Skip to main content

Overview of Next Generation, High-Throughput Molecular Genetic Methods

  • Chapter
  • First Online:
Molecular Genetics of Pediatric Orthopaedic Disorders
  • 658 Accesses

Abstract

Recent advances in genome-wide technologies have revolutionized how researchers identify disease-causing genes. Both microarray-based genotyping analysis for copy number variations and high-throughput next-generation sequencing (NGS) for sequence variations have enabled a surge in the discovery of genes associated with disease. Application of these technologies in large population studies has shown the extent of sequence and copy-number variations throughout the genome and their contributions to human quantitative traits and diseases. This chapter will highlight both technologies and will provide examples of how each has been used to identify genes causing pediatric orthopaedic disorders.

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

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Paria N, Copley LA, Herring JA, Kim HK, Richards BS, Sucato DJ, Rios JJ, Wise CA. The impact of large-scale genomic methods in orthopaedic disorders: insights from genome-wide association studies. J Bone Joint Surg Am. 2014;96(5):e38.

    Article  PubMed  Google Scholar 

  2. Lander ES. Initial impact of the sequencing of the human genome. Nature. 2011;470(7333):187–97.

    Article  CAS  PubMed  Google Scholar 

  3. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. The sequence of the human genome. Science. 2001;291(5507):1304–51.

    Article  CAS  PubMed  Google Scholar 

  4. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.

    Article  CAS  PubMed  Google Scholar 

  5. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931–45.

    Google Scholar 

  6. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, ­Makhijani V, Roth GT, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452(7189):872–6.

    Article  CAS  PubMed  Google Scholar 

  7. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature. 2006;444(7118):444–54.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Girirajan S, Campbell CD, Eichler EE. Human copy number variation and complex genetic disease. Annu Rev Genet. 2011;45:203–26.

    Google Scholar 

  9. Yagerman SE, Cross MB, Green DW, Scher DM. Pediatric orthopedic conditions in ­Charcot-Marie-Tooth disease: a literature review. Curr Opin Pediatr. 2012;24(1):50–6.

    Article  CAS  PubMed  Google Scholar 

  10. Lupski JR, de Oca-Luna RM, Slaugenhaupt S, Pentao L, Guzzetta V, Trask BJ, ­Saucedo-Cardenas O, Barker DF, Killian JM, Garcia CA, et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell. 1991;66(2):219–32.

    Article  CAS  PubMed  Google Scholar 

  11. Pentao L, Wise CA, Chinault AC, Patel PI, Lupski JR. Charcot-Marie-Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit. Nat Genet. 1992;2(4):292–300.

    Article  CAS  PubMed  Google Scholar 

  12. Boerkoel CF, Takashima H, Garcia CA, Olney RK, Johnson J, Berry K, Russo P, Kennedy S, Teebi AS, Scavina M, et al. Charcot-Marie-Tooth disease and related neuropathies: mutation distribution and genotype-phenotype correlation. Ann Neurol. 2002;51(2):190–201.

    Article  CAS  PubMed  Google Scholar 

  13. Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 1998;14(10):417–22.

    Article  CAS  PubMed  Google Scholar 

  14. Alvarado DM, Aferol H, McCall K, Huang JB, Techy M, Buchan J, Cady J, Gonzales PR, Dobbs MB, Gurnett CA. Familial isolated clubfoot is associated with recurrent chromosome 17q23.1q23.2 microduplications containing TBX4. Am J Hum Genet. 2010;87(1):154–60.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Alvarado DM, Buchan JG, Frick SL, Herzenberg JE, Dobbs MB, Gurnett CA. Copy number analysis of 413 isolated talipes equinovarus patients suggests role for transcriptional ­regulators of early limb development. Eur J Hum Genet. 2013;21(4):373–80.

    Google Scholar 

  16. Duboc V, Logan MP. Regulation of limb bud initiation and limb-type morphology. Dev Dyn. 2011;240(5):1017–27.

    Article  CAS  PubMed  Google Scholar 

  17. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007;315(5813):848–53.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, et al. Runs of homozygosity in ­European populations. Am J Hum Genet. 2008;83(3):359–72.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Jen J, Coulin CJ, Bosley TM, Salih MA, Sabatti C, Nelson SF, Baloh RW. Familial ­horizontal gaze palsy with progressive scoliosis maps to chromosome 11q23–25. Neurology. 2002;59(3):432–5.

    Article  PubMed  Google Scholar 

  20. Jen JC, Chan WM, Bosley TM, Wan J, Carr JR, Rub U, Shattuck D, Salamon G, Kudo LC, Ou J, et al. Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science. 2004;304(5676):1509–13.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Senderek J, Bergmann C, Stendel C, Kirfel J, Verpoorten N, De Jonghe P, Timmerman V, Chrast R, Verheijen MH, Lemke G, et al. Mutations in a gene encoding a novel SH3/TPR domain protein cause autosomal recessive Charcot-Marie-Tooth type 4C neuropathy. Am J Hum Genet. 2003;73(5):1106–19.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet. 2007;80(4):727–39.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Consortium TGP. A map of human genome variation from population-scale sequencing. ­Nature. 2010;467(7319):1061–73.

    Article  Google Scholar 

  24. Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, Bouffard GG, Chines PS, Cruz P, Hansen NF, et al. The ClinSeq project: piloting large-scale genome ­sequencing for research in genomic medicine. Genome Res. 2009;19(9):1665–74.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745–55.

    Article  CAS  PubMed  Google Scholar 

  26. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009;461(7261):272–6.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Gilissen C, Hoischen A, Brunner HG, Veltman JA. Disease gene identification strategies for exome sequencing. Eur J Hum Genet. 2012;20(5):490–7.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Paria N, Copley LA, Herring JA, Kim HK, Richards BS, Sucato DJ, Wise CA, Rios JJ. Whole-exome sequencing: discovering genetic causes of orthopaedic disorders. J Bone Joint Surg Am. 2013;95(23):e1851–8.

    Article  PubMed  Google Scholar 

  29. Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337(6090):64–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, et al. Exome sequencing identifies the cause of a Mendelian disorder. Nat Genet. 2010;42(1):30–5.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC. Identification by whole-genome ­resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet. 2010;19(22):4313–8.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010;42(9):790–3.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Weedon MN, Hastings R, Caswell R, Xie W, Paszkiewicz K, Antoniadi T, Williams M, King C, Greenhalgh L, Newbury-Ecob R, et al. Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease. Am J Hum Genet. 2011;89(2):308–12.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Becker J, Semler O, Gilissen C, Li Y, Bolz HJ, Giunta C, Bergmann C, Rohrbach M, Koerber F, Zimmermann K, et al. Exome sequencing identifies truncating mutations in human ­SERPINF1 in autosomal-recessive osteogenesis imperfecta. Am J Hum Genet. 2011;88(3):362–71.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Vissers LE, Lausch E, Unger S, Campos-Xavier AB, Gilissen C, Rossi A, Del Rosario M, Venselaar H, Knoll U, Nampoothiri S, et al. Chondrodysplasia and abnormal joint ­development associated with mutations in IMPAD1, encoding the golgi-resident nucleotide phosphatase, gPAPP. Am J Hum Genet. 2011;88(5):608–15.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Gammill HS, Rubens CE, Santillan DA, Murray JC, et al. Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med. 2012;4(137):137ra76.

    Article  PubMed Central  PubMed  Google Scholar 

  37. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, et al. Accurate whole-genome sequencing and haplotyping from 10–20 human cells. Nature. 2012;487(7406):190–5.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, 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(3):255–62.

    Article  PubMed  Google Scholar 

  39. Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, Reid JG, Fink JK, Morgan MB, Gingras MC, et al. Whole-genome sequencing for ­optimized patient management. Sci Transl Med. 2011;3(87):87re83.

    Article  Google Scholar 

  40. Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, et al. Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med. 2012;4(138):138ra178.

    Article  Google Scholar 

  41. Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012;4(154):154ra135.

    Article  PubMed Central  PubMed  Google Scholar 

  42. Lindhurst MJ, Sapp JC, Teer JK, Johnston JJ, Finn EM, Peters K, Turner J, Cannons JL, Bick D, Blakemore L, et al. A mosaic activating mutation in AKT1 associated with the Proteus syndrome. New Engl J Med. 2011;365(7):611–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, et al. Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Am J Hum Genet. 2012;90(6):1108–15.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Lee JH, Huynh M, Silhavy JL, Kim S, Dixon-Salazar T, Heiberg A, Scott E, Bafna V, Hill KJ, Collazo A, et al. De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet. 2012;44(8):941–5.

    Article  CAS  PubMed  Google Scholar 

  45. Riviere JB, Mirzaa GM, O’Roak BJ, Beddaoui M, Alcantara D, Conway RL, St-Onge J, Schwartzentruber JA, Gripp KW, Nikkel SM, et al. De novo germline and postzygotic ­mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly ­syndromes. Nat Genet. 2012;44(8):934–40.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Lindhurst MJ, Parker VE, Payne F, Sapp JC, Rudge S, Harris J, Witkowski AM, Zhang Q, Groeneveld MP, Scott CE, et al. Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA. Nat Genet. 2012;44(8):928–33.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Rios JJ, Paria N, Burns DK, Israel BA, Cornelia R, Wise CA, Ezaki M. Somatic ­gain-of-function mutations in PIK3CA in patients with macrodactyly. Hum Mol Genet. 2012.

    Google Scholar 

  48. Rios JJ, Paria N, Burns DK, Israel BA, Cornelia R, Wise CA, Ezaki M. Somatic gain-of-function mutations in PIK3CA in patients with macrodactyly. Hum Mol Genet. 2013;22(3):444–51.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jonathan J. Rios PhD .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this chapter

Cite this chapter

Rios, J. (2015). Overview of Next Generation, High-Throughput Molecular Genetic Methods. In: Wise, C., Rios, J. (eds) Molecular Genetics of Pediatric Orthopaedic Disorders. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2169-0_1

Download citation

Publish with us

Policies and ethics