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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Comparing Copy Number Variations and SNPs02:26

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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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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

Updated: May 24, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Identification of functional non-coding variants associated with orofacial cleft.

Priyanka Kumari, Ryan Z Friedman, Lira Pi

    Biorxiv : the Preprint Server for Biology
    |March 3, 2025
    PubMed
    Summary
    This summary is machine-generated.

    Researchers identified specific genetic variations, or single nucleotide polymorphisms (SNPs), linked to oral facial clefts (OFC). These functional SNPs near the IRF6 gene significantly increase the risk for cleft lip with or without cleft palate (CL/P).

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    Quantification of Orofacial Phenotypes in Xenopus
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    Area of Science:

    • Genetics and Genomics
    • Developmental Biology
    • Human Disease Pathogenesis

    Background:

    • Oral facial cleft (OFC) is a common birth defect with complex genetic and environmental causes.
    • Genome-wide association studies (GWAS) have identified numerous genetic loci associated with OFC, but the functional variants remain largely unknown.
    • The IRF6 gene locus is a key region implicated in OFC risk.

    Purpose of the Study:

    • To identify functional single nucleotide polymorphisms (SNPs) associated with oral facial cleft (OFC) risk at eight specific genetic loci.
    • To investigate the mechanism by which these functional SNPs influence gene expression in embryonic oral epithelium.
    • To determine the contribution of identified functional SNPs to cleft lip with or without cleft palate (CL/P) risk.

    Main Methods:

    • Utilized massively parallel reporter assays (MPRAs) in an oral epithelium cell line to screen for SNPs affecting enhancer activity.
    • Integrated chromatin-mark data to prioritize enhancers in relevant cell types.
    • Validated candidate functional SNPs using traditional reporter assays and genome engineering in induced pluripotent stem cells (iPSCs) differentiated into oral epithelium.

    Main Results:

    • Identified six candidate functional SNPs in five loci: 1q32/IRF6, 3q28/TP63, 6p24.3/TFAP2A, 20q12/MAFB, and 9q22.33/FOXE1.
    • Demonstrated allele-specific enhancer activity for identified SNPs in oral epithelium.
    • Genome engineering experiments confirmed the regulatory roles of two SNPs near IRF6 and one near FOXE1.
    • Conditional analysis of GWAS meta-analysis indicated that two functional SNPs near IRF6 explain most of the CL/P risk associated with this locus.

    Conclusions:

    • This study successfully identified functional genetic variants contributing to oral facial cleft pathogenesis.
    • The findings highlight the importance of the IRF6 locus and specific SNPs in regulating gene expression critical for oral development.
    • Connects genetic variations in OFC to underlying molecular mechanisms, paving the way for future research and potential therapeutic strategies.