Neurotherapeutics

, Volume 11, Issue 4, pp 699–707 | Cite as

Next Generation Sequencing and the Future of Genetic Diagnosis

Review

Abstract

The introduction of next generation sequencing (NGS) has led to an exponential increase of elucidated genetic causes in both extremely rare diseases and common but heterogeneous disorders. It can be applied to the whole or to selected parts of the genome (genome or exome sequencing, gene panels). NGS is not only useful in large extended families with linkage information, but may also be applied to detect de novo mutations or mosaicism in sporadic patients without a prior hypothesis about the mutated gene. Currently, NGS is applied in both research and clinical settings, and there is a rapid transition of research findings to diagnostic applications. These developments may greatly help to minimize the “diagnostic odyssey” for patients as whole-genome analysis can be performed in a few days at reasonable costs compared with gene-by-gene analysis based on Sanger sequencing following diverse clinical tests. Despite the enthusiasm about NGS, one has to keep in mind its limitations, such as a coverage and accuracy of < 100 %, resulting in missing variants and false positive findings. In addition, variant interpretation is challenging as there is usually more than one candidate variant found. Therefore, there is an urgent need to define standards for NGS with respect to run quality and variant interpretation, as well as mechanisms of quality control. Further, there are ethical challenges including incidental findings and how to guide unaffected probands seeking direct-to-customer testing. However, taken together, the application of NGS in research and diagnostics provides a tremendous opportunity to better serve our patients.

Keywords

Exome sequencing Massively parallel sequencing Incidental findings Diagnostic yield Gene panel 

Notes

Acknowledgments

KL receives funding from the German Research Foundation (LO 1555/3-2, LO 1555/8-1) and the Dystonia Coalition (NS065701). CK is supported by a career development award from the Hermann and Lilly Schilling Foundation, and by the German Research Foundation (SFB936 and SFB TR134).

Required Author Forms

Disclosure forms provided by the authors are available with the online version of this article.

Supplementary material

13311_2014_288_MOESM1_ESM.pdf (1.2 mb)
ESM 1(PDF 1225 kb)

