Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

Ultra-rare Disease and Genomics-Driven Precision Medicine

  • Lee, Sangmoon (Department of Biomedical Sciences, Seoul National University College of Medicine) ;
  • Choi, Murim (Department of Biomedical Sciences, Seoul National University College of Medicine)
  • Received : 2015.07.31
  • Accepted : 2016.05.26
  • Published : 2016.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Since next-generation sequencing (NGS) technique was adopted into clinical practices, revolutionary advances in diagnosing rare genetic diseases have been achieved through translating genomic medicine into precision or personalized management. Indeed, several successful cases of molecular diagnosis and treatment with personalized or targeted therapies of rare genetic diseases have been reported. Still, there are several obstacles to be overcome for wider application of NGS-based precision medicine, including high sequencing cost, incomplete variant sensitivity and accuracy, practical complexities, and a shortage of available treatment options.

Keywords

References

  1. Hagemann IS, Cottrell CE, Lockwood CM. Design of targeted, capture-based, next generation sequencing tests for precision cancer therapy. Cancer Genet 2013;206:420-431. https://doi.org/10.1016/j.cancergen.2013.11.003
  2. Yadav SS, Li J, Lavery HJ, Yadav KK, Tewari AK. Next-generation sequencing technology in prostate cancer diagnosis, prognosis, and personalized treatment. Urol Oncol 2015;33:267.e1-267.e13. https://doi.org/10.1016/j.urolonc.2015.02.009
  3. Hennekam RC. Care for patients with ultra-rare disorders. Eur J Med Genet 2011;54:220-224. https://doi.org/10.1016/j.ejmg.2010.12.001
  4. Mencacci NE, Rubio-Agusti I, Zdebik A, Asmus F, Ludtmann MH, Ryten M, et al. A missense mutation in KCTD17 causes autosomal dominant myoclonus-dystonia. Am J Hum Genet 2015;96:938-947. https://doi.org/10.1016/j.ajhg.2015.04.008
  5. Zech M, Lam DD, Francescatto L, Schormair B, Salminen AV, Jochim A, et al. Recessive mutations in the ${\alpha}3$ (VI) collagen gene COL6A3 cause early-onset isolated dystonia. Am J Hum Genet 2015;96:883-893. https://doi.org/10.1016/j.ajhg.2015.04.010
  6. Lee S, Moon JS, Lee CR, Kim HE, Baek SM, Hwang S, et al. Abatacept alleviates severe autoimmune symptoms in a patient carrying a de novo variant in CTLA-4. J Allergy Clin Immunol 2016;137:327-330. https://doi.org/10.1016/j.jaci.2015.08.036
  7. Mousallem T, Urban TJ, McSweeney KM, Kleinstein SE, Zhu M, Adeli M, et al. Clinical application of whole-genome sequencing in patients with primary immunodeficiency. J Allergy Clin Immunol 2015;136:476-479.e6. https://doi.org/10.1016/j.jaci.2015.02.040
  8. Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet 2012;13:565-575. https://doi.org/10.1038/nrg3241
  9. Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature 2015;519:223-228. https://doi.org/10.1038/nature14135
  10. Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Al Turki S, et al. Timing, rates and spectra of human germline mutation. Nat Genet 2016;48:126-133. https://doi.org/10.1038/ng.3469
  11. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 2013;14:681-691. https://doi.org/10.1038/nrg3555
  12. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009;106:19096-19101. https://doi.org/10.1073/pnas.0910672106
  13. Seo J, Choi IH, Lee JS, Yoo Y, Kim NK, Choi M, et al. Rare cases of congenital arthrogryposis multiplex caused by novel recurrent CHRNG mutations. J Hum Genet 2015;60:213-215. https://doi.org/10.1038/jhg.2015.2
  14. Grosu DS, Hague L, Chelliserry M, Kruglyak KM, Lenta R, Klotzle B, et al. Clinical investigational studies for validation of a next-generation sequencing in vitro diagnostic device for cystic fibrosis testing. Expert Rev Mol Diagn 2014;14:605-622. https://doi.org/10.1586/14737159.2014.916618
  15. Kuk K, Taylor-Cousar JL. Lumacaftor and ivacaftor in the management of patients with cystic fibrosis: current evidence and future prospects. Ther Adv Respir Dis 2015;9:313-326. https://doi.org/10.1177/1753465815601934
  16. Rogan MP, Stoltz DA, Hornick DB. Cystic fibrosis transmembrane conductance regulator intracellular processing, trafficking, and opportunities for mutation-specific treatment. Chest 2011;139:1480-1490. https://doi.org/10.1378/chest.10-2077
  17. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 2011;13:255-262. https://doi.org/10.1097/GIM.0b013e3182088158
  18. Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, et al. Whole-genome sequencing for optimized patient management. Sci Transl Med 2011;3:87re3.
  19. Mordechai O, Postovsky S, Vlodavsky E, Eran A, Constantini S, Dotan E, et al. Metastatic rhabdoid meningioma with BRAF V600E mutation and good response to personalized therapy: case report and review of the literature. Pediatr Hematol Oncol 2015;32:207-211. https://doi.org/10.3109/08880018.2014.936058
  20. Yu C, Sonnen AF, George R, Dessailly BH, Stagg LJ, Evans EJ, et al. Rigid-body ligand recognition drives cytotoxic T-lymphocyte antigen 4 (CTLA-4) receptor triggering. J Biol Chem 2011;286:6685-6696. https://doi.org/10.1074/jbc.M110.182394
  21. Stamper CC, Zhang Y, Tobin JF, Erbe DV, Ikemizu S, Davis SJ, et al. Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses. Nature 2001;410:608-611. https://doi.org/10.1038/35069118
  22. Nepomnyashchaya YN, Artemov AV, Roumiantsev SA, Roumyantsev AG, Zhavoronkov A. Non-invasive prenatal diagnostics of aneuploidy using next-generation DNA sequencing technologies, and clinical considerations. Clin Chem Lab Med 2013;51:1141-1154.
  23. Stahlberg A, Krzyzanowski PM, Jackson JB, Egyud M, Stein L, Godfrey TE. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing. Nucleic Acids Res 2016;44:e105. https://doi.org/10.1093/nar/gkw224
  24. Lee JS, Lee S, Lim BC, Kim KJ, Hwang YS, Choi M, et al. Alpha-thalassemia X-linked intellectual disability syndrome identified by whole exome sequencing in two boys with white matter changes and developmental retardation. Gene 2015;569:318-322. https://doi.org/10.1016/j.gene.2015.04.075
  25. Chong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, et al. The genetic basis of Mendelian phenotypes: discoveries, challenges, and opportunities. Am J Hum Genet 2015;97:199-215. https://doi.org/10.1016/j.ajhg.2015.06.009
  26. Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 2015;16:114. https://doi.org/10.1186/s13059-015-0677-2
  27. Li YY, Jones SJ. Drug repositioning for personalized medicine. Genome Med 2012;4:27.