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Candidate pathway based analysis for cleft lip with or without cleft palate.

Tian-Xiao Zhang1, Terri H Beaty, Ingo Ruczinski

  • 1Johns Hopkins University.

Statistical Applications in Genetics and Molecular Biology
|April 14, 2012
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Summary
This summary is machine-generated.

This study investigated genetic pathways linked to non-syndromic cleft lip with or without cleft palate (NSCL/P). While no single pathway reached statistical significance, the overall results suggest a role for the studied genes and biological pathways in NSCL/P.

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Area of Science:

  • Genetics
  • Developmental Biology
  • Bioinformatics

Background:

  • Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with complex genetic underpinnings.
  • Previous genome-wide association studies (GWAS) have identified genetic associations, but the underlying biological mechanisms remain largely unexplored.

Purpose of the Study:

  • To identify potential biological pathways associated with NSCL/P.
  • To explore the biological mechanisms contributing to NSCL/P risk.

Main Methods:

  • Utilized data from a large GWAS of 1,908 NSCL/P case-parent trios (5,742 individuals).
  • Selected 42 candidate biological pathways involving 1,564 genes and 40,208 single nucleotide polymorphisms (SNPs).
  • Employed a pathway-based analysis with permutation testing to assess statistical significance.

Main Results:

  • Several pathways showed nominally significant p-values, indicating potential associations.
  • No pathways remained statistically significant after controlling for the family-wise error rate.
  • A permutation test indicated an overall significant pattern (p=0.029) of low p-values, suggesting a collective role for the pathways.

Conclusions:

  • This pathway-based analysis did not pinpoint a single significant pathway for NSCL/P.
  • The collective evidence suggests that one or more of the investigated genes and pathways likely contribute to the risk of oral clefting.