Hybridization capture-based next-generation sequencing to evaluate coding sequence and deep intronic mutations in the NF1 gene

Genes

Volumn 7, Issue 12, 2016, Pages

  Cunha, Karin Soares ^a,b   Oliveira, Nathalia Silva ^c   Fausto, Anna Karoline ^c   De Souza, Carolina Cruz ^a   Gros, Audrey ^d,e   Bandres, Thomas ^d   Idrissi, Yamina ^e   Merlio, Jean Philippe ^d,e   De Moura Neto, Rodrigo Soares ^f   Silva, Rosane ^f   Geller, Mauro ^f,g   Cappellen, David ^d,e  

^a FLUMINENSE FEDERAL UNIVERSITY   (Brazil)

^b Centro Nacional de Neurofibromatose (CNNF)   (Brazil)

^c HOSPITAL UNIVERSITÁRIO ANTÔNIO PEDRO   (Brazil)

^d HAUT LÉVÊQUE HOSPITAL   (France)

^e UNIVERSITÉ DE BORDEAUX   (France)

^f FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^g Centro Universitario Serra Dos Orgaos   (Brazil)

Author keywords

Neurofibromatosis 1; Next generation sequencing; NF1 gene

Indexed keywords

GENOMIC DNA;

ADOLESCENT; ADULT; AGED; ARTICLE; CLINICAL ARTICLE; EXON; FEMALE; FRAMESHIFT MUTATION; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC CODE; GENETIC SCREENING; HUMAN; HYBRIDIZATION CAPTURE BASED NEXT GENERATION SEQUENCING; INTRON; MALE; MIDDLE AGED; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NEUROFIBROMATOSIS TYPE 1; NEXT GENERATION SEQUENCING; NF1 GENE; RNA SPLICING; YOUNG ADULT;

EID: 85010408529     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes7120133     Document Type: Article

References (37)

1. Uusitalo, E.; Leppävirta, J.; Koffert, A.; Suominen, S.; Vahtera, J.; Vahlberg, T.; Pöyhönen, M.; Peltonen, J.; Peltonen, S. Incidence and mortality of neurofibromatosis: A total population study in Finland. J. Investig. Dermatol. 2015, 135, 904-906.
2. Cunha, K.S.G.; Geller, M. Advances in Neurofibromatosis Research; Nova Science Publishers Inc.: Hauppauge, NY, USA, 2011.
3. Pasmant, E.; Parfait, B.; Luscan, A.; Goussard, P.; Briand-Suleau, A.; Laurendeau, I.; Fouveaut, C.; Leroy, C.; Montadert, A.; Wolkenstein, P. et al. Neurofibromatosis type 1 molecular diagnosis: What can NGS do for you when you have a large gene with loss of function mutations? Eur. J. Hum. Genet. EJHG 2015, 23, 596-601.
4. Clementi, M.; Barbujani, G.; Turolla, L.; Tenconi, R. Neurofibromatosis-1: A maximum likelihood estimation of mutation rate. Hum. Genet. 1990, 84, 116-118.
5. De Luca, A.; Schirinzi, A.; Buccino, A.; Bottillo, I.; Sinibaldi, L.; Torrente, I.; Ciavarella, A.; Dottorini, T.; Porciello, R.; Giustini, S. et al. Novel and recurrent mutations in the NF1 gene in Italian patients with neurofibromatosis type 1. Hum. Mutat. 2004, 23, 629.
6. Griffiths, S.; Thompson, P.; Frayling, I.; Upadhyaya, M. Molecular diagnosis of neurofibromatosis type 1: 2 years experience. Fam. Cancer 2007, 6, 21-34.
7. Uusitalo, E.; Hammais, A.; Palonen, E.; Brandt, A.; Mäkelä, V.-V.; Kallionpää, R.; Jouhilahti, E.-M.; Pöyhönen, M.; Soini, J.; Peltonen, J. et al. Neurofibromatosis type 1 gene mutation analysis using sequence capture and high-throughput sequencing. Acta Derm. Venereol. 2014, 94, 663-666.
8. Upadhyaya, M. The Molecular Biology of Neurofibromatosis Type 1; Morgan & Claypool: Williston, VT, USA, 2014.
9. Messiaen, L.M.; Callens, T.; Mortier, G.; Beysen, D.; Vandenbroucke, I.; Van Roy, N.; Speleman, F.; Paepe, A.D. Exhaustive mutation analysis of the NF1 gene allows identification of 95% of mutations and reveals a high frequency of unusual splicing defects. Hum. Mutat. 2000, 15, 541-555.
10. Flanagan, S.E.; Xie, W.; Caswell, R.; Damhuis, A.; Vianey-Saban, C.; Akcay, T.; Darendeliler, F.; Bas, F.; Guven, A.; Siklar, Z. et al. Next-Generation Sequencing Reveals Deep Intronic Cryptic ABCC8 and HADH Splicing Founder Mutations Causing Hyperinsulinism by Pseudoexon Activation. Am. J. Hum. Genet. 2013, 92, 131-136.
11. Stumpf, D.A.; Alksne, J.F.; Annegers, J.F.; Brown, S.S.; Conneally, P.M.; Housman, D.; Leppert, M.F.; Miller, J.P.; Moss, M.L.; Pileggi, A.J. et al. Neurofibromatosis. Conference statement. National Institutes of Health Consensus Development Conference. Arch Neurol. 1988, 45, 575-578.
12. Ars, E.; Kruyer, H.; Morell, M.; Pros, E.; Serra, E.; Ravella, A.; Estivill, X.; Lázaro, C. Recurrent mutations in the NF1 gene are common among neurofibromatosis type 1 patients. J. Med. Genet. 2003, 40, e82.
13. Forzan, M. Functional Splicing Assay mediante l’utilizzo di minigeni plasmidici nel gene NF1. Ph.D. Thesis, Università degli Studi di Padova, Padova, Italy, 2010.
14. Mattocks, C.; Baralle, D.; Tarpey, P. Automated comparative sequence analysis identifies mutations in 89% of NF1 patients and confirms a mutation cluster in exons 11-17 distinct from the GAP related domain. Br. Med. J. 2004, 41, e48.
15. Van Minkelen, R.; van Bever, Y.; Kromosoeto, J.N.R.; Withagen-Hermans, C.J.; Nieuwlaat, A.; Halley, D.J.J.; van den Ouweland, A.M.W. A clinical and genetic overview of 18 years neurofibromatosis type 1 molecular diagnostics in the Netherlands. Clin. Genet. 2014, 85, 318-327.
16. Balla, B.; Árvai, K.; Horváth, P.; Tobiás, B.; Takács, I.; Nagy, Z.; Dank, M.; Fekete, G.; Kósa, J.P.; Lakatos, P. Fast and robust next-generation sequencing technique using ion torrent personal genome machine for the screening of neurofibromatosis type 1 (NF1) gene. J. Mol. Neurosci. MN 2014, 53, 204-210.
17. Chou, L.-S.; Liu, C.-S.J.; Boese, B.; Zhang, X.; Mao, R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: Neurofibromatosis type 1 gene as a model. Clin. Chem. 2010, 56, 62-72.
18. Hutter, S.; Piro, R.M.; Waszak, S.M.; Kehrer-Sawatzki, H.; Friedrich, R.E.; Lassaletta, A.; Witt, O.; Korbel, J.O.; Lichter, P.; Schuhmann, M.U. et al. No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients. Hum. Genet. 2016, 135, 469-475.
