Sequencing methods in dermatology


Cite item

Full Text

Abstract

Review of the literature devoted to the application of sequencing methods (genome research method) at various dermatological diseases. DNA sequencing technology is described in the article. Sanger Sequencing Method and Next-Generation Sequencing are discussed. Examples of genes and mutations found by sequencing methods are presented. Clinical meaning of mutations in BRAF, NRAS, KIT, GNAQ, GNA11 genes that play an important role in the pathogenesis of different clinical pathological forms of melanoma is described. Reveling tumor subtypes provides a selective approach in treatment of cutaneous melanoma, that can be useful in different therapeutic methods and makes it possible to predict the development of chemoresistance. Furthermore, data about another genes, that play an important role in pathogenesis of different dermatological diseases with tumor and non-tumor genesis are presented.

About the authors

Maria B. Aksenenko

Krasnoyarsk State Medical University

Email: aksenenko_mariya@mail.ru
Candidate of Medical Sciences, Docent, Department of Pathophysiology with a Course of a Clinical Pathophysiology 660022, Krasnoyarsk, Russia

T. G Ruksha

Krasnoyarsk State Medical University

660022, Krasnoyarsk, Russia

References

  1. Griffith M., Miller C.A., Griffith O.L., Krysiak K., Skidmore Z.L., Ramu A., et al. Optimizing cancer genome sequencing and analysis. Cell Syst. 2015; 1(3): 210-33.
  2. Ребриков Д.В., Коростин Д.О., Шубина Е.С., Ильинский В.В. NGS: высокопроизводительное секвенирование. М.: БИНОМ; 2014.
  3. Wang Y., Navin N.E. Advances and applications of single-cell sequencing technologies. Mol. Cell. 2015; 58(4):598-609. doi: 10.1016/j.molcel. 2015.05.005.
  4. Mardis E.R. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. (Palo Alto Calif). 2013; 6: 287-303. doi: 10.1146/annurev-anchem-062012-092628.
  5. Latta R.G., Gardner K.M., Staples D.A. Quantitative trait locus mapping of genes under selection across multiple years and sites in Avena barbata: epistasis, pleiotropy, and genotype-by-environment interactions. Genetics. 2010; 185(1): 375-385.
  6. Jelani M., Wasif N., Ali G., Chishti M., Ahmad W. A novel deletion mutation in LIPH gene causes autosomal recessive hypotrichosis (LAH2). Clin. Genet. 2006; 74(2): 184-8. doi: 10.1111/j.1399-0004.2008.01011.
  7. Yang Y., Xie B., Yan J. Application of next-generation sequencing technology in forensic science. Genomics Proteomics Bioinformatics. 2014; 12(5):190-7. doi: 10.1016/j.gpb.2014.09.001.
  8. Hodis E., Watson I.R., Kryukov G.V., Arold S.T., Imielinski M., Theurillat J.P., et al. A landscape of driver mutations in melanoma. Cell. 2012; 150(2): 251-63. doi: 10.1016/j.cell.2012.06.024.
  9. Laine A., Topisirovic I., Zhai D., Reed J.C., Borden K.L., Ronai Z. Regulation of p53 localization and activity by Ubc13. Mol. Cell Biol. 2006; 26(23): 8901-13.
  10. Davies H., Bignell G.R., Cox C., Stephens P., Edkins S., Clegg S., et al. Mutations of the BRAF gene in human cancer. Nature. 2002; 417(6892): 949-54.
