Skip to main content

Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues

  • Protocol
  • First Online:
Odontogenesis

Abstract

This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Thesleff I (2003) Epithelial-mesenchymal signalling regulating tooth morphogenesis. J Cell Sci 116(9):1647–1648

    Article  CAS  PubMed  Google Scholar 

  2. Jussila M, Thesleff I (2012) Signaling networks regulating tooth organogenesis and regeneration, and the specification of dental mesenchymal and epithelial cell lineages. Cold Spring Harbor Perspect Biol 4(4):a008425

    Article  CAS  Google Scholar 

  3. Brook A (2009) Multilevel complex interactions between genetic, epigenetic and environmental factors in the aetiology of anomalies of dental development. Arch Oral Biol 54:S3–S17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Townsend G, Bockmann M, Hughes T et al (2012) Genetic, environmental and epigenetic influences on variation in human tooth number, size and shape. Odontology 100(1):1–9

    Article  CAS  PubMed  Google Scholar 

  5. Wang J, Sun K, Shen Y et al (2016) DNA methylation is critical for tooth agenesis: implications for sporadic non-syndromic anodontia and hypodontia. Sci Rep 6:19162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bailleul-Forestier I, Berdal A, Vinckier F et al (2008) The genetic basis of inherited anomalies of the teeth. Part 2: syndromes with significant dental involvement. Eur J Med Genet 51(5):383–408

    Article  PubMed  Google Scholar 

  7. Cobourne MT, Sharpe PT (2013) Diseases of the tooth: the genetic and molecular basis of inherited anomalies affecting the dentition. Wiley Interdiscip Rev Dev Biol 2(2):183–212

    Article  PubMed  Google Scholar 

  8. Vastardis H, Karimbux N, Guthua SW et al (1996) A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Nat Genet 13(4):417–421

    Article  CAS  PubMed  Google Scholar 

  9. Prasad MK, Geoffroy V, Vicaire S et al (2016) A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement. J Med Genet 53(2):98–110

    Article  CAS  PubMed  Google Scholar 

  10. Vastardis H (2000) The genetics of human tooth agenesis: new discoveries for understanding dental anomalies. Am J Orthod Dentofac Orthop 117(6):650–656

    Article  CAS  Google Scholar 

  11. Pagnan NAB, Visinoni ÁF (2014) Update on ectodermal dysplasias clinical classification. Am J Med Genet A 164(10):2415–2423

    Article  Google Scholar 

  12. Ye X, Attaie AB (2016) Genetic basis of nonsyndromic and syndromic tooth agenesis. J Pediatr Genet 5(4):198–208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sarkar T, Bansal R, Das P (2014) Whole genome sequencing reveals novel non-synonymous mutation in ectodysplasin a (EDA) associated with non-syndromic X-linked dominant congenital tooth agenesis. PLoS One 9(9):e106811

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Lammi L, Arte S, Somer M et al (2004) Mutations in AXIN2 cause familial tooth agenesis and predispose to colorectal cancer. Am J Hum Genet 74(5):1043–1050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Bergendal B, Klar J, Stecksén-Blicks C et al (2011) Isolated oligodontia associated with mutations in EDARADD, AXIN2, MSX1, and PAX9 genes. Am J Med Genet A 155(7):1616–1622

    Article  CAS  Google Scholar 

  16. Arte S, Parmanen S, Pirinen S et al (2013) Candidate gene analysis of tooth agenesis identifies novel mutations in six genes and suggests significant role for WNT and EDA signaling and allele combinations. PLoS One 8(8):e73705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Crawford PJ, Aldred M, Bloch-Zupan A (2007) Amelogenesis imperfecta. Orphanet J Rare Dis 2(1):17

    Article  PubMed  PubMed Central  Google Scholar 

  18. Smith CE, Murillo G, Brookes SJ et al (2016) Deletion of amelotin exons 3–6 is associated with amelogenesis imperfecta. Hum Mol Genet 25(16):3578–3587

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Sillence D, Senn A, Danks D (1979) Genetic heterogeneity in osteogenesis imperfecta. J Med Genet 16(2):101–116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Goldblatt J, Carman P, Sprague P (1991) Unique dwarfing, spondylometaphyseal skeletal dysplasia, with joint laxity and dentinogenesis imperfecta. Am J Med Genet 39(2):170–172

