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Related Concept Videos

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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Factors Affecting Dissolution: Polymorphism, Amorphism and Pseudopolymorphism01:21

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Polymorphism refers to the existence of a drug substance in multiple crystalline forms, known as polymorphs. Recently, this term has been expanded to include solvates (forms containing a solvent), amorphous forms (non-crystalline forms), and desolvated solvates (forms from which the solvent has been removed).
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Pharmaceutical Alternatives: Polymorphic Form-Related and Particle Size-Related Therapeutic Nonequivalence01:27

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Changes in polymorphic forms can significantly influence the bioavailability of poorly soluble drugs. Although the FDA defines pharmaceutical equivalence based on having the same active ingredient, dosage form, and route of administration, it does not automatically disqualify products with different polymorphic forms. This means two products with different polymorphs can still be deemed pharmaceutically equivalent. However, polymorphic differences can affect properties like wettability,...
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Effects of EDTA on End-Point Detection Methods01:18

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Different methods, such as visual observance of metal-ion indicators, spectroscopic techniques, and potentiometric methods, can determine the endpoint of an EDTA titration.
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In argentometric precipitation titrations, endpoints can be detected visually by the Mohr, Volhard, and Fajans methods. In the Mohr method, adding a soluble chromate indicator gives an initial yellow color to the analyte solution. As the titrant is added, the first excess of silver ions forms a red silver chromate precipitate, marking the endpoint. The solution pH should be maintained at about 8 by adding solid CaCO3.
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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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The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform
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Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing

Akio Miyao1, Jianyu Song Kiyomiya2, Keiko Iida2

  • 1Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan. miyao@affrc.go.jp.

BMC Bioinformatics
|June 30, 2019
PubMed
Summary

We developed two new methods for detecting genetic variations using Polymorphic Edge Detection (PED). These methods accurately identify single nucleotide polymorphisms (SNPs) and structural variations from next-generation sequencing data without needing a reference genome.

Keywords:
IndelMutationNGSPolymorphismSV

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Accurate detection of genetic polymorphisms is crucial for genetic analysis.
  • Current next-generation sequencing pipelines for polymorphism detection lack complete reliability.

Purpose of the Study:

  • To introduce two novel methods for detecting genetic polymorphisms, focusing on the Polymorphic Edge (PED).
  • To provide reliable tools for identifying both single nucleotide polymorphisms (SNPs) and structural variations.

Main Methods:

  • Developed a k-mer based method for detecting SNPs by direct comparison of short reads between target and control datasets, eliminating the need for a reference genome.
  • Developed a bidirectional alignment method to detect various polymorphic edges, including SNPs, insertions, deletions, inversions, and translocations, even from single-end reads.

Main Results:

  • Successfully created a high-quality comparison map between rice cultivars, aligning with theoretical introgression values.
  • Identified specific large deletions across different rice cultivars.
  • Demonstrated the ability to detect SNPs without a reference genome using the k-mer method.

Conclusions:

  • Polymorphic Edge Detection (PED) offers an efficient tool for accurate genetic data acquisition.
  • The k-mer method enables SNP detection via direct short-read comparison, bypassing genomic alignment.
  • The bidirectional alignment method detects SNPs and structural variations effectively, even with single-end reads.