  11. Riveiro-Falkenbach E., Villanueva C.A., Garrido M.C., Ruano Y., García Martín R.M., Godoy E., et al. Intra- and inter-tumoral homogeneity of BRAF (V600E) mutations in melanoma tumors. J. Invest. Dermatol. 2015; 135(12): 3078-85. doi: 10.1038/jid.2015.229.
  12. Имянитов Е.Н. Эпидемиология и биология опухолей кожи. Практическая онкология. 2012; 13 (2): 61-8.
  13. Jakob J.A, Bassett R.L.Jr., Ng C.S., Curry J.L., Joseph R.W., Alvarado G.C., et al. NRAS mutation status is an independent prognostic factor in metastatic melanoma. Cancer. 2012; 118 (16): 4014-23. doi: 10.1002/cncr.26724.
  14. Monsel G., Ortonne N., Bagot M., Bensussan A., Dumaz N. c-Kit mutants require hypoxia-inducible factor 1alpha to transform melanocytes. Oncogene. 2010; 29(2): 227-36.
  15. Yilmaz I., Gamsizkan M., Kucukodaci Z., Berber U., Demirel D., Haholu A., et al. BRAF, KIT, NRAS, GNAQ and GNA11 mutation analysis in cutaneous melanomas in Turkish population. Indian J. Pathol. Microbiol. 2015; 58(3): 279-84.
  16. Garcia-Marcos M., Ghosh P., Farquhar M.G. Molecular basis of a novel oncogenic mutation in GNAO1. Oncogene. 2011; 30(23): 2691-6.
  17. Xia J., Jia P., Hutchinson K.E., Dahlman K.B., Johnson D., Sosman J., et al. A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance. Mol. Cancer Ther. 2014; 13(7): 1918-28.
  18. Davies H., Bignell G.R., Cox C., Stephens P., Edkins S., Clegg S., et al. Mutations of the BRAF gene in human cancer. Nature; 2002; 417(6892): 949-54.
  19. Hauschild A., Agarwala S.S., Trefzer U., Hogg D., Robert C., Hersey P., et al. Results of a phase III, randomized, placebo-controlled study of sorafenib in combination with carboplatin and paclitaxel as second-line treatment in patients with unresectable stage III or stage IV melanoma. J. Clin. Oncol. 2009; 27(17): 2823-30.
  20. Grimaldi A.M., Simeone E., Festino L., Vanella V., Palla M., Ascierto P.A. Novel mechanisms and therapeutic approaches in melanoma: targeting the MAPK pathway. Discov. Med. 2015; 19(107): 455-61.
  21. Sun C., Wang L., Huang S., Heynen G.J., Prahallad A., Robert C., et al. Reversible and adaptive resistance to BRAF (V600E) inhibition in melanoma. Nature. 2014; 508(7494): 118-22.
  22. Hauschild A., Grob J.J., Demidov L.V., Jouary T., Gutzmer R., Millward M., et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012; 380(9839): 358-65. doi: 10.1016/S0140-6736(12)60868-X.
  23. Colombino M., Capone M., Lissia A., Cossu A., Rubino C., De Giorgi V., et al. BRAF/NRAS mutation frequencies among primary tumors and metastases in patients with melanoma. J. Clin. Oncol. 2012; 30(20): 2522-9. doi: 10.1200/JCO.2011.41.2452.
  24. Zebary A., Jangard M., Omholt K., Ragnarsson-Olding B., Hansson J. KIT, NRAS and BRAF mutations in sinonasal mucosal melanoma: a study of 56 cases. Br. J. Cancer. 2013; 109(3): 559-64. doi: 10.1038/bjc.2013.373.
  25. Beadling C., Jacobson-Dunlop E., Hodi F.S., Le C., Warrick A., Patterson J., et al. KIT gene mutations and copy number in melanoma subtypes. Clin. Cancer Res. 2008; 14(21): 6821-8. doi: 10.1158/1078-0432.
  26. Curtin J.A., Busam K., Pinkel D., Bastian B.C. Somatic activation of KIT in distinct subtypes of melanoma. J. Clin. Oncol. 2006; 24(26): 4340-6.
  27. Poynter J.N., Elder J.T., Fullen D.R., Nair R.P., Soengas M.S., Johnson T.M., et al. BRAF and NRAS mutations in melanoma and melanocytic nevi. Melanoma Res. 2006; 16(4): 267-73.
  28. Krishnamurthy S., Gu K., Ali S.M., Parvatappa N.J. Interdiscipl Histopathol. 2014; 2(2): 108-11. doi: 10.5455/jihp.20140225013612.
  29. Paulson K.G., Iyer J.G., Nghiem P. Asymmetric lateral distribution of melanoma and Merkel cell carcinoma in the United States J. Am. Acad. Dermatol. 2011; 65(1): 35-9. doi: 10.1016/j.jaad.2010.05.026.
  30. Giglia-Mari G., Sarasin A. TP53 mutations in human skin cancers. Hum. Mutat. 2003; 21(3): 217-28.
  31. Yan W., Wistuba I.I., Emmert-Buck M.R., Erickson H.S. Squamous cell carcinoma - similarities and differences among anatomical sites. Am. J. Cancer Res. 2011; 1(3): 275-300.
  32. Griewank K.G., Schadendorf D. Panel sequencing melanomas. J. Invest. Dermatol. 2015; 135(2): 335-36. doi: 10.1038/jid.2014.420.
  33. South A.P., Li Q., Uitto J. Next generation sequencing for mutation detection in heritable skin diseases: the paradigm of pseudoxanthoma elasticum. J. Invest. Dermatol. 2015; 135(4): 937-40. doi: 10.1038/jid.2014.521.
  34. Scott C.A., Plagnol V., Nitoiu D., Bland P.J., Blaydon D.C., Chronnell C.M., et al. Targeted sequence capture and high throughput sequencing in the molecular diagnosis of ichthyosis and other skin diseases. J. Invest. Dermatol. 2013; 133(2): 573-6. doi: 10.1038/jid.2012.332.
  35. Fitz-Gibbon S., Tomida S., Chiu B.H., Nguyen L., Du C., Liu M., et al. Propionibacterium acnes strain population in the human skin microbiome associated with acne. J. Invest. Dermatol. 2013; 133(9): 2152-60. doi: 10.1038/jid.2013.21.
  36. Capon F., Boulding H., Quaranta M., Mortimer N.J., Setterfield J.F., Black M.M., et al. Genetic analysis of desmoglein 3 (DSG3) sequence variants in patients with pemphigus vulgaris. Br. J. Dermatol. 2009; 161(6): 1403-5. doi: 10.1111/j.1365-2133.2009.09429.x.
  37. Saleh M.A. Pemphigus in the Arab world. J. Dermatol. 2015; 42(1): 27-30.
  38. Nagai M., Nagai H., Tominaga C., Sakaguchi Y., Jitsukawa O., Ohgo N., et al. Localised dominant dystrophic epidermolysis bullosa with a novel de novo mutation in COL7A1 Diagnosed by Next-generation Sequencing. Acta Dermatol. Venereol. 2015; 95(5): 629-31.
  39. Abe M. Novel gene therapy for epidermolysis bullosa using recombinant human VII type collagen protein. Hokkaido Igaku Zasshi. 2006; 81(3): 245-52.
  40. Pasmant E., Parfait B., Luscan A., Goussard P., Briand-Suleau A., Laurendeau I., 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.
  41. Balla B., Árvai K., Horváth P., Tobiás B., Takács I., Nagy Z., et al. 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. 2014; 53(2): 204-10.
  42. Ahmed M.S., Rauf S., Naeem M., Khan M.N., Mir A. Identification of novel mutation in the HR gene responsible for atrichia with papular lesions in a Pakistani family. J. Dermatol. 2013; 40(11): 927-8.
  43. Stahl J.M., Cheung M., Sharma A. Trivedi N.R., Shanmugam S., Robertson G.P. Loss of PTEN promotes tumor development in malignant melanoma. Cancer Res. 2003; 63(11): 2881-990.

Copyright (c) 2016 Eco-Vector


 


This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies