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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Next-generation Sequencing03:00

Next-generation Sequencing

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.
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Sanger Sequencing01:57

Sanger Sequencing

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...
RNA-seq03:21

RNA-seq

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 microarray-based...

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Related Experiment Video

Updated: May 10, 2026

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

Single nucleotide polymorphism typing with massively parallel sequencing for human identification.

Seung Bum Seo1, Jonathan L King, David H Warshauer

  • 1Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.

International Journal of Legal Medicine
|June 6, 2013
PubMed
Summary
This summary is machine-generated.

Massively parallel sequencing effectively genotypes single nucleotide polymorphisms (SNPs) using the Ion AmpliSeq™ HID panel. High accuracy was achieved even with low DNA input, demonstrating feasibility for large-scale SNP genotyping.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Single nucleotide polymorphisms (SNPs) are crucial genetic markers.
  • Massively parallel sequencing offers high-throughput genotyping potential.
  • Evaluating SNP genotyping platforms is essential for genetic analysis.

Purpose of the Study:

  • To evaluate the Ion AmpliSeq™ HID SNP panel for genotyping.
  • To assess performance across different DNA input quantities.
  • To compare results with another sequencing platform.

Main Methods:

  • Utilized the Ion AmpliSeq™ HID SNP panel (103 autosomal, 33 Y-SNPs) on an Ion PGM™ Sequencer.
  • Sequenced four DNA samples at three target quantities (10 ng, 1 ng, 100 pg).
  • Compared results with the Genome Analyzer IIx platform.

Main Results:

  • All 136 SNPs genotyped successfully at 10 ng DNA.
  • Reduced DNA input (1 ng, 100 pg) showed minor genotype imbalances and dropouts.
  • High concordance (95 SNPs) with Genome Analyzer IIx, with one SNP error attributed to homopolymer misalignment.

Conclusions:

  • Massively parallel sequencing is feasible for large-scale SNP genotyping.
  • The Ion AmpliSeq™ HID panel demonstrates robust performance.
  • Improvements in barcode systems and software could enhance cost-effectiveness and comprehensiveness.