SJ. An intact PDZ motif is essential for correct P2Y12 purinoceptor traffic in human platelets. Blood 2011; 118: 5641-51.
22. Nurden P, Nurden AT. Congenital disorders associated with platelet dysfunctions. J Thromb Haemost 2008; 99: 253-63.
23. Yang J, Wu J, Jiang H, Mortensen R, Austin S, Manning DR, Woulfe D, Brass LF. Signaling through Gi family members in platelets. Redundancy and specificity in the regulation of adenylyl cyclase and other effectors. J Biol Chem 2002; 277: 46035-42.
24. Remijn JA, IJsseldijk MJ, Strunk AL, Abbes AP, Engel H, Dikkeschei B, Dompeling EC, de Groot PG, Slingerland RJ. Novel molecular defect in the platelet ADP receptor P2Y12 of a patient with haemorrhagic diathesis. Clin Chem Lab Med 2007; 45: 187-9.
25. Patel YM, Lordkipanidzé M, Lowe GC, Nisar SP, Garner K, Stockley J, Daly ME, Mitchell M, Watson SP, Austin SK, Mundell SJ. A novel mutation in the P2Y12 receptor and a function-reducing polymorphism in protease-activated receptor 1 in a patient with chronic bleeding. J Thromb Haemost 2014; 12: 716-25.
26. Smolenski A. Novel roles of cAMP/cGMP-dependent signaling in platelets. J Thromb Haemost 2012; 10: 167-76.
27. Kasai K, Akagawa K. Roles of the cytoplasmic and transmembrane domains of syntaxins in intracellular localization and trafficking. J Cell Sci 2001; 114: 3115-24.
28. Walenta JH, Didier AJ, Liu X, Kramer H. The Golgi-associated hook3 protein is a member of a novel family of microtubule-binding proteins. J Cell Biol 2001; 152: 923-34.