References

  1. 1.
    Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463-5467.PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Metzker ML. Emerging technologies in DNA sequencing. Genome Res 2005;15:1767-1776.PubMedCrossRefGoogle Scholar
  3. 3.
    Lin B, Wang J, Cheng Y. Recent patents and advances in the next-generation sequencing technologies. Recent Pat Biomed Eng 2008;2008:60-67.PubMedCrossRefPubMedCentralGoogle Scholar
  4. 4.
    Lam HY, Clark MJ, Chen R, et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 2012;30:78-82.CrossRefPubMedCentralGoogle Scholar
  5. 5.
    Gilissen C, Hoischen A, Brunner HG, Veltman JA. Disease gene identification strategies for exome sequencing. Eur J Hum Genet 2012;20:490-497.PubMedCrossRefPubMedCentralGoogle Scholar
  6. 6.
    Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet 2012;13:565-575.PubMedCrossRefGoogle Scholar
  7. 7.
    Weise A, Timmermann B, Grabherr M, et al. High-throughput sequencing of microdissected chromosomal regions. Eur J Hum Genet 2010;18:457-462.PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Selmer KK, Gilfillan GD, Stromme P, et al. A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions. Eur J Hum Genet 2012;20:58-63.PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Gilissen C, Hoischen A, Brunner HG, Veltman JA. Unlocking Mendelian disease using exome sequencing. Genome Biol 2011;12:228.PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Kumar KR, Lohmann K, Klein C. Genetics of Parkinson disease and other movement disorders. Curr Opin Neurol 2012;25:466-474.PubMedCrossRefGoogle Scholar
  11. 11.
    Lemke JR, Riesch E, Scheurenbrand T, et al. Targeted next generation sequencing as a diagnostic tool in epileptic disorders. Epilepsia 2012;53:1387-1398.PubMedCrossRefGoogle Scholar
  12. 12.
    de Ligt J, Willemsen MH, van Bon BW, et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 2012;367:1921-1929.PubMedCrossRefGoogle Scholar
  13. 13.
    Zimprich A, Benet-Pages A, Struhal W, et al. A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet 2011;89:168-175.PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Vilarino-Guell C, Wider C, Ross OA, et al. VPS35 mutations in Parkinson disease. Am J Hum Genet 2011;89:162-167.PubMedCrossRefPubMedCentralGoogle Scholar
  15. 15.
    Haack TB, Hogarth P, Kruer MC, et al. Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA. Am J Hum Genet 2012;91:1144-1149.PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Fuchs T, Saunders-Pullman R, Masuho I, et al. Mutations in GNAL cause primary torsion dystonia. Nat Genet 2012;45:88-92.PubMedCrossRefPubMedCentralGoogle Scholar
  17. 17.
    Chen WJ, Lin Y, Xiong ZQ, et al. Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia. Nat Genet 2011;43:1252-1255.PubMedCrossRefGoogle Scholar
  18. 18.
    Soong BW, Huang YH, Tsai PC, et al. Exome sequencing identifies GNB4 mutations as a cause of dominant intermediate Charcot-Marie-Tooth disease. Am J Hum Genet 2013;92:422-430.PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Neph S, Vierstra J, Stergachis AB, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012;489:83-90.PubMedCrossRefPubMedCentralGoogle Scholar
  20. 20.
    Herdewyn S, Zhao H, Moisse M, et al. Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis. Hum Mol Genet 2012;21:2412-2419.PubMedCrossRefPubMedCentralGoogle Scholar
  21. 21.
    Lohmann K, Wilcox RA, Winkler S, et al. Whispering dysphonia (DYT4 dystonia) is caused by a mutation in the TUBB4 gene. Ann Neurol 2013;73:537-545.PubMedCrossRefGoogle Scholar
  22. 22.
    Nishiguchi KM, Tearle RG, Liu YP, et al. Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene. Proc Natl Acad Sci U S A 2013;110:16139-16144.PubMedCrossRefPubMedCentralGoogle Scholar
  23. 23.
    Jiang YH, Yuen RK, Jin X, et al. Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet 2013;93:249-263.PubMedCrossRefPubMedCentralGoogle Scholar
  24. 24.
    Pagnamenta AT, Lise S, Harrison V, et al. Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies. J Hum Genet 2012;57:70-72.PubMedCrossRefGoogle Scholar
  25. 25.
    Tapper WJ, Foulds N, Cross NC, et al. Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations. PLoS One 2014;9:e86940.PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Huisman SA, Redeker EJ, Maas SM, Mannens MM, Hennekam RC. High rate of mosaicism in individuals with Cornelia de Lange syndrome. J Med Genet 2013;50:339-344.PubMedCrossRefGoogle Scholar
  27. 27.
    Simons C, Wolf NI, McNeil N, et al. A de novo mutation in the beta-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum. Am J Hum Genet 2013;92:767-773.PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Suls A, Jaehn JA, Kecskes A, et al. De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome. Am J Hum Genet 2013;93:967-975.PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Michaelson JJ, Shi Y, Gujral M, et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 2012;151:1431-1442.PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Erdmann J, Stark K, Esslinger UB, et al. Dysfunctional nitric oxide signalling increases risk of myocardial infarction. Nature 2013;504:432-436.PubMedCrossRefGoogle Scholar
  31. 31.
    Tang B, Xiong H, Sun P, et al. Association of PINK1 and DJ-1 confers digenic inheritance of early-onset Parkinson's disease. Hum Mol Genet 2006;15:1816-1825.PubMedCrossRefGoogle Scholar
