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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,...
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...
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%...
Pleiotropy01:33

Pleiotropy

Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
Multiple Allele Traits01:49

Multiple Allele Traits

The Concept of Multiple Allelism
Multiple Allele Traits01:49

Multiple Allele Traits

The Concept of Multiple Allelism

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Related Experiment Video

Updated: Jun 1, 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

HAPGEN2: simulation of multiple disease SNPs.

Zhan Su1, Jonathan Marchini, Peter Donnelly

  • 1Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK. zhan@well.ox.ac.uk

Bioinformatics (Oxford, England)
|June 10, 2011
PubMed
Summary
This summary is machine-generated.

We developed HAPGEN2, a novel simulation tool for genome-wide association studies (GWAS). This method efficiently simulates multiple nearby disease SNPs on the same chromosome, improving genetic study designs.

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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

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Last Updated: Jun 1, 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
05:53

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

Published on: June 21, 2018

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Simulated data experiments offer a cost-effective method for evaluating experimental designs and analysis techniques in genome-wide association studies (GWAS).
  • Resampling-based haplotype simulation is efficient, producing samples with linkage disequilibrium (LD) patterns similar to real data.
  • Current simulation methods face limitations in simulating multiple nearby disease SNPs on the same chromosome.

Purpose of the Study:

  • To introduce an advanced simulation algorithm capable of generating multiple nearby disease SNPs on the same chromosome.
  • To enhance the capabilities of existing GWAS simulation tools.

Main Methods:

  • Developed HAPGEN2, a novel simulation algorithm building upon the HAPGEN resampling method.
  • The algorithm retains the advantages of resampling techniques while expanding the scope of applicable disease models.

Main Results:

  • HAPGEN2 successfully simulates multiple nearby disease single nucleotide polymorphisms (SNPs) on the same chromosome.
  • The new method expands the range of disease models that can be simulated compared to previous tools.

Conclusions:

  • HAPGEN2 provides a more versatile tool for simulating complex genetic scenarios in GWAS.
  • This advancement facilitates more robust evaluation of experimental designs and analysis methods for genetic studies.