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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.
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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
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An innovative SNP genotyping method adapting to multiple platforms and throughputs.

Y M Long1, W S Chao2, G J Ma3

  • 1Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
|December 13, 2016
PubMed
Summary

A new semi-thermal asymmetric reverse PCR (STARP) method offers accurate and cost-effective genotyping of single nucleotide polymorphisms (SNPs). This innovative technique improves upon existing PCR-based methods for diverse applications in agriculture, medicine, and forensics.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • Multiplex chip-based technology has advanced genome-scale SNP genotyping.
  • Existing PCR-based methods for individual SNP genotyping face challenges in accuracy, throughput, cost, and platform compatibility.

Purpose of the Study:

  • To develop a novel, accurate, and cost-effective method for genotyping single nucleotide polymorphisms (SNPs).
  • To create a versatile genotyping assay with flexible throughput and broad platform compatibility.

Main Methods:

  • Developed semi-thermal asymmetric reverse PCR (STARP) using unique PCR conditions.
  • Employed two universal priming element-adjustable primers (PEA-primers) and three locus-specific primers (two allele-specific AMAS-primers and a common reverse primer).
  • Designed AMAS-primers with 3' modifications for allele specificity and 5' tails for PEA-primer binding.

Main Results:

  • STARP demonstrated high accuracy, flexible throughputs, and simple assay design.
  • The method offers low operational costs and compatibility with multiple platforms.
  • STARP successfully genotyped both SNPs and insertion-deletion polymorphisms (indels).

Conclusions:

  • STARP is an innovative genotyping method with significant advantages over existing PCR-based techniques.
  • The method's accuracy, cost-effectiveness, and versatility make it suitable for various applications.
  • STARP is expected to have wide applications in agriculture, medicine, and forensics for analyzing DNA variations.