Next-generation sequencing identifies rare variants associated with Noonan syndrome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 31, 2014, Pages 11473-11478

  Chen, Peng Chieh ^a,b,c   Yin, Jiani ^d   Yu, Hui Wen ^c   Yuan, Tao ^b   Fernandez, Minerva ^d   Yung, Christina K ^e   Trinh, Quang M ^e   Peltekova, Vanya D ^e   Reid, Jeffrey G ^f   Tworog Dube, Erica ^b   Morgan, Margaret B ^f   Muzny, Donna M ^f   Stein, Lincoln ^e   McPherson, John D ^e   Roberts, Amy E ^g   Gibbs, Richard A ^f   Neel, Benjamin G ^d   Kucherlapati, Raju ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c NATIONAL CHENG KUNG UNIVERSITY HOSPITAL   (Taiwan)

^d UNIVERSITY HEALTH NETWORK   (Canada)

^e ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^f BAYLOR COLLEGE OF MEDICINE   (United States)

^g BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

Developmental diseases; Human genetics; PTPN11; RAS; Whole exome sequencing

Indexed keywords

DNA; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; PEPTIDES AND PROTEINS; RAS LIKE WITHOUT CAAX 1 PROTEIN; RAS P21 PROTEIN ACTIVATOR 2; RAS PROTEIN; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CLINICAL ARTICLE; COFFIN LOWRY SYNDROME; CONTROLLED STUDY; GENETIC PARAMETERS; GENETIC VARIABILITY; HUMAN; LOSS OF FUNCTION MUTATION; MEDICAL RECORD REVIEW; MISSENSE MUTATION; NEXT GENERATION SEQUENCING; NONSENSE MUTATION; NOONAN SYNDROME; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN STABILITY;

DEVELOPMENTAL DISEASES; HUMAN GENETICS; PTPN11; RAS; WHOLE EXOME SEQUENCING;

ALLELES; GENETIC ASSOCIATION STUDIES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MAP KINASE KINASE 1; MAP KINASE SIGNALING SYSTEM; MUTATION; NEUROFIBROMIN 1; NOONAN SYNDROME; RAS PROTEINS;

EID: 84905639695     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1324128111     Document Type: Article

References (53)