    Article  CAS  PubMed  Google Scholar 

  21. Unger S, Antoniazzi F, Brugnara M et al (2008) Clinical and radiographic delineation of odontochondrodysplasia. Am J Med Genet A 146(6):770–778

    Article  Google Scholar 

  22. Shields E, Bixler D, El-Kafrawy A (1973) A proposed classification for heritable human dentine defects with a description of a new entity. Arch Oral Biol 18(4):543–553, IN7

    Article  CAS  PubMed  Google Scholar 

  23. MacDougall M, Dong J, Acevedo AC (2006) Molecular basis of human dentin diseases. Am J Med Genet A 140(23):2536–2546

    Article  PubMed  CAS  Google Scholar 

  24. de La Dure-Molla M, Fournier BP, Berdal A (2015) Isolated dentinogenesis imperfecta and dentin dysplasia: revision of the classification. Eur J Hum Genet 23(4):445–451

    Article  PubMed  CAS  Google Scholar 

  25. MacDougall M, Simmons D, Luan X et al (1997) Dentin phosphoprotein and dentin sialoprotein are cleavage products expressed from a single transcript coded by a gene on human chromosome 4 Dentin phosphoprotein DNA sequence determination. J Biol Chem 272(2):835–842

    Article  CAS  PubMed  Google Scholar 

  26. Fisher LW, Fedarko NS (2003) Six genes expressed in bones and teeth encode the current members of the SIBLING family of proteins. Connect Tissue Res 44(1):33–40

    Article  CAS  PubMed  Google Scholar 

  27. Yamakoshi Y, Hu JC-C, Fukae M et al (2005) Dentin glycoprotein the protein in the middle of the dentin sialophosphoprotein chimera. J Biol Chem 280(17):17472–17479

    Article  CAS  PubMed  Google Scholar 

  28. Yang Q, Chen D, Xiong F et al (2016) A splicing mutation in VPS4B causes dentin dysplasia I. J Med Genet 53(9):624–633

    Article  CAS  PubMed  Google Scholar 

  29. Xiong F, Ji Z, Liu Y et al (2017) Mutation in SSUH2 causes autosomal-dominant dentin dysplasia type I. Hum Mutat 38(1):95–104

    Article  CAS  PubMed  Google Scholar 

  30. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci 74(2):560–564

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  PubMed  Google Scholar 

  33. Smith M (2017) DNA sequence analysis in clinical medicine, proceeding cautiously. Front Mol Biosci 4:24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Kircher M, Kelso J (2010) High-throughput DNA sequencing—concepts and limitations. BioEssays 32(6):524–536

    Article  CAS  PubMed  Google Scholar 

  35. Koboldt DC, Larson DE, Chen K et al (2012) Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol 838:369–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Biesecker LG, Green RC (2014) Diagnostic clinical genome and exome sequencing. N Engl J Med 370(25):2418–2425

    Article  PubMed  CAS  Google Scholar 

  37. Schouten JP, McElgunn CJ, Waaijer R et al (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30(12):e57–e57

    Article  PubMed  PubMed Central  Google Scholar 

  38. Schwartz M, Dunø M (2004) Improved molecular diagnosis of dystrophin gene mutations using the multiplex ligation-dependent probe amplification method. Genet Test 8(4):361–367

    Article  CAS  PubMed  Google Scholar 

  39. Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genom Proteom Bioinformatics 13(5):278–289

    Article  Google Scholar 

  40. O’Sullivan J, Bitu CC, Daly SB et al (2011) Whole-Exome sequencing identifies FAM20A mutations as a cause of amelogenesis imperfecta and gingival hyperplasia syndrome. Am J Hum Genet 88(5):616–620

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Poulter JA, Brookes SJ, Shore RC et al (2014) A missense mutation in ITGB6 causes pitted hypomineralized amelogenesis imperfecta. Hum Mol Genet 23(8):2189–2197

    Article  CAS  PubMed  Google Scholar 

  42. Poulter JA, El-Sayed W, Shore RC et al (2014) Whole-exome sequencing, without prior linkage, identifies a mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta. Eur J Hum Genet 22(1):132–135

    Article  CAS  PubMed  Google Scholar 

  43. Acevedo AC, Poulter JA, Alves PG et al (2015) Variability of systemic and oro-dental phenotype in two families with non-lethal Raine syndrome with FAM20C mutations. BMC Med Genet 16(1):8

