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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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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB.

Joon-Ho Lee1, Taeheon Lee2, Hak-Kyo Lee1

  • 1Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

Asian-Australasian Journal of Animal Sciences
|September 3, 2014
PubMed
Summary
This summary is machine-generated.

A new Horse Single Nucleotide Polymorphism and Expression Database (HSDB) was created to catalog horse genomic variants and expression data. This resource aids in understanding horse genetics for improved breeding and selection strategies.

Keywords:
DatabaseExpressionHorseThoroughbredVariants

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Area of Science:

  • Genomics
  • Animal Genetics
  • Bioinformatics

Background:

  • Genetics plays a crucial role in horse breeding and selection.
  • A lack of comprehensive horse-specific genomic browsers and databases hinders research.
  • Understanding genomic variants and their expression is vital for horse improvement.

Purpose of the Study:

  • To construct a comprehensive horse genomic variants database.
  • To integrate genomic variant data with transcriptional profiles.
  • To facilitate genetic improvement and breeding strategies for Thoroughbreds.

Main Methods:

  • Utilized population genome sequences from eighteen horses.
  • Incorporated RNA-sequencing data from four horses.
  • Identified and validated single nucleotide polymorphisms (SNPs) against SNP chip and RNA-seq data.

Main Results:

  • Developed the Horse Single Nucleotide Polymorphism and Expression Database (HSDB).
  • Identified numerous genomic variants, including rare variants, in the horse genome.
  • Achieved high concordance levels (99.02% with SNP chip, 96.6% with RNA-seq) for identified SNPs.
  • Integrated genomic variants with corresponding transcriptional profiles.

Conclusions:

  • The HSDB provides valuable genomic and expression data for horses.
  • The database aids in understanding the functional impact of genomic variants.
  • HSDB will support advancements in horse genetic improvement and breeding programs.