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Pedigree Analysis01:35

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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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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Published on: June 21, 2018

Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data.

B J Hayes1

  • 1Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia 3083. ben.hayes@dip.vic.gov.au

Journal of Dairy Science
|March 24, 2011
PubMed
Summary
This summary is machine-generated.

This study presents an efficient algorithm for assigning parentage in dairy cattle using single nucleotide polymorphism (SNP) data. The method accurately identifies sires and dams, even with large datasets, aiding in pedigree reconstruction.

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Area of Science:

  • Animal Genetics
  • Bioinformatics
  • Dairy Science

Background:

  • Dairy cattle are routinely genotyped using single nucleotide polymorphism (SNP) arrays for genomic estimated breeding values.
  • SNP arrays offer valuable data for parentage assignment and pedigree reconstruction in livestock.

Purpose of the Study:

  • To develop a computationally efficient algorithm for parentage assignment using SNP data.
  • To demonstrate the accuracy of the algorithm with varying SNP panel densities.

Main Methods:

  • An efficient algorithm was developed for parentage assignment using SNP data.
  • The algorithm's performance was evaluated using 50,000-SNP and 3,000-SNP panels.

Main Results:

  • The developed algorithm provides computationally efficient parentage assignment.
  • Very accurate parentage assignment was achieved with both dense (50,000-SNP) and sparse (3,000-SNP) panels.

Conclusions:

  • The efficient algorithm facilitates accurate parentage assignment and pedigree reconstruction in dairy cattle.
  • This method is effective across different SNP densities, supporting large-scale genomic applications.