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Yang J, Kawasaki K, Lee M et al (2016) The dentin phosphoprotein repeat region and inherited defects of dentin. Mol Genet Genomic Med 4(1):28–38

    Article  CAS  PubMed  Google Scholar 

  45. Aidar M, Line SRP (2007) A simple and cost-effective protocol for DNA isolation from buccal epithelial cells. Braz Dent J 18(2):148–152

    Article  PubMed  Google Scholar 

  46. Lahiri DK, Nurnberger JI Jr (1991) A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies. Nucl Acids Res 19(19):5444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Thiede C, Prange-Krex G, Freiberg-Richter J et al (2000) Buccal swabs but not mouthwash samples can be used to obtain pretransplant DNA fingerprints from recipients of allogeneic bone marrow transplants. Bone Marrow Transplantation 25(5):575

    Article  CAS  PubMed  Google Scholar 

  48. Abraham JE, Maranian MJ, Spiteri I et al (2012) Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping. BMC Med Genomics 5(1):19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ishmael FT, Stellato C (2008) Principles and applications of polymerase chain reaction: basic science for the practicing physician. Ann Allergy Asthma Immunol 101(4):437–443

    Article  CAS  PubMed  Google Scholar 

  50. Kolmodin LA, Birch DE (2002) Polymerase chain reaction. Basic principles and routine practice. Methods Mol Biol 192:3–18

    CAS  PubMed  Google Scholar 

  51. Untergasser A, Cutcutache I, Koressaar T et al (2012) Primer3—new capabilities and interfaces. Nucl Acids Res 40(15):e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23(10):1289–1291

    Article  CAS  PubMed  Google Scholar 

  53. Landre P, Gelfand D, Watson R (1995) The use of cosolvents to enhance amplification by the polymerase chain reaction. In: PCR strategies. Academic, New York, pp 316

    Google Scholar 

  54. Tang M, Xu W, Wang Q et al (2009) Potential of DNMT and its epigenetic regulation for lung cancer therapy. Curr Genomics 10(5):336–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Stewart SK, Morris TJ, Guilhamon P et al (2015) oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips. Methods 72:9–15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Gross JA, Lefebvre F, Lutz P-E et al (2016) Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array. Biol Methods Protocols 1(1):bpw002

    Article  Google Scholar 

  57. Field SF, Beraldi D, Bachman M et al (2015) Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array). PLoS One 10(2):e0118202

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  58. Skvortsova K, Zotenko E, Luu P-L et al (2017) Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA. Epigenet Chromatin 10(1):16

    Article  CAS  Google Scholar 

  59. Pastor WA, Pape UJ, Huang Y et al (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473(7347):394–397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Taiwo O, Wilson GA, Morris T et al (2012) Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7(4):617–636

    Article  CAS  PubMed  Google Scholar 

  61. Nestor CE, Meehan RR (2014) Hydroxymethylated DNA immunoprecipitation (hmeDIP). Func Anal DNA Chromatin 1094:259–267

    Article  CAS  Google Scholar 

  62. Buenrostro JD, Wu B, Chang HY et al (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21.29.21–21.29.29

    Article  Google Scholar 

  63. Chen S, Santos L, Wu Y et al (2005) Altered gene expression in human cleidocranial dysplasia dental pulp cells. Arch Oral Biol 50(2):227–236

    Article  CAS  PubMed  Google Scholar 

  64. Yan W, Zhang C, Yang X et al (2015) Abnormal differentiation of dental pulp cells in cleidocranial dysplasia. J Dent Res 94(4):577–583

    Article  CAS  PubMed  Google Scholar 

  65. Mosmann T (1983) Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J Immunol Methods 65(1–2):55–63

    Article  CAS  PubMed  Google Scholar 

  66. Liang C-C, Park AY, Guan J-L (2007) In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro. Nat Protoc 2(2):329–333

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Amorim, B.R., dos Santos, P.A.C., de Lima, C.L., Andia, D.C., Mazzeu, J.F., Acevedo, A.C. (2019). Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues. In: Papagerakis, P. (eds) Odontogenesis. Methods in Molecular Biology, vol 1922. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9012-2_37

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9012-2_37

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9011-5

  • Online ISBN: 978-1-4939-9012-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics