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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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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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Updated: Jul 12, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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AGIDB: a versatile database for genotype imputation and variant decoding across species.

Kaili Zhang1, Jiete Liang1, Yuhua Fu1

  • 1Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.

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AGIDB is a new website that provides tools and a database for animal genomics research. It offers comprehensive variant decoding and genotype imputation for 89 species, supporting genetic research and breeding.

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Area of Science:

  • Genomics and Genetics
  • Bioinformatics
  • Animal Science

Background:

  • High costs of whole-genome sequencing limit research applications.
  • Imputation from SNP chips or low-coverage WGS (lcWGS) are common but have limitations.
  • Processing lcWGS data and meeting imputation requirements are challenging.

Purpose of the Study:

  • To develop AGIDB, a comprehensive website for animal genomics research.
  • To overcome limitations in processing lcWGS data and genotype imputation.
  • To provide a user-friendly platform with extensive variant data and tools.

Main Methods:

  • Integrated whole-genome sequencing and chip data from 17,360 and 174,945 individuals, respectively.
  • Processed data from 89 species, identifying over one billion variants across 688.57 TB.
  • Developed user-friendly searching, data analysis modules, and downloadable reference panels.

Main Results:

  • Created AGIDB (agidb.pro) with an unprecedented sample size and variant decoding for animals.
  • Integrated diverse genotype imputation scenarios.
  • Enabled comprehensive annotation of genetic variants for specific populations.

Conclusions:

  • AGIDB serves as a foundational resource for animal genetics and breeding research.
  • The platform supports researchers with extensive datasets, variant decoding, and utility tools.
  • AGIDB facilitates advanced genetic variant analysis and imputation across numerous species.