Skip to main content

Homozygosity Mapping for Autosomal Recessive Ocular Diseases

  • Chapter
  • First Online:
Advances in Vision Research, Volume I

Abstract

Genetic eye diseases play a major role in causing visual impairment and blindness affecting all the structures of the eye from the anterior to posterior segment. They are inherited as either Mendelian or complex and in Mendelian inheritance, auotosomal dominant, autosomal recessive or X-linked recessive patterns are commonly observed. Linkage and homozygosity mapping is based on the information provided by the non-recombinants on the chromosomal segments to map disease genes. In Homozygosity mapping the large stretches of homozygous alleles inherited due to identity-by-descent (IBD) and shared between the affected individual(s) and absent in the unaffected in the family are compared to map the disease gene locus. A small family with one each of affected and unaffected provides sufficient data to map disease locus/gene using homozygosity mapping unlike linkage studies where larger multi-generation families with many affected and unaffected are required. An increased prevalence of autosomal recessive disorders observed in genetically isolated or highly inbred families have aided in mapping many ocular diseases genes using homozygosity mapping. This chapter details the history, methodology and the different ocular diseases where homozygosity mapping has been applied to identify the causative genes.

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

Access this chapter

Chapter
USD 29.95
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
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
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. Sadagopan KA, Capasso J, Levin AV. Genetics for the ophthalmologist. Oman J Ophthalmol. 2012;5:144–9.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Hurst JA. Genetics of blindness. Br J Hosp Med. 1992;47:495–500.

    CAS  PubMed  Google Scholar 

  3. Fan BJ, Tam PO, Choy KW, Wang DY, Lam DS, Pang CP. Molecular diagnostics of genetic eye diseases. Clin Biochem. 2006;39:231–9.

    Article  CAS  PubMed  Google Scholar 

  4. Neveling K, den Hollander AI, Cremers FP, Collin RW. Identification and analysis of inherited retinal disease genes. Methods Mol Biol. 2013;935:3–23.

    Article  CAS  PubMed  Google Scholar 

  5. Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171:737–8.

    Article  CAS  PubMed  Google Scholar 

  6. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol. 1986;51(Pt 1):263–73.

    Article  CAS  PubMed  Google Scholar 

  7. MacDonald IM, Sasi R. Molecular genetics of inherited eye disorders. Clin Invest Med. 1994;17:474–98.

    CAS  PubMed  Google Scholar 

  8. Nollau P, Wagener C. Methods for detection of point mutations: performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin Chem. 1997;43:1114–28.

    CAS  PubMed  Google Scholar 

  9. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A. 1989;86:2766–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Pasternak JJ. Genetics and physical mapping of the human genome. In: An introduction to human molecular genetics: mechanisms of inherited diseases. Hoboken: Wiley; 2005. p. 153–88.

    Chapter  Google Scholar 

  11. Guttmacher AE, Collins FS. Welcome to the genomic era. N Engl J Med. 2003;349:996–8.

    Article  CAS  PubMed  Google Scholar 

  12. Brookes AJ. The essence of SNPs. Gene. 1999;234:177–86.

    Article  CAS  PubMed  Google Scholar 

  13. Wang DG, Fan JB, Siao CJ, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998;280:1077–82.

    Article  CAS  PubMed  Google Scholar 

  14. Lindblad-Toh K, Tanenbaum DM, Daly MJ, et al. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol. 2000;18:1001–5.

    Article  CAS  PubMed  Google Scholar 

  15. Mei R, Galipeau PC, Prass C, et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 2000;10:1126–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Swaroop A, Sieving PA. The golden era of ocular disease gene discovery: race to the finish. Clin Genet. 2013;84:99–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet. 2010;11:476–86.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Dryja TP. Gene-based approach to human gene-phenotype correlations. Proc Natl Acad Sci U S A. 1997;94:12117–21.

    Article  CAS  PubMed  Google Scholar 

  19. Rosenfeld PJ, McKusick VA, Amberger JS, Dryja TP. Recent advances in the gene map of inherited eye disorders: primary hereditary diseases of the retina, choroid, and vitreous. J Med Genet. 1994;31:903–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhang L, Yang W, Ying D, et al. Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data. Hum Mutat. 2011;32:345–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hildebrandt F, Heeringa SF, Ruschendorf F, et al. A systematic approach to mapping recessive disease genes in individuals from outbred populations. PLoS Genet. 2009;5:e1000353.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Alkuraya FS. Homozygosity mapping: one more tool in the clinical geneticist's toolbox. Genet Med Off J Am College Med Genet. 2010;12:236–9.

    Google Scholar 

  23. Arbour NC, Zlotogora J, Knowlton RG, et al. Homozygosity mapping of achromatopsia to chromosome 2 using DNA pooling. Hum Mol Genet. 1997;6:689–94.

    Article  CAS  PubMed  Google Scholar 

  24. Ben Hamida C, Doerflinger N, Belal S, et al. Localization of Friedreich ataxia phenotype with selective vitamin E deficiency to chromosome 8q by homozygosity mapping. Nat Genet. 1993;5:195–200.

    Article  CAS  PubMed  Google Scholar 

  25. Hillaire D, Leclerc A, Faure S, et al. Localization of merosin-negative congenital muscular dystrophy to chromosome 6q2 by homozygosity mapping. Hum Mol Genet. 1994;3:1657–61.

    Article  CAS  PubMed  Google Scholar 

  26. Pollak MR, Chou YH, Cerda JJ, et al. Homozygosity mapping of the gene for alkaptonuria to chromosome 3q2. Nat Genet. 1993;5:201–4.

    Article  CAS  PubMed  Google Scholar 

  27. Sheffield VC, Carmi R, Kwitek-Black A, et al. Identification of a Bardet-Biedl syndrome locus on chromosome 3 and evaluation of an efficient approach to homozygosity mapping. Hum Mol Genet. 1994;3:1331–5.

    Article  CAS  PubMed  Google Scholar 

  28. Hamel C. Retinitis pigmentosa. Orphanet J Rare Dis. 2006;1:40.

    Article  PubMed  Google Scholar 

  29. van Huet RA, Pierrache LH, Meester-Smoor MA, et al. The efficacy of microarray screening for autosomal recessive retinitis pigmentosa in routine clinical practice. Mol Vis. 2015;21:461–76.

    PubMed  PubMed Central  Google Scholar 

  30. Kajiwara K, Berson EL, Dryja TP. Digenic retinitis pigmentosa due to mutations at the unlinked peripherin/RDS and ROM1 loci. Science. 1994;264:1604–8.

    Article  CAS  PubMed  Google Scholar 

  31. Dryja TP, Hahn LB, Kajiwara K, Berson EL. Dominant and digenic mutations in the peripherin/RDS and ROM1 genes in retinitis pigmentosa. Invest Ophthalmol Vis Sci. 1997;38:1972–82.

    CAS  PubMed  Google Scholar 

  32. Mansergh FC, Millington-Ward S, Kennan A, et al. Retinitis pigmentosa and progressive sensorineural hearing loss caused by a C12258A mutation in the mitochondrial MTTS2 gene. Am J Hum Genet. 1999;64:971–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. A SFaT. Neuropathy, ataxia and retinitis pigmentosa (NARP) syndrome. In: Bertini E, editor. Orphanet encyclopedia. Turkey: Orphanet; 2004.

    Google Scholar 

  34. Bandah-Rozenfeld D, Mizrahi-Meissonnier L, Farhy C, et al. Homozygosity mapping reveals null mutations in FAM161A as a cause of autosomal-recessive retinitis pigmentosa. Am J Hum Genet. 2010;87:382–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Peluso I, Conte I, Testa F, et al. The ADAMTS18 gene is responsible for autosomal recessive early onset severe retinal dystrophy. Orphanet J Rare Dis. 2013;8:16.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Tuson M, Marfany G, Gonzalez-Duarte R. Mutation of CERKL, a novel human ceramide kinase gene, causes autosomal recessive retinitis pigmentosa (RP26). Am J Hum Genet. 2004;74:128–38.