19. Maruoka, R.; Takenouchi, T.; Torii, C.; Shimizu, A.; Misu, K.; Higasa, K.; Matsuda, F.; Ota, A.; Tanito, K.; Kuramochi, A. et al. The use of next-generation sequencing in molecular diagnosis of neurofibromatosis type 1: A validation study. Genet. Test. Mol. Biomark. 2014, 18, 722-735.
20. Banerjee, S.; Dai, Y.; Liang, S.; Chen, H.; Wang, Y.; Tang, L.; Wu, J.; Huang, H. A novel mutation in NF1 is associated with diverse intra-familial phenotypic variation and astrocytoma in a Chinese family. J. Clin. Neurosci. Off. J. Neurosurg. Soc. Australas. 2016, 31, 182-184.
21. Calì, F.; Chiavetta, V.; Ruggeri, G.; Piccione, M.; Selicorni, A.; Palazzo, D.; Bonsignore, M.; Cereda, A.; Elia, M.; Failla, P. et al. Mutation spectrum of NF1 gene in Italian patients with neurofibromatosis type 1 using Ion Torrent PGMTM platform. Eur. J. Med. Genet. 2016.
22. Mamanova, L.; Coffey, A.J.; Scott, C.E.; Kozarewa, I.; Turner, E.H.; Kumar, A.; Howard, E.; Shendure, J.; Turner, D.J. Target-enrichment strategies for next-generation sequencing. Nat. Methods 2010, 7, 111-118.
23. Galindo-González, L.; Pinzón-Latorre, D.; Bergen, E.A.; Jensen, D.C.; Deyholos, M.K. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. Plant Methods 2015, 11, 19.
24. Valero, M.C.; Martín, Y.; Hernández-Imaz, E.; Marina Hernández, A.; Meleán, G.; Valero, A.M.; Javier Rodríguez-Álvarez, F.; Tellería, D.; Hernández-Chico, C. A highly sensitive genetic protocol to detect NF1 mutations. J. Mol. Diagn. JMD 2011, 13, 113-122.
25. Summerer, D.; Schracke, N.; Wu, H.; Cheng, Y.; Bau, S.; Stähler, C.F.; Stähler, P.F.; Beier, M. Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform. Genomics 2010, 95, 241-246.
26. Chilamakuri, C.S.R.; Lorenz, S.; Madoui, M.-A.; Vodák, D.; Sun, J.; Hovig, E.; Myklebost, O.; Meza-Zepeda, L.A. Performance comparison of four exome capture systems for deep sequencing. BMC Genom. 2014, 15.
27. Sabbagh, A.; Pasmant, E.; Imbard, A.; Luscan, A.; Soares, M.; Blanché, H.; Laurendeau, I.; Ferkal, S.; Vidaud, M.; Pinson, S. et al. NF1 molecular characterization and neurofibromatosis type I genotype-phenotype correlation: The French experience. Hum. Mutat. 2013, 34, 1510-1518.
28. Ars, E.; Serra, E.; Garcia, J.; Kruyer, H.; Gaona, A.; Lazaro, C.; Estivill, X. Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. Hum. Mol. Genet. 2000, 9, 237.
29. Wang, H.; Nettleton, D.; Ying, K. Copy number variation detection using next generation sequencing read counts. BMC Bioinform. 2014, 15, 109.
30. Abou Tayoun, A.N.; Tunkey, C.D.; Pugh, T.J.; Ross, T.; Shah, M.; Lee, C.C.; Harkins, T.T.; Wells, W.A.; Tafe, L.J.; Amos, C.I. et al. A comprehensive assay for CFTR mutational analysis using next-generation sequencing. Clin. Chem. 2013, 59, 1481-1488.
31. Poliseno, L. (Ed.) Pseudogenes; Methods in Molecular Biology Series; Springer: New York, NY, USA, 2014; Volume 1167.
32. Messiaen, L.; Wimmer, K. Mutation analysis of the NF1 gene by cDNA-based sequencing of the coding region. In Advances in Neurofibromatosis Research; Cunha, K.S.G., Geller, M., Eds.; Nova Science Publishers Inc.: New York, NY, USA, 2012; pp. 89-108.
33. Wimmer, K.; Roca, X.; Beiglböck, H.; Callens, T.; Etzler, J.; Rao, A.R.; Krainer, A.R.; Fonatsch, C.; Messiaen, L. Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 50 splice-site disruption. Hum. Mutat. 2007, 28, 599-612.
34. Svaasand, E.K.; Engebretsen, L.F.; Ludvigsen, T.; Brechan, W.; Sjursen, W. A Novel Deep Intronic Mutation Introducing a Cryptic Exon Causing Neurofibromatosis Type 1 in a Family with Highly Variable Phenotypes: A Case Study. Hered. Genet. Curr. Res. 2015, 4, 3.
35. Castellanos, E.; Rosas, I.; Solanes, A.; Bielsa, I.; Lázaro, C.; Carrato, C.; Hostalot, C.; Prades, P.; Roca-Ribas, F.; Blanco, I. et al. In vitro antisense therapeutics for a deep intronic mutation causing Neurofibromatosis type 2. Eur. J. Hum. Genet. 2013, 21, 769-773.
36. Coutinho, G.; Xie, J.; Du, L.; Brusco, A.; Krainer, A.R.; Gatti, R.A. Functional significance of a deep intronic mutation in the ATM gene and evidence for an alternative exon 28a. Hum. Mutat. 2005, 25, 118-124.
37. Jian, X.; Boerwinkle, E.; Liu, X. In silico tools for splicing defect prediction: A survey from the viewpoint of end users. Genet. Med. 2014, 16, 497-503.