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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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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Development of a 25-plex SNP assay for traceability in cattle.

B Karniol¹, A Shirak, E Baruch

¹Agricultural Research Organization, Institute of Animal Science, Bet-Dagan, Israel.

Animal Genetics

|March 19, 2009

Summary

A new DNA profiling method using 25 single nucleotide polymorphisms (SNPs) offers high precision for cattle traceability. This SNaPshot assay provides accurate genetic identification and parentage control for major commercial breeds.

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Area of Science:

Animal Genetics
Molecular Biology
Forensic Science

Background:

Single nucleotide polymorphisms (SNPs) are crucial genetic markers for DNA profiling due to their abundance and suitability for automation.
The SNaPshot method offers a robust platform for multiplex SNP genotyping, enabling efficient analysis of multiple genetic loci simultaneously.

Purpose of the Study:

To develop and validate a multiplex assay for genotyping 25 SNPs in cattle using the SNaPshot method.
To assess the utility of this assay for DNA-based traceability, including parentage control and sample identification in commercial cattle breeds.

Main Methods:

Utilized the SNaPshot primer extension method to multiplex 25 validated SNPs for cattle identity control.
Employed four different fluorochromes and specifically designed extension primers for precise detection and length control of amplified products.
Estimated allele frequencies and calculated genotype probabilities for Holstein, Simmental, Limousin, Angus, Charolais, and Tux Cattle breeds.

Main Results:

Achieved high genotyping precision (>0.998) and a low probability of identical genotypes between unrelated individuals (10^-8 to 10^-10).
Demonstrated a high exclusion power of 99.9% for parentage control when both putative parents' genotypes are known.
Validated the assay's accuracy through traceability tests and analysis of parent-sib pairs and trio families.

Conclusions:

The 25-plex SNaPshot assay is a reliable and efficient tool for DNA-based traceability in major commercial cattle breeds.
The assay is adaptable for both low- and high-throughput applications, offering a valuable alternative for genetic identification and parentage verification.