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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,...
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%...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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.
GWAS does not require the identification of the target gene involved in...
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.

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Related Experiment Video

Updated: May 12, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

SNPnexus: an enhanced web platform for large-scale and multi-sample variant analysis (2025 update).

Jorge Oscanoa1, Qianqian Zhu1, Emanuela Gadaleta1

  • 1Centre for Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom.

Nucleic Acids Research
|May 11, 2026
PubMed
Summary

SNPnexus is a powerful web platform for annotating and prioritizing genetic variants. Its recent upgrade enhances performance, supports larger datasets, and offers advanced filtering for efficient variant analysis.

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Related Experiment Videos

Last Updated: May 12, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

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

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • SNPnexus is an established web platform for genetic variant analysis.
  • Previous versions required updates for performance and data structure.

Purpose of the Study:

  • To detail the significant backend re-engineering and interface redesign of SNPnexus.
  • To highlight enhanced capabilities for large-scale and comparative genetic variant analysis.

Main Methods:

  • Substantial backend re-engineering and dataset restructuring.
  • Redesigned user interface supporting larger queries and multi-sample analysis.
  • Implementation of pre-annotation filters and updated annotation databases (GRCh37/GRCh38).

Main Results:

  • Major performance improvements and increased query capacity (150,000 variants).
  • New features include comparative workflows, advanced filtering, and interactive visualizations.
  • Expanded annotations cover pathogenicity, population frequencies, conservation, and clinical associations.

Conclusions:

  • SNPnexus offers a significantly improved, efficient, and versatile platform for functional annotation and prioritization of genetic variants.
  • The updated platform supports complex analyses for disease cohort studies and evolutionary research.
  • SNPnexus remains freely accessible with enhanced features for all users.