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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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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Infinium Assay for Large-scale SNP Genotyping Applications
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A New SNP Genotyping Technology by Target SNP-Seq.

Jian Zhang1, Jingjing Yang1, Changlong Wen2

  • 1Beijing Institute of Vegetable Science, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China.

Methods in Molecular Biology (Clifton, N.J.)
|February 13, 2023
PubMed
Summary

A new target SNP-seq method offers accurate, cost-effective genotyping of hundreds of single-nucleotide polymorphisms (SNPs) in massive DNA samples. This high-throughput sequencing approach advances genetic research and plant breeding.

Keywords:
High-throughput sequencingMultiplex PCRPerfect SNPTarget SNP-seq

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single-nucleotide polymorphism (SNP) genotyping is crucial for genetic research and crop improvement.
  • Existing methods like KASP, microarrays, and GBS have limitations in scalability, cost, or accuracy for certain applications.

Purpose of the Study:

  • To develop and validate a novel, efficient, and cost-effective SNP genotyping method.
  • To provide a flexible platform for middle-scale SNP genotyping in large populations.

Main Methods:

  • Developed target SNP-seq by combining multiplex PCR amplification and high-throughput sequencing on the Illumina X Ten platform.
  • Utilized perfect SNPs identified through variome analysis (whole-genome sequence data).
  • Compared target SNP-seq performance against KASP, microchips, and GBS.

Main Results:

  • Target SNP-seq demonstrated high accuracy and flexibility for genotyping hundreds of SNPs.
  • The method can process massive DNA samples within 3 days at a cost of $7 per sample.
  • Achieved cost-effectiveness and high efficiency compared to existing SNP genotyping techniques.

Conclusions:

  • Target SNP-seq is a competitive and powerful tool for middle-scale SNP genotyping.
  • The method has significant potential to accelerate genetic research and enhance plant breeding programs.