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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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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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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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CandiHap: a haplotype analysis toolkit for natural variation study.

Xukai Li1,2, Zhiyong Shi2, Jianhua Gao1,2

  • 1Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taigu, 030031 China.

Molecular Breeding : New Strategies in Plant Improvement
|June 14, 2023
PubMed
Summary

CandiHap software streamlines gene haplotype analysis for identifying candidate genes and causal variants. This tool accelerates genetic association studies by enabling rapid, robust analysis across various species and platforms.

Keywords:
CandiHapGWASHaplotypeInDelsSNPs

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Haplotype blocks are crucial for association-based mapping of candidate genes, reducing genotyping workload.
  • Gene haplotype analysis aids in evaluating trait-variant associations within gene regions.
  • Current gene haplotype analysis is often manual, limiting efficiency.

Purpose of the Study:

  • To introduce CandiHap, a software tool for rapid and robust gene haplotype analysis.
  • To enable preselection of candidate causal single-nucleotide polymorphisms and insertions/deletions (InDels).
  • To facilitate the exploration of favorable haplotypes for target traits.

Main Methods:

  • CandiHap analyzes genetic data from Sanger or next-generation sequencing.
  • Users can specify genes or linkage sites identified through genome-wide association studies.
  • The software supports both graphical user interface and command-line operations.

Main Results:

  • CandiHap provides rapid and robust haplotype analysis and candidate identification.
  • It allows for the preselection of candidate causal single-nucleotide polymorphisms and InDels.
  • The software is applicable to diverse species including plants, animals, and microbes.

Conclusions:

  • CandiHap significantly enhances the efficiency of gene haplotype analysis.
  • It supports researchers in identifying candidate genes and causal variants for trait-associated studies.
  • The software is freely available and versatile for various biological research applications.