  32. 32.
    Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013;132:1077-1130.PubMedCrossRefPubMedCentralGoogle Scholar
  33. 33.
    Arif B, Kumar KR, Seibler P, et al. A novel OPA3 mutation revealed by exome sequencing: an example of reverse phenotyping. JAMA Neurol 2013;70:783-787.PubMedCrossRefGoogle Scholar
  34. 34.
    Might M, Wilsey M. The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med 2014 Mar 20.Google Scholar
  35. 35.
    Erdmann J, Schunkert H. Forty-five years to diagnosis. Neuromuscul Disord 2013;23:503-505.PubMedCrossRefGoogle Scholar
  36. 36.
    Baasch AL, Huning I, Gilissen C, et al. Exome sequencing identifies a de novo SCN2A mutation in a patient with intractable seizures, severe intellectual disability, optic atrophy, muscular hypotonia, and brain abnormalities. Epilepsia 2014;55:e25-29.Google Scholar
  37. 37.
    Abecasis GR, Altshuler D, Auton A, et al. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-1073.PubMedCrossRefGoogle Scholar
  38. 38.
    Dorschner MO, Amendola LM, Turner EH, et al. Actionable, pathogenic incidental findings in 1,000 participants’ exomes. Am J Hum Genet 2013;93:631-640.PubMedCrossRefPubMedCentralGoogle Scholar
  39. 39.
    Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat 2011;32:358-368.PubMedCrossRefGoogle Scholar
  40. 40.
    Cassa CA, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat 2013;34:1216-1220.PubMedCrossRefPubMedCentralGoogle Scholar
  41. 41.
    Klein C, Konig IR, Lohmann K. Exome sequencing for gene discovery: time to set standard criteria. Ann Neurol 2012;72:627-628.PubMedCrossRefGoogle Scholar
  42. 42.
    Ma L, Chen R, Wang L, Yang Y, Wan X. No mutations in CIZ1 in twelve adult-onset primary cervical dystonia families. Mov Disord 2013;28:1899-1901.PubMedCrossRefGoogle Scholar
  43. 43.
    Zech M, Gross N, Jochim A, et al. Rare sequence variants in ANO3 and GNAL in a primary torsion dystonia series and controls. Mov Disord 2014;29:143-147.PubMedCrossRefGoogle Scholar
  44. 44.
    Schrijver I, Aziz N, Jennings LJ, et al. Methods-based proficiency testing in molecular genetic pathology. J Mol Diagn 2014;16:283-287.PubMedCrossRefGoogle Scholar
  45. 45.
    Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-574.PubMedCrossRefPubMedCentralGoogle Scholar
  46. 46.
    Burke W, Matheny Antommaria AH, Bennett R, et al. Recommendations for returning genomic incidental findings? We need to talk! Genet Med 2013;15:854-859.PubMedCrossRefGoogle Scholar
  47. 47.
    Holtzman NA. ACMG recommendations on incidental findings are flawed scientifically and ethically. Genet Med 2013;15:750-751.PubMedCrossRefGoogle Scholar
  48. 48.
    Shahmirzadi L, Chao EC, Palmaer E, et al. Patient decisions for disclosure of secondary findings among the first 200 individuals undergoing clinical diagnostic exome sequencing. Genet Med 2014;16:395-399.PubMedCrossRefPubMedCentralGoogle Scholar
  49. 49.
    Hudson K, Javitt G, Burke W, Byers P. ASHG Statement on direct-to-consumer genetic testing in the United States. Obstet Gynecol 2007;110:1392-1395.PubMedCrossRefGoogle Scholar
  50. 50.
    Nalls MA, Plagnol V, Hernandez DG, et al. Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet 2011;377:641-649.PubMedCrossRefGoogle Scholar
  51. 51.
    Klein C, Ziegler A. From GWAS to clinical utility in Parkinson's disease. Lancet 2011;377:613-614.PubMedCrossRefGoogle Scholar
  52. 52.
    Skirton H, Goldsmith L, Jackson L, O'Connor A. Direct to consumer genetic testing: a systematic review of position statements, policies and recommendations. Clin Genet 2012;82:210-218.PubMedCrossRefGoogle Scholar
  53. 53.
    Kassahn KS, Scott HS, Caramins MC. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge. Hum Mutat 2014;35:413-423.PubMedCrossRefGoogle Scholar
  54. 54.
    Nemeth AH, Kwasniewska AC, Lise S, et al. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain 2013;136:3106-3118.PubMedCrossRefPubMedCentralGoogle Scholar
  55. 55.
    Beck J, Pittman A, Adamson G, et al. Validation of next-generation sequencing technologies in genetic diagnosis of dementia. Neurobiol Aging 2014;35:261-265.PubMedCrossRefGoogle Scholar
  56. 56.
    Yang Y, Muzny DM, Reid JG, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369:1502-1511.PubMedCrossRefGoogle Scholar
  57. 57.
    Neveling K, Feenstra I, Gilissen C, et al. A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum Mutat 2013;34:1721-1726.PubMedCrossRefGoogle Scholar
  58. 58.
    Saunders CJ, Miller NA, Soden SE, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 2012;4:154ra135.PubMedCrossRefGoogle Scholar
  59. 59.
    Veenstra DL, Piper M, Haddow JE, et al. Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update. Genet Med 2013;15:14-24.PubMedCrossRefPubMedCentralGoogle Scholar
  60. 60.
    Bowdin S, Ray P, Cohn RD, Meyn MS. The genome clinic: A multidisciplinary approach to assessing the opportunities and challenges of integrating genomic analysis into clinical care. Hum Mutat 2014;35:513-519.PubMedCrossRefGoogle Scholar
  61. 61.
    Polvi A, Linturi H, Varilo T, et al. The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era. Hum Mutat 2013;34:1458-1466.PubMedCrossRefGoogle Scholar

Copyright information

© The American Society for Experimental NeuroTherapeutics, Inc. 2014

Authors and Affiliations

  1. 1.Institute of NeurogeneticsUniversity of LübeckLübeckGermany

Personalised recommendations