    Article  CAS  PubMed  Google Scholar 

  37. Ajmal M, Khan MI, Neveling K, et al. A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma. J Med Genet. 2014;51:444–8.

    Article  CAS  PubMed  Google Scholar 

  38. Avila-Fernandez A, Perez-Carro R, Corton M, et al. Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. Hum Mol Genet. 2015;24:4037–48.

    Article  CAS  PubMed  Google Scholar 

  39. Coussa RG, Otto EA, Gee HY, et al. WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome. Clin Genet. 2013;84:150–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Bocquet B, Marzouka NA, Hebrard M, et al. Homozygosity mapping in autosomal recessive retinitis pigmentosa families detects novel mutations. Mol Vis. 2013;19:2487–500.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Collin RW, van den Born LI, Klevering BJ, et al. High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population. Invest Ophthalmol Vis Sci. 2011;52:2227–39.

    Article  CAS  PubMed  Google Scholar 

  42. Siemiatkowska AM, Arimadyo K, Moruz LM, et al. Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping. Mol Vis. 2011;17:3013–24.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Sohocki MM, Bowne SJ, Sullivan LS, et al. Mutations in a new photoreceptor-pineal gene on 17p cause Leber congenital amaurosis. Nat Genet. 2000;24:79–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. den Hollander AI, Roepman R, Koenekoop RK, Cremers FP. Leber congenital amaurosis: genes, proteins and disease mechanisms. Prog Retin Eye Res. 2008;27:391–419.

    Article  Google Scholar 

  45. Roger JE, Hiriyanna A, Gotoh N, et al. OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness. J Clin Invest. 2014;124:631–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wang X, Wang H, Cao M, et al. Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. Hum Mutat. 2011;32:1450–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. den Hollander AI, Koenekoop RK, Mohamed MD, et al. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. Nat Genet. 2007;39:889–95.

    Article  Google Scholar 

  48. Wang H, den Hollander AI, Moayedi Y, et al. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am J Hum Genet. 2009;84:380–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Frank V, den Hollander AI, Bruchle NO, et al. Mutations of the CEP290 gene encoding a centrosomal protein cause Meckel-Gruber syndrome. Hum Mutat. 2008;29:45–52.

    Article  CAS  PubMed  Google Scholar 

  50. Janecke AR, Thompson DA, Utermann G, et al. Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy. Nat Genet. 2004;36:850–4.

    Article  CAS  PubMed  Google Scholar 

  51. Aldahmesh MA, Al-Owain M, Alqahtani F, Hazzaa S, Alkuraya FS. A null mutation in CABP4 causes Leber's congenital amaurosis-like phenotype. Mol Vis. 2010;16:207–12.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Abu-Safieh L, Alrashed M, Anazi S, et al. Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes. Genome Res. 2013;23:236–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Chacon-Camacho OF, Zenteno JC. Review and update on the molecular basis of Leber congenital amaurosis. World J Clin Cases. 2015;3:112–24.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Ramprasad VL, Soumittra N, Nancarrow D, et al. Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis. Mol Vis. 2008;14:481–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Srilekha S, Arokiasamy T, Srikrupa NN, et al. Homozygosity Mapping in Leber Congenital Amaurosis and Autosomal Recessive Retinitis Pigmentosa in South Indian Families. PLoS One. 2015;10:e0131679.

    Article  PubMed  PubMed Central  Google Scholar 

  56. Beales PL, Elcioglu N, Woolf AS, Parker D, Flinter FA. New criteria for improved diagnosis of Bardet-Biedl syndrome: results of a population survey. J Med Genet. 1999;36:437–46.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Billingsley G, Deveault C, Heon E. BBS mutational analysis: a strategic approach. Ophthalmic Genet. 2011;32:181–7.

    Article  CAS  PubMed  Google Scholar 

  58. Sathya Priya C, Sen P, Umashankar V, et al. Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort. Clin Genet. 2015;87:161–6.

    Article  CAS  PubMed  Google Scholar 

  59. Weiss JS, Moller HU, Aldave AJ, et al. IC3D classification of corneal dystrophies--edition 2. Cornea. 2015;34:117–59.

    Article  PubMed  Google Scholar 

  60. Toma NM, Ebenezer ND, Inglehearn CF, Plant C, Ficker LA, Bhattacharya SS. Linkage of congenital hereditary endothelial dystrophy to chromosome 20. Hum Mol Genet. 1995;4:2395–8.

    Article  CAS  PubMed  Google Scholar 

  61. Callaghan M, Hand CK, Kennedy SM, FitzSimon JS, Collum LM, Parfrey NA. Homozygosity mapping and linkage analysis demonstrate that autosomal recessive congenital hereditary endothelial dystrophy (CHED) and autosomal dominant CHED are genetically distinct. Br J Ophthalmol. 1999;83:115–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Vithana EN, Morgan P, Sundaresan P, et al. Mutations in sodium-borate cotransporter SLC4A11 cause recessive congenital hereditary endothelial dystrophy (CHED2). Nat Genet. 2006;38:755–7.

    Article  CAS  PubMed  Google Scholar 

  63. Ramprasad VL, Ebenezer ND, Aung T, et al. Novel SLC4A11 mutations in patients with recessive congenital hereditary endothelial dystrophy (CHED2). Mutation in brief #958. Online. Hum Mutat. 2007;28:522–3.

    Article  PubMed  Google Scholar 

  64. Ali M, Buentello-Volante B, McKibbin M, et al. Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma. Mol Vis. 2010;16:1162–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Williamson KA, FitzPatrick DR. The genetic architecture of microphthalmia, anophthalmia and coloboma. Eur J Med Genet. 2014;57:369–80.

    Article  PubMed  Google Scholar 

  66. Casey J, Kawaguchi R, Morrissey M, et al. First implication of STRA6 mutations in isolated anophthalmia, microphthalmia, and coloboma: a new dimension to the STRA6 phenotype. Hum Mutat. 2011;32:1417–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Christensen AE, Fiskerstrand T, Knappskog PM, Boman H, Rodahl E. A novel ADAMTSL4 mutation in autosomal recessive ectopia lentis et pupillae. Invest Ophthalmol Vis Sci. 2010;51:6369–73.

    Article  PubMed  Google Scholar 

  68. Paun CC, Pijl BJ, Siemiatkowska AM, et al. A novel crumbs homolog 1 mutation in a family with retinitis pigmentosa, nanophthalmos, and optic disc drusen. Mol Vis. 2012;18:2447–53.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Uz E, Alanay Y, Aktas D, et al. Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia. Am J Hum Genet. 2010;86:789–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Iseri SU, Wyatt AW, Nurnberg G, et al. Use of genome-wide SNP homozygosity mapping in small pedigrees to identify new mutations in VSX2 causing recessive microphthalmia and a semidominant inner retinal dystrophy. Hum Genet. 2010;128:51–60.

    Article  CAS  PubMed  Google Scholar 

  71. Hmani-Aifa M, Ben Salem S, Benzina Z, et al. A genome-wide linkage scan in Tunisian families identifies a novel locus for non-syndromic posterior microphthalmia to chromosome 2q37.1. Hum Genet. 2009;126:575–87.

    Article  CAS  PubMed  Google Scholar 

  72. Miano MG, Jacobson SG, Carothers A, et al. Pitfalls in homozygosity mapping. Am J Hum Genet. 2000;67:1348–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nagasamy Soumittra .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Japan KK

About this chapter

Cite this chapter

SatyaPriya, C., Srilekha, S., Sudha, K., Sripriya, S., Soumittra, N. (2017). Homozygosity Mapping for Autosomal Recessive Ocular Diseases. In: Prakash, G., Iwata, T. (eds) Advances in Vision Research, Volume I. Essentials in Ophthalmology. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56511-6_32

Download citation

  • DOI: https://doi.org/10.1007/978-4-431-56511-6_32

  • Published:

  • Publisher Name: Springer, Tokyo

  • Print ISBN: 978-4-431-56509-3

  • Online ISBN: 978-4-431-56511-6

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics