Mosaic and Intronic Mutations in Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing

English version České info

Tuberous sclerosis complex (TSC) is a human genetic disorder due to mutations in the TSC1 or TSC2 genes. A mystery for many years has been the fact that with standard genetic testing 10–15% of TSC patients have had no mutation identified (NMI) in either TSC1 or TSC2. We examined the genetic cause of TSC in patients who were ‘NMI’ after previous testing. We found a mutation in TSC1 or TSC2 in the vast majority of the subjects studied: 45 of 53 (85%). The majority of mutations identified were either in introns or mosaic or both. Usually we expect to find mutations causing human disease in exons, coding parts of genes. However, mutations can also be found in introns, the non-coding parts of genes, and we found intronic mutations in 18 of 45 subjects (40%). Mosaic mutations were seen in 26 of 45 subjects (58%). Mosaicism is the situation in which different cells in the body have a different genetic make-up, and in this case the mutations in TSC1/TSC2 were present in only a fraction of the cells from the patient. So these two types of hard-to-find mutations (in introns and/or mosaic) explain the majority of TSC patients who were NMI.

Vyšlo v časopise: Mosaic and Intronic Mutations in Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing. PLoS Genet 11(11): e32767. doi:10.1371/journal.pgen.1005637
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005637

Souhrn

Zdroje

1. Online Mendelian Inheritance in Man, OMIM. Johns Hopkins University, Baltimore, MD. MIM Numbers: 191100, 613254. http://www.omim.org.

2. Crino PB, Nathanson KL, Henske EP. The tuberous sclerosis complex. N Engl J Med. 2006;355(13):1345–56. 17005952

3. Kwiatkowski DJ, Thiele EA, Whittemore VH. Tuberous sclerosis complex. Weinheim, Germany: Wiley-VCH; 2010. 409 p.

4. Northrup H, Krueger DA. Tuberous sclerosis complex diagnostic criteria update: recommendations of the 2012 Iinternational Tuberous Sclerosis Complex Consensus Conference. Pediatr Neurol. 2013;49(4):243–54. Epub 2013/09/24. doi: 10.1016/j.pediatrneurol.2013.08.001 24053982

5. Ali M, Girimaji SC, Markandaya M, Shukla AK, Sacchidanand S, Kumar A. Mutation and polymorphism analysis of TSC1 and TSC2 genes in Indian patients with tuberous sclerosis complex. Acta Neurol Scand. 2005;111(1):54–63. 15595939

6. Apak A, Haliloglu G, Kose G, Yilmaz E, Anlar B, Aysun S. Mutation analysis of TSC2 gene in 33 Turkish familial cases with tuberous sclerosis. Turk J Pediatr. 2003;45(1):1–5. 12718362

7. Au K- S, Rodriguez JA, Finch JL, Volcik KA, Roach ES, Delgado MR, et al. Germ-line mutational analysis of the TSC2 gene in 90 tuberous-sclerosis patients. Am J Hum Genet. 1998;62:286–94. 9463313

8. Au KS, Williams AT, Roach ES, Batchelor L, Sparagana SP, Delgado MR, et al. Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States. Genet Med. 2007;9(2):88–100. 17304050

9. Choi JE, Chae JH, Hwang YS, Kim KJ. Mutational analysis of TSC1 and TSC2 in Korean patients with tuberous sclerosis complex. Brain Dev. 2006;28(7):440–6. 16554133

10. Dabora SL, Jozwiak S, Franz DN, Roberts PS, Nieto A, Chung J, et al. Mutational Analysis in a Cohort of 224 Tuberous Sclerosis Patients Indicates Increased Severity of TSC2, Compared with TSC1, Disease in Multiple Organs. Am J Hum Genet. 2001;68(1):64–80. 11112665

11. Hung CC, Su YN, Chien SC, Liou HH, Chen CC, Chen PC, et al. Molecular and clinical analyses of 84 patients with tuberous sclerosis complex. BMC Med Genet. 2006;7:72. 16981987

12. Langkau N, Martin N, Brandt R, Zugge K, Quast S, Wiegele G, et al. TSC1 and TSC2 mutations in tuberous sclerosis, the associated phenotypes and a model to explain observed TSC1/ TSC2 frequency ratios. Eur J Pediatr. 2002;161(7):393–402. 12111193

13. Niida Y, Lawrence-Smith N, Banwell A, Hammer E, Lewis J, Beauchamp RL, et al. Analysis of both TSC1 and TSC2 for germline mutations in 126 unrelated patients with tuberous sclerosis. Hum Mutat. 1999;14(5):412–22. 10533067

14. Rendtorff ND, Bjerregaard B, Frodin M, Kjaergaard S, Hove H, Skovby F, et al. Analysis of 65 tuberous sclerosis complex (TSC) patients by TSC2 DGGE, TSC1/TSC2 MLPA, and TSC1 long-range PCR sequencing, and report of 28 novel mutations. Hum Mutat. 2005;26(4):374–83. 16114042

