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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
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Functional Validation of Noncoding Variants Associated With Nonsyndromic Orofacial Cleft.

Siying Zhu1, Hongxu Tao1, Robert A Cornell2

  • 1State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.

Human Mutation
|September 8, 2025
PubMed
Summary

Genome-wide association studies identified genetic variants linked to nonsyndromic orofacial cleft (NSOFC). This research focuses on noncoding variants and methods to understand their role in craniofacial development and NSOFC.

Keywords:
cisregulatory elementgenome-wide association studynoncoding variantnonsyndromic orofacial cleft

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Area of Science:

  • Genetics
  • Developmental Biology
  • Human Disease

Background:

  • Genome-wide association studies (GWASs) have identified numerous genetic variants associated with nonsyndromic orofacial cleft (NSOFC).
  • Translating these GWAS findings into a mechanistic understanding of NSOFC pathogenesis is challenging due to uncertainties about causal variants and the prevalence of variants in noncoding genomic regions.
  • Current research on NSOFC-associated noncoding variants primarily investigates their impact on transcriptional regulation and gene expression.

Purpose of the Study:

  • To systematically summarize recent GWAS findings for NSOFC.
  • To explore statistical and functional methods for identifying and validating causal variants, particularly those in noncoding regions.
  • To bridge the gap between GWAS-identified variants and the underlying pathogenic mechanisms of NSOFC.

Main Methods:

  • Systematic review of recent NSOFC-associated GWAS findings.
  • Focus on variants located in noncoding regions.
  • Discussion of current statistical and functional approaches for variant identification and validation.

Main Results:

  • GWASs have identified genetic variants linked to NSOFC risk.
  • Noncoding variants, especially those in regulatory elements, are a key focus for understanding NSOFC.
  • Methods are being developed to identify and validate causal variants in NSOFC.

Conclusions:

  • Deciphering causal variants in NSOFC is crucial for understanding craniofacial development.
  • Identifying causal variants can lead to improved early diagnosis and risk stratification for NSOFC.
  • Understanding the genetic basis of NSOFC may reveal novel therapeutic targets.