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Genome-wide Association Studies-GWAS01:11

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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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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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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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Genome-wide Analyses Identify a Novel Risk Locus for Nonsyndromic Cleft Palate.

M He1, X Zuo2,3,4, H Liu1

  • 1The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China.

Journal of Dental Research
|August 8, 2020
PubMed
Summary
This summary is machine-generated.

Genetic factors for nonsyndromic cleft palate only (NSCPO) were investigated. A genome-wide association study identified a novel locus at 15q24.3 and a known locus at 1q32.2, advancing understanding of cleft palate development.

Keywords:
common variantsfunctional variantsgenetic risk locigenome-wide association studyorofacial cleftssusceptibility

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Area of Science:

  • Genetics
  • Developmental Biology
  • Human Health

Background:

  • Nonsyndromic orofacial clefts (NSOFCs) present as cleft lip only (NSCLO), cleft lip with palate (NSCLP), and cleft palate only (NSCPO).
  • The genetic underpinnings of NSCPO remain largely uncharacterized, hindering a comprehensive understanding of NSOFC pathogenesis.

Purpose of the Study:

  • To identify genetic loci associated with nonsyndromic cleft palate only (NSCPO) in the Chinese Han population.
  • To explore the genetic overlap and differential effects of identified loci across NSOFC subphenotypes.

Main Methods:

  • A two-stage genome-wide association study (GWAS) was conducted for NSCPO.
  • Replication analyses of selected variants were performed in other NSOFC cohorts.
  • Functional annotation of risk alleles and candidate genes was integrated with existing biological knowledge.

Main Results:

  • A novel genetic locus at 15q24.3 and a known locus at 1q32.2 were significantly associated with NSCPO.
  • A variant at 15q24.3 showed opposing effects on risk for NSCPO and NSCLP.
  • Candidate genes within the identified loci are implicated in embryonic patterning and cellular processes crucial for palate development.

Conclusions:

  • The study identifies novel genetic risk factors for NSCPO, contributing to the understanding of its genetic architecture.
  • The findings highlight the complex genetic basis of NSOFCs, with loci potentially influencing different subphenotypes distinctly.
  • This research provides critical insights into the molecular mechanisms underlying palate development and the etiology of cleft palate.