15. Sancak O, Nellist M, Goedbloed M, Elfferich P, Wouters C, Maat-Kievit A, et al. Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype—phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex. Eur J Hum Genet. 2005;13(6):731–41. 15798777

16. van Slegtenhorst M, Verhoef S, Tempelaars A, Bakker L, Wang Q, Wessels M, et al. Mutational spectrum of the TSC1 gene in a cohort of 225 tuberous sclerosis complex patients: no evidence for genotype-phenotype correlation. J Med Genet. 1999;36(4):285–9. 10227394

17. Yamashita Y, Ono J, Okada S, Wataya-Kaneda M, Yoshikawa K, Nishizawa M, et al. Analysis of all exons of TSC1 and TSC2 genes for germline mutations in Japanese patients with tuberous sclerosis: report of 10 mutations. Am J Med Genet. 2000;90(2):123–6. 10607950

18. Chromosome European 16 Tuberous Sclerosis Consortium. Identification and characterization of the tuberous sclerosis gene on chromosome 16. Cell. 1993;75:1305–15.

19. Sampson JR, Scahill SJ, Stephenson JB, Mann L, Connor JM. Genetic aspects of tuberous sclerosis in the west of Scotland. J Med Genet. 1989;26(1):28–31. 2918523

20. van Slegtenhorst M, de Hoogt R, Hermans C, Nellist M, Janssen B, Verhoef S, et al. Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. Science. 1997;277(5327):805–8. 9242607

21. Camposano SE, Greenberg E, Kwiatkowski DJ, Thiele EA. Distinct clinical characteristics of tuberous sclerosis complex patients with no mutation identified. Ann Hum Genet. 2009;73(2):141–6. doi: 10.1111/j.1469-1809.2008.00496.x 19133941

22. Boronat S, Shaaya EA, Doherty CM, Caruso P, Thiele EA. Tuberous sclerosis complex without tubers and subependymal nodules: a phenotype-genotype study. Clin Genet. 2014;86(2):149–54. doi: 10.1111/cge.12245 23909698

23. Tyburczy ME, Wang JA, Li S, Thangapazham R, Chekaluk Y, Moss J, et al. Sun exposure causes somatic second-hit mutations and angiofibroma development in tuberous sclerosis complex. Hum Mol Genet. 2014;23(8):2023–9. doi: 10.1093/hmg/ddt597 24271014

24. Jones AC, Shyamsundar MM, Thomas MW, Maynard J, Idziaszczyk S, Tomkins S, et al. Comprehensive Mutation Analysis of TSC1 and TSC2-and Phenotypic Correlations in 150 Families with Tuberous Sclerosis. Am J Hum Genet. 1999;64(5):1305–15. 10205261

25. Young JM, Burley MW, Jeremiah SJ, Jeganathan D, Ekong R, Osborne JP, et al. A mutation screen of the TSC1 gene reveals 26 protein truncating mutations and 1 splice site mutation in a panel of 79 tuberous sclerosis patients. Ann Hum Genet. 1998;62(Pt 3):203–13. 9803264

26. Mayer K, Ballhausen W, Leistner W, Rott H. Three novel types of splicing aberrations in the tuberous sclerosis TSC2 gene caused by mutations apart from splice consensus sequences. Biochim Biophys Acta. 2000;1502(3):495–507. 11068191

27. Povey S, Ekong R. Tuberous sclerosis database. http://chromium.lovd.nl/LOVD2/TSC.

28. Jeganathan D, Fox MF, Young JM, Yates JR, Osborne JP, Povey S. Nonsense-mediated RNA decay in the TSC1 gene suggests a useful tool pre- and post-positional cloning. Hum Genet. 2002;111(6):555–65. 12436247

29. King K, Flinter FA, Nihalani V, Green PM. Unusual deep intronic mutations in the COL4A5 gene cause X linked Alport syndrome. Hum Genet. 2002;111(6):548–54. 12436246

30. Hutton M, Lendon CL, Rizzu P, Baker M, Froelich S, Houlden H, et al. Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17. Nature. 1998;393(6686):702–5. 9641683

31. Harland M, Mistry S, Bishop DT, Bishop JA. A deep intronic mutation in CDKN2A is associated with disease in a subset of melanoma pedigrees. Hum Mol Genet. 2001;10(23):2679–86. 11726555

32. Nellist M, Brouwer RW, Kockx CE, van Veghel-Plandsoen M, Withagen-Hermans C, Prins-Bakker L, et al. Targeted Next Generation Sequencing reveals previously unidentified TSC1 and TSC2 mutations. BMC Med Genet. 2015;16:10. doi: 10.1186/s12881-015-0155-4 25927202

33. Mayer K, Ballhausen W, Rott HD. Mutation screening of the entire coding regions of the TSC1 and the TSC2 gene with the protein truncation test (PTT) identifies frequent splicing defects. Hum Mutat. 1999;14(5):401–11. 10533066

34. Kwiatkowska J, Wigowska-Sowinska J, Napierala D, Slomski R, Kwiatkowski DJ. Mosaicism in tuberous sclerosis as a potential cause of the failure of molecular diagnosis. N Engl J Med. 1999;340(9):703–7. 10053179

