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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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Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

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Software solutions for the livestock genomics SNP array revolution.

E L Nicolazzi1, S Biffani2, F Biscarini1

  • 1Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.

Animal Genetics
|April 25, 2015
PubMed
Summary
This summary is machine-generated.

Navigating complex single nucleotide polymorphism (SNP) array data is challenging due to a lack of standardization. This toolkit aids SNP array data management and analysis, but standardization remains a critical issue for researchers.

Keywords:
genome-wide association studiesgenomic selectionimputationlivestock speciesmanagementpopulation geneticssingle nucleotide polymorphism

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Area of Science:

  • Genomics
  • Bioinformatics
  • Animal Breeding

Background:

  • The increasing availability of single nucleotide polymorphism (SNP) arrays, particularly in bovine species, presents challenges in data management and integration.
  • Genomic and genotype data lack standardization, hindering efficient exchange and analysis.
  • Existing analysis software often requires non-standard, case-specific input files, demanding programming skills for data preparation.

Purpose of the Study:

  • To introduce a software toolkit designed for comprehensive SNP array data management.
  • To facilitate analyses including imputation, genome-wide association studies (GWAS), population genetics, and genomic selection.
  • To highlight the ongoing data standardization issues in SNP array research.

Main Methods:

  • Development of a software toolkit for handling SNP array data.
  • Integration of functionalities for data management, imputation, GWAS, population genetics, and genomic selection.
  • Review and advice on navigating existing tools for SNP array data complexity.

Main Results:

  • The developed toolkit provides a centralized solution for various SNP array data analyses.
  • The toolkit assists researchers in managing large datasets and performing complex genomic analyses.
  • The study underscores the persistent lack of standardized genotypic data formats and software input files.

Conclusions:

  • While the toolkit offers valuable solutions for SNP array data analysis, it does not resolve the fundamental need for data standardization.
  • Researchers must still contend with a chaotic data landscape, necessitating careful tool selection and data preparation.
  • The toolkit aims to empower researchers by providing guidance and tools to navigate the complexities of SNP array data.