1. Gelb BD, Tartaglia M (2006) Noonan syndrome and related disorders: Dysregulated RAS-mitogen activated protein kinase signal transduction. Hum Mol Genet 15(Spec No 2):R220-R226. (Pubitemid 44446797)
2. Aoki Y, Matsubara Y (2013) Ras/MAPK syndromes and childhood hemato-oncological diseases. Int J Hematol 97(1):30-36.
3. Rauen KA (2013) The RASopathies. Annu Rev Genomics Hum Genet 14:355-369.
4. Kontaridis MI, Swanson KD, David FS, Barford D, Neel BG (2006) PTPN11 (Shp2) mutations in LEOPARD syndrome have dominant negative, not activating, effects. J Biol Chem 281(10):6785-6792. (Pubitemid 43847615)
5. Marin TM, et al. (2011) Rapamycin reverses hypertrophic cardiomyopathy in a mouse model of LEOPARD syndrome-associated PTPN11 mutation. J Clin Invest 121(3):1026-1043.
6. Roberts AE, Allanson JE, Tartaglia M, Gelb BD (2013) Noonan syndrome. Lancet 381(9863):333-342.
7. Tartaglia M, et al. (2001) Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat Genet 29(4):465-468. (Pubitemid 34326699)
8. Roberts AE, et al. (2007) Germline gain-of-function mutations in SOS1 cause Noonan syndrome. Nat Genet 39(1):70-74. (Pubitemid 46026503)
9. Tartaglia M, et al. (2007) Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet 39(1):75-79. (Pubitemid 46026504)
10. Razzaque MA, et al. (2007) Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat Genet 39(8):1013-1017. (Pubitemid 47185179)
11. Schubbert S, et al. (2006) Germline KRAS mutations cause Noonan syndrome. Nat Genet 38(3):331-336.
12. Martinelli S, et al. (2010) Heterozygous germline mutations in the CBL tumor-suppressor gene cause a Noonan syndrome-like phenotype. Am J Hum Genet 87(2):250-257.
13. Cordeddu V, et al. (2009) Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet 41(9):1022-1026.
14. Cirstea IC, et al. (2010) A restricted spectrum of NRAS mutations causes Noonan syndrome. Nat Genet 42(1):27-29.
15. Niemeyer CM, et al. (2010) Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia. Nat Genet 42(9):794-800.
16. Pandit B, et al. (2007) Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet 39(8):1007-1012. (Pubitemid 47185177)
17. Colley A, Donnai D, Evans DG (1996) Neurofibromatosis/Noonan phenotype: A variable feature of type 1 neurofibromatosis. Clin Genet 49(2):59-64. (Pubitemid 26116815)
18. Wallace MR, et al. (1990) Type 1 neurofibromatosis gene: Identification of a large transcript disrupted in three NF1 patients. Science 249(4965):181-186.
19. Kaufmann D, et al. (2001) Spinal neurofibromatosis without café-au-lait macules in two families with null mutations of the NF1 gene. Am J Hum Genet 69(6):1395-1400. (Pubitemid 33124221)
20. Klose A, et al. (1998) Selective disactivation of neurofibromin GAP activity in neurofibromatosis type 1. Hum Mol Genet 7(8):1261-1268. (Pubitemid 28383059)
21. Upadhyaya M, et al. (1997) Mutational and functional analysis of the neurofibromatosis type 1 (NF1) gene. Hum Genet 99(1):88-92. (Pubitemid 26419862)
22. Thomas L, et al. (2012) Assessment of the potential pathogenicity of missense mutations identified in the GTPase-activating protein (GAP)-related domain of the neurofibromatosis type-1 (NF1) gene. Hum Mutat 33(12):1687-1696.
23. De Luca A, et al. (2005) NF1 gene mutations represent the major molecular event underlying neurofibromatosis-Noonan syndrome. Am J Hum Genet 77(6):1092-1101. (Pubitemid 41698528)
24. Croonen EA, Yntema HG, van Minkelen R, van den Ouweland AM, van der Burgt I (2012) Patient with a neurofibromatosis type 1 mutation but a clinical diagnosis of Noonan syndrome. Clin Dysmorphol 21(4):212-214.
25. Trivier E, et al. (1996) Mutations in the kinase Rsk-2 associated with Coffin-Lowry syndrome. Nature 384(6609):567-570. (Pubitemid 26415934)
26. Nava C, et al. (2007) Cardio-facio-cutaneous and Noonan syndromes due to mutations in the RAS/MAPK signalling pathway: Genotype-phenotype relationships and overlap with Costello syndrome. J Med Genet 44(12):763-771. (Pubitemid 350275049)
27. Shi GX, Andres DA (2005) Rit contributes to nerve growth factor-induced neuronal differentiation via activation of B-Raf-extracellular signal-regulated kinase and p38 mitogen-activated protein kinase cascades. Mol Cell Biol 25(2):830-846.