35. Rose VM, Au KS, Pollom G, Roach ES, Prashner HR, Northrup H. Germ-Line Mosaicism in Tuberous Sclerosis: How Common? Am J Hum Genet. 1999;64(4):986–92. 10090883

36. Sampson JR, Maheshwar MM, Aspinwall R, Thompson P, Cheadle JP, Ravine D, et al. Renal cystic disease in tuberous sclerosis: role of the polycystic kidney disease 1 gene. Am J Hum Genet. 1997;61(4):843–51. 9382094

37. Jones AC, Sampson JR, Cheadle JP. Low level mosaicism detectable by DHPLC but not by direct sequencing. Hum Mutat. 2001;17(3):233–4. 11241845

38. Emmerson P, Maynard J, Jones S, Butler R, Sampson JR, Cheadle JP. Characterizing mutations in samples with low-level mosaicism by collection and analysis of DHPLC fractionated heteroduplexes. Hum Mutat. 2003;21(2):112–5. 12552557

39. Verhoef S, Bakker L, Tempelaars AM, Hesseling-Janssen AL, Mazurczak T, Jozwiak S, et al. High rate of mosaicism in tuberous sclerosis complex. Am J Hum Genet. 1999;64(6):1632–7. 10330349

40. Yates JR, van Bakel I, Sepp T, Payne SJ, Webb DW, Nevin NC, et al. Female germline mosaicism in tuberous sclerosis confirmed by molecular genetic analysis. Hum Mol Genet. 1997;6(13):2265–9. 9361032

41. Kozlowski P, Roberts P, Dabora S, Franz D, Bissler J, Northrup H, et al. Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations. Hum Genet. 2007;121(3–4):389–400. 17287951

42. Verhoef S, Vrtel R, van ET, Bakker L, Sikkens E, Halley D, et al. Somatic mosaicism and clinical variation in tuberous sclerosis complex. Lancet. 1995;345(8943):202. 7823706

43. Roberts PS, Dabora S, Thiele EA, Franz DN, Jozwiak S, Kwiatkowski DJ. Somatic mosaicism is rare in unaffected parents of patients with sporadic tuberous sclerosis. J Med Genet. 2004;41(5):e69. 15121797

44. Sampson JR. TSC1 and TSC2: genes that are mutated in the human genetic disorder tuberous sclerosis. Biochem Soc Trans. 2003;31(Pt 3):592–6. 12773162

45. Qin W, Kozlowski P, Taillon BE, Bouffard P, Holmes AJ, Janne P, et al. Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Hum Genet. 2010;127(5):573–82. Epub 2010/02/19. doi: 10.1007/s00439-010-0801-z 20165957

46. Evans DG, Ramsden RT, Shenton A, Gokhale C, Bowers NL, Huson SM, et al. Mosaicism in neurofibromatosis type 2: an update of risk based on uni/bilaterality of vestibular schwannoma at presentation and sensitive mutation analysis including multiple ligation-dependent probe amplification. J Med Genet. 2007;44(7):424–8. 17307835

47. Kluwe L, Mautner V, Heinrich B, Dezube R, Jacoby LB, Friedrich RE, et al. Molecular study of frequency of mosaicism in neurofibromatosis 2 patients with bilateral vestibular schwannomas. J Med Genet. 2003;40(2):109–14. 12566519

48. Evans DG, Trueman L, Wallace A, Collins S, Strachan T. Genotype/phenotype correlations in type 2 neurofibromatosis (NF2): evidence for more severe disease associated with truncating mutations. J Med Genet. 1998;35(6):450–5. 9643284

49. Tyburczy ME, Jozwiak S, Malinowska IA, Chekaluk Y, Pugh TJ, Wu CL, et al. A shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis complex. Hum Mol Genet. 2015;24(7):1836–42. doi: 10.1093/hmg/ddu597 25432535

50. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–95. Epub 2010/01/19. doi: 10.1093/bioinformatics/btp698 20080505

51. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. Epub 2010/07/21. doi: 10.1101/gr.107524.110 20644199

52. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. Epub 2009/06/10. doi: 10.1093/bioinformatics/btp352 19505943

53. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6. Epub 2011/01/12. doi: 10.1038/nbt.1754 21221095

54. Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56–65 (01 November 2012). http://www.1000genomes.org/. doi: 10.1038/nature11632 23128226

55. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA. http://evs.gs.washington.edu/EVS/.

56. Exome Aggregation Consortium (ExAC), Cambridge, MA. http://exac.broadinstitute.org/.

57. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9. Epub 2010/04/01. doi: 10.1038/nmeth0410-248 20354512

58. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7(4):248–249. http://genetics.bwh.harvard.edu/pph2/. doi: 10.1038/nmeth0410-248 20354512

59. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001;11(5):863–74. Epub 2001/05/05 11337480

60. 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):1073–81. http://sift.jcvi.org/. doi: 10.1038/nprot.2009.86 19561590