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Related Concept Videos

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.
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Single Nucleotide Polymorphisms-SNPs01:05

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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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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Comparing Copy Number Variations and SNPs02:26

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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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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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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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Genome-wide SNP calling using next generation sequencing data in tomato.

Ji-Eun Kim1, Sang-Keun Oh, Jeong-Hee Lee

  • 1SEEDERS Inc., Daejeon 305-509, Korea.

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Researchers developed a sensitive SNP calling method for tomatoes, discovering millions of genome-wide single nucleotide polymorphisms (SNPs). This advance aids tomato genetic research and marker-assisted breeding programs.

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Area of Science:

  • Plant Genomics
  • Molecular Biology
  • Crop Science

Background:

  • The tomato (Solanum lycopersicum L.) is a key model organism for Solanaceae research and crop breeding.
  • Genome-wide single nucleotide polymorphisms (SNPs) are crucial for genetic research and breeding, but their discovery often requires costly high-depth sequencing.

Purpose of the Study:

  • To develop a cost-effective and sensitive method for discovering genome-wide SNPs in tomato.
  • To identify a large number of non-redundant SNPs from diverse tomato datasets.

Main Methods:

  • A modified SAMtools algorithm was employed to enhance SNP calling sensitivity.
  • Analysis of 90 Gb of next-generation sequencing data from whole genome resequencing and transcriptome datasets of multiple tomato accessions.
  • Alignment of reference genomes with their own raw data to optimize SNP discovery workflow.

Main Results:

  • Identification of 4,812,432 non-redundant SNPs across all datasets.
  • Discovery of 131,785 SNPs from seven transcriptome datasets.
  • Identification of 4,680,647 SNPs from the S. pimpinellifolium genome, significantly exceeding previous transcriptome-based SNP counts.

Conclusions:

  • The developed SNP calling method offers high sensitivity and efficiency for genome-wide SNP discovery in tomatoes.
  • The substantial number of identified SNPs provides a valuable resource for marker-assisted breeding and genome-wide association studies in tomato.
  • Comparative analysis of SNP distribution in whole genome versus transcriptome data provides insights into genomic variation.