28. Aoki Y, et al. (2013) Gain-of-function mutations in RIT1 cause Noonan syndrome, a RAS/MAPK pathway syndrome. Am J Hum Genet 93(1):173-180.
29. Araki T, et al. (2009) Noonan syndrome cardiac defects are caused by PTPN11 acting in endocardium to enhance endocardial-mesenchymal transformation. Proc Natl Acad Sci USA 106(12):4736-4741.
30. Gómez-Seguí I, et al. (2013) Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies. Leukemia 27(9):1943-1946.
31. Forbes SA, et al. (2011) COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39(Database issue):D945-D950.
32. Maekawa M, et al. (1994) A novel mammalian Ras GTPase-activating protein which has phospholipid-binding and Btk homology regions. Mol Cell Biol 14(10):6879-6885.
33. Scheffzek K, Lautwein A, Kabsch W, Ahmadian MR, Wittinghofer A (1996) Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras. Nature 384(6609):591-596. (Pubitemid 26415941)
34. Lockyer PJ, et al. (1997) Distinct subcellular localisations of the putative inositol 1,3,4,5-tetrakisphosphate receptors GAP1IP4BP and GAP1m result from the GAP1IP4BP PH domain directing plasma membrane targeting. Curr Biol 7(12):1007-1010. (Pubitemid 28017081)
35. Guy GR, Jackson RA, Yusoff P, Chow SY (2009) Sprouty proteins: Modified modulators, matchmakers or missing links? J Endocrinol 203(2):191-202.
36. Basson MA, et al. (2005) Sprouty1 is a critical regulator of GDNF/RET-mediated kidney induction. Dev Cell 8(2):229-239. (Pubitemid 40197739)
37. Patriotis C, Makris A, Chernoff J, Tsichlis PN (1994) Tpl-2 acts in concert with Ras and Raf-1 to activate mitogen-activated protein kinase. Proc Natl Acad Sci USA 91(21):9755-9759. (Pubitemid 24311886)
38. Ekvall S, Hagenäs L, Allanson J, Annerén G, Bondeson ML (2011) Co-occurring SHOC2 and PTPN11 mutations in a patient with severe/complex Noonan syndrome-like phenotype. Am J Med Genet A 155A(6):1217-1224.
39. Brasil AS, et al. (2010) PTPN11 and KRAS gene analysis in patients with Noonan and Noonan-like syndromes. Genetic Testing Molec Biomarkers 14(3):425-432.
40. Brasil AS, et al. (2010) Co-occurring PTPN11 and SOS1 gene mutations in Noonan syndrome: Does this predict a more severe phenotype? Arq Bras Endocrinol Metabol 54(8):717-722.
41. Boileau C, et al.; National Heart, Lung, and Blood Institute (NHLBI) Go Exome Sequencing Project (2012) TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nat Genet 44(8):916-921.
42. Lindsay ME, et al. (2012) Loss-of-function mutations in TGFB2 cause a syndromic presentation of thoracic aortic aneurysm. Nat Genet 44(8):922-927.
43. van Haelst MM, et al.; Fraser Syndrome Collaboration Group (2008) Molecular study of 33 families with Fraser syndrome new data and mutation review. Am J Med Genet A 146A(17):2252-2257.
44. Castaman G (2013) New development in von Willebrand disease. Curr Opin Hematol 20(5):424-429.
45. Riddell AF, et al. (2009) Characterization of W1745C and S1783A: 2 novel mutations causing defective collagen binding in the A3 domain of von Willebrand factor. Blood 114(16):3489-3496.
46. Schubbert S, Shannon K, Bollag G (2007) Hyperactive Ras in developmental disorders and cancer. Nat Rev Cancer 7(4):295-308. (Pubitemid 46480970)
47. Chen PC, et al. (2010) Activation of multiple signaling pathways causes developmental defects in mice with a Noonan syndrome-associated Sos1 mutation. J Clin Invest 120(12):4353-4365.
48. Wu X, et al. (2011) MEK-ERK pathway modulation ameliorates disease phenotypes in a mouse model of Noonan syndrome associated with the Raf1(L613V) mutation. J Clin Invest 121(3):1009-1025.
49. van der Burgt I, et al. (1994) Clinical and molecular studies in a large Dutch family with Noonan syndrome. Am J Med Genet 53(2):187- 191.
50. Green RC, et al. (2013) ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Gen Med 15(7):565-574.
51. McKenna A, et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297-1303.
52. Binkley J, et al. (2010) ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses. Genome Res 20(1):142-154.
53. Wu G, Feng X, Stein L (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol 11(5):R53.