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Genome-wide Association Studies-GWAS

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.
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Stratified Sampling Method

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Trihybrid Crosses

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Single Nucleotide Polymorphisms-SNPs

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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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Updated: Jun 10, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

A haplotype inference algorithm for trios based on deterministic sampling.

Alexandros Iliadis¹, John Watkinson, Dimitris Anastassiou

¹Department of Electrical Engineering, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.

|August 24, 2010

Summary

This summary is machine-generated.

We developed a new Tree-Based Deterministic Sampling (TDS) method for haplotype phase inference in trio datasets. This method offers improved speed and accuracy compared to existing tools like BEAGLE, making it suitable for genome-wide association studies.

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Last Updated: Jun 10, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

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Published on: December 27, 2010

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Published on: February 3, 2013

Area of Science:

Genetics
Bioinformatics
Computational Biology

Background:

Genome-wide association studies (GWAS) involve genotyping numerous single nucleotide polymorphisms (SNPs) across thousands of individuals.
Haplotype phase inference (phasing) enhances statistical power in GWAS compared to using genotypes alone.
Existing phasing algorithms are available for unrelated individuals and some for trio data.

Purpose of the Study:

To introduce a novel technique for haplotype phasing specifically for trio datasets.
To evaluate the performance of the new method against existing algorithms in terms of speed and accuracy.

Main Methods:

Development of a tree-based deterministic sampling scheme for phasing trio data.
Comparison with publicly available algorithms: PHASE v2.1, BEAGLE v3.0.2, and 2SNP v1.7.
Evaluation on datasets with varying numbers of markers and trios.

Main Results:

PHASE v2.1 exhibits prohibitive computational complexity for routine use.
2SNP v1.7 is fast for small datasets but significantly inaccurate.
The proposed Tree-Based Deterministic Sampling (TDS) method outperforms BEAGLE in speed and accuracy for small to intermediate trio datasets across all marker sizes.
The TDS method is available as a downloadable package.

Conclusions:

A conceptually simple and intuitive phasing algorithm for trio data has been developed using Tree-Based Deterministic Sampling.
The algorithm achieves a favorable trade-off between speed and accuracy, positioning it as a strong candidