The Journal of Pediatrics
Volume 155, Issue 6 , Pages 909-913 , December 2009

A Genome-Wide Association Study Identifies a Locus for Nonsyndromic Cleft Lip with or without Cleft Palate on 8q24

  • Struan F.A. Grant, PhD

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
    • Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
    • Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA
    • Corresponding Author InformationReprint requests: Struan Grant, PhD, Center for Applied Genomics, 1216 E. Abramson Research Center, 3615 Civic Center Blvd, Philadelphia, PA 19104-4318.
  • ,
  • Kai Wang, PhD

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Haitao Zhang, PhD

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Wendy Glaberson, BA

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Kiran Annaiah, MSc

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Cecilia E. Kim, BA

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Jonathan P. Bradfield, BS

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Joseph T. Glessner, MSc

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Kelly A. Thomas, BA

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Maria Garris, BA

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Edward C. Frackelton, BA

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • F. George Otieno, MSc

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Rosetta M. Chiavacci, BSN

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Hyun-Duck Nah, PhD

      Affiliations

    • Division of Plastic Surgery, School of Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Richard E. Kirschner, MD

      Affiliations

    • Division of Plastic Surgery, School of Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, PA
  • ,
  • Hakon Hakonarson, MD, PhD

      Affiliations

    • Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA
    • Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
    • Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA

Received 18 March 2009 ,Revised 28 April 2009 ,Accepted 11 June 2009.

References 

  1. Murray JC. Gene/environment causes of cleft lip and/or palate. Clin Genet. 2002;61:248–256
  2. Wyszynski DF, Beaty TH, Maestri NE. Genetics of nonsyndromic oral clefts revisited. Cleft Palate Craniofac J. 1996;33:406–417
  3. Strauss RP. The organization and delivery of craniofacial health services: the state of the art. Cleft Palate Craniofac J. 1999;36:189–195
  4. Christensen K, Juel K, Herskind AM, Murray JC. Long term follow up study of survival associated with cleft lip and palate at birth. BMJ. 2004;328:1405
  5. Stanier P, Moore GE. Genetics of cleft lip and palate: syndromic genes contribute to the incidence of non-syndromic clefts. Hum Mol Genet 2004;13 Spec No 1:R73-81.
  6. Mitchell LE, Risch N. Mode of inheritance of nonsyndromic cleft lip with or without cleft palate: a reanalysis. Am J Hum Genet. 1992;51:323–332
  7. Mossey PA, Little J. Epidemiology of oral clefts: An international perspective. In:  Wyszynski DF editors. Cleft Lip and Palate. New York: Oxford University Press; 2002;p. 127–144
  8. Vanderas AP. Incidence of cleft lip, cleft palate, and cleft lip and palate among races: a review. Cleft Palate J. 1987;24:216–225
  9. Fraser FC. The genetics of cleft lip and cleft palate. Am J Hum Genet. 1970;22:336–352
  10. Ardinger HH, Buetow KH, Bell GI, Bardach J, VanDemark DR, Murray JC. Association of genetic variation of the transforming growth factor-alpha gene with cleft lip and palate. Am J Hum Genet. 1989;45:348–353
  11. Mitchell LE. Transforming growth factor alpha locus and nonsyndromic cleft lip with or without cleft palate: a reappraisal. Genet Epidemiol. 1997;14:231–240
  12. Cummings AM, Kavlock RJ. Gene-environment interactions: a review of effects on reproduction and development. Crit Rev Toxicol. 2004;34:461–485
  13. Mitchell LE, Christensen K. Analysis of the recurrence patterns for nonsyndromic cleft lip with or without cleft palate in the families of 3,073 Danish probands. Am J Med Genet. 1996;61:371–376
  14. Marazita ML, Murray JC, Lidral AC, Arcos-Burgos M, Cooper ME, Goldstein T, et al. Meta-analysis of 13 genome scans reveals multiple cleft lip/palate genes with novel loci on 9q21 and 2q32-35. Am J Hum Genet. 2004;75:161–173
  15. Juriloff DM, Harris MJ, Brown CJ. Unravelling the complex genetics of cleft lip in the mouse model. Mamm Genome. 2001;12:426–435
  16. Kondo S, Schutte BC, Richardson RJ, Bjork BC, Knight AS, Watanabe Y, et al. Mutations in IRF6 cause Van der Woude and popliteal pterygium syndromes. Nat Genet. 2002;32:285–289
  17. Rahimov F, Marazita ML, Visel A, Cooper ME, Hitchler MJ, Rubini M, et al. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet. 2008;40:1341–1347
  18. Hakonarson H, Grant SFA, Bradfield JP, Marchand L, Kim CE, Glessner JT, et al. A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature. 2007;448:591–594
  19. Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet. 2005;37:549–554
  20. Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL. Whole-genome genotyping with the single-base extension assay. Nat Methods. 2006;3:31–33
  21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–575
  22. Birnbaum S, Ludwig KU, Reutter H, Herms S, Steffens M, Rubini M, et al. Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet. 2009;41:473–477
  23. Spritz RA. The genetics and epigenetics of orofacial clefts. Curr Opin Pediatr. 2001;13:556–560
  24. Yoshiura K, Machida J, Daack-Hirsch S, Patil SR, Ashworth LK, Hecht JT, et al. Characterization of a novel gene disrupted by a balanced chromosomal translocation t(2;19)(q11.2;q13.3) in a family with cleft lip and palate. Genomics. 1998;54:231–240
  25. FitzPatrick DR, Carr IM, McLaren L, Leek JP, Wightman P, Williamson K, et al. Identification of SATB2 as the cleft palate gene on 2q32-q33. Hum Mol Genet. 2003;12:2491–2501
  26. Colmenares C, Heilstedt HA, Shaffer LG, Schwartz S, Berk M, Murray JC, et al. Loss of the SKI proto-oncogene in individuals affected with 1p36 deletion syndrome is predicted by strain-dependent defects in Ski-/- mice. Nat Genet. 2002;30:106–109
  27. Shaikh TH, Kurahashi H, Emanuel BS. Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review. Genet Med. 2001;3:6–13
  28. Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D. A chromosomal deletion map of human malformations. Am J Hum Genet. 1998;63:1153–1159
  29. Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D. A chromosomal duplication map of malformations: regions of suspected haplo- and triplolethality–and tolerance of segmental aneuploidy–in humans. Am J Hum Genet. 1999;64:1702–1708

 This research was financially supported by the Children's Hospital of Philadelphia and in part by a Research Development Award from the Cotswold Foundation (H.H. & S.F.A.G). The authors declare no conflicts of interest.

PII: S0022-3476(09)00575-7

doi: 10.1016/j.jpeds.2009.06.020

The Journal of Pediatrics
Volume 155, Issue 6 , Pages 909-913 , December 2009