Şükrü ÖZTÜRK, Şükrü PALANDUZ, Shahrashoub SHARIFI, Tuğba KALAYCI, Kıvanç CEFLE

Clinical Characteristics and Mutation Spectrum of Neurofibromatosis Type 1 in 27 Turkish Families

Background: Neurofibromatosis type 1 (NF1) is a neurocutaneous disorder that results in a predisposition to the growth of multiple tumors in the central nervous system, the peripheral nervous system, and the skin. The clinical manifestations of neurofibromatosis are associated with loss of neurofibromin expression which causes the upregulation of the RAS pathway. Although neurofibromatosis type 1 can be diagnosed based on the National Institutes of Health criteria, sometimes the diagnosis is difficult, in cases where the characteristic features do not develop. Moreover, other RAS-related disorders may present with significantly overlapping clinical features. Aims: To determine the clinical and molecular genetic characteristics of Turkish patients with neurofibromatosis type 1. Study design: Cross-sectional study. Methods: For the genetic analysis of 27 Turkish families clinically diagnosed with NF1 between 1990 and 2019, we used a multi-step process consisting of next-generation sequencing, multiplex ligation-dependent probe amplification, and array-comparative genomic hybridization. Results: In this study, we identified 11 novel and 11 previously reported single-nucleotide variants in 22 families. Whole gene deletions were detected by multiplex ligation-dependent probe amplification analysis in 3 families. Of those, array comparative genomic hybridization analysis defined a 17q11.2 deletion in 4 patients from 2 families and 1.2-Mb involving 1 unrelated patient. All patients with a deletion had facial dysmorphism, suggesting a peculiar phenotype in this group. We could not find any pathogenic variant in the 2 families that met the National Institutes of Health criteria. Conclusion: The novel pathogenic variants identified in this study broaden the spectrum of pathogenic variants in NF1 and provide better clinical characterization of NF1. RNA-seq experiments are recommended in patients who meet the National Institutes of Health diagnostic criteria for NF but have not identified any variants in nextgeneration sequencing, multiplex ligation-dependent probe amplification, or array-comparative genomic hybridization analysis.

PDF

___

1. Sabbagh A, Pasmant E, Imbard A, et al. NF1 molecular characterization and neurofibromatosis type I genotype-phenotype correlation: the French experience. Hum Mutat. 2013;34(11):1510-1518. [CrossRef]
2. Venturin M, Carra S, Gaudenzi G, et al. ADAP2 in heart development: a candidate gene for the occurrence of 132 cardiovascular malformations in NF1 microdeletion syndrome. J Med Genet. 2014;51(7):436-443. [CrossRef]
3. Pasmant E, Parfait B, Luscan A, 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. 2015;23(5):596-601. [CrossRef]
4. Tsipi M, Poulou M, Fylaktou I, et al. Phenotypic expression of a spectrum of neurofibromatosis type 1 (NF1) mutations identified through NGS and MLPA. J Neurol Sci. 2018;395:95-105. [CrossRef]
5. Yoshida Y, Sato N, Furumura M, Nakayama J. Treatment of pigmented lesions of neurofibromatosis 1 with intense pulsed-radio frequency in combination with topical application of of vitamin D3 ointment. J Dermatol. 2007;34(4):227-230. [CrossRef]
6. Barrea C, Vaessen S, Bulk S, Harvengt J, Misson JP. Phenotype–genotype correlation in children with neurofibromatosis type 1. Neuropediatrics. 2018;49(3):180-184. [CrossRef]
7. Nyström AM, Ekvall S, Allanson J, et al. Noonan syndrome and neurofibromatosis type I in a family with a novel mutation in NF1. Clin Genet. 2009;76(6):524-534. [CrossRef]
8. Yap P, Super L, Qin J, et al. Congenital retroperitoneal teratoma in neurofibromatosis type 1. Pediatr Blood Cancer. 2016 ;63(4):706-708. [CrossRef]
9. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;76:7.20.1-7.20.41. [CrossRef]
10. 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(7):1073- 1081. [CrossRef]
11. Schwarz JM, Cooper DN, Schuelke M, Seelow D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods. 2014;11(4):361-362. [CrossRef]
12. Karczewski KJ, Francioli LC, Tiao G, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581:434-443. [CrossRef]
13. 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. [CrossRef]
14. Richards S, Aziz N, Bale S, et al. 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(5):405-424. [CrossRef]
15. Coffa J, van den Berg J. Analysis of MLPA Data Using Novel Software Coffalyser. NET by MRC-Holland. Mod Approaches Qual Control. 2011;7:125-150.[CrossRef]
16. Frayling IM, Mautner V-F, van Minkelen R, et al. Breast cancer risk in neurofibromatosis type 1 is a function of the type of NF1 gene mutation: a new genotype-phenotype correlation. J Med Genet. 2019;56(4):209-219. [CrossRef]
17. Momozawa Y, Iwasaki Y, Parsons MT, et al. Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. Nat Commun. 2018;9(1):4083. [CrossRef]
18. Wilson CH, Griffith CD, Shrimankar J, Douglas F. Gynaecomastia, neurofibromatosis and breast cancer. Breast. 2004;13(1):77-79. [CrossRef]
19. Cassiman C, Casteels I, Jacob J, et al. Choroidal abnormalities in café-au-lait syndromes: a new differential diagnostic tool? Clin Genet. 2017;91(4):529-535. [CrossRef]
20. De Luca AD, Schirinzi A, Buccino A, et al. Novel and recurrent mutations in the NF1 gene in Italian patients with neurofibromatosis type 1. Hum Mutat. 2004;23(6):629. [CrossRef]
21. Serra G, Antona V, Corsello G, et al. NF1 microdeletion syndrome: case report of two new patients. Ital J Pediatr. 2019;45(1):138. [CrossRef]
22. Kehrer-Sawatzki H, Kluwe L, Sandig C, et al. High frequency of mosaicism among patients with neurofibromatosis type 1 (NF1) with microdeletions caused by somatic recombination of the JJAZ1 gene. Am J Hum Genet. 2004;75(3):410-423. [CrossRef]
23. Mautner VF, Kluwe L, Friedrich RE, et al. Clinical characterisation of 29 neurofibromatosis type-1 patients with molecularly ascertained 1.4 Mb type-1 NF1 deletions. J Med Genet. 2010;47(9):623-630. [CrossRef]
24. Ulusal SD, Gürkan H, Atlı E, et al. Genetic analyses of the NF1 gene in Turkish neurofibromatosis type I patients and definition of three novel variants. Balkan J Med Genet. 2017;20(1):13-20. [CrossRef]
25. Matsumoto K, Ogawa H, Nozawa S, Akiyama H. An analysis of osteoporosis in patients with hereditary multiple exostoses. Osteoporos Int. 2020;31(12):2355-2361. [CrossRef]
26. Xiong HY, Alipanahi B, Lee LJ, et al. The human splicing code reveals new insights into the genetic determinants of disease. Science. 2014;347(6218):1254806. [CrossRef]
27. Maquat LE. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol. 2004;5(2):89-99. [CrossRef]
28. Vogt J, Nguyen R, Kluwe L, et al. Delineation of the clinical phenotype associated with non-mosaic type-2 NF1 deletions: two case reports. J Med Case Rep. 2011;5:577. [CrossRef]
29. Venturin M, Moncini S, Villa V, et al. Mutations and novel polymorphisms in coding regions and UTRs of CDK5R1 and OMG genes in patients with non-syndromic mental retardation. Neurogenetics. 2006;7(1):59-66. [CrossRef]
30. Ben-Shachar S, Constantini S, Hallevi H, et al. Increased rate of missense/in-frame mutations in individuals with NF1-related pulmonary stenosis: a novel genotype–phenotype correlation. Eur J Hum Genet. 2013;21(5):535-539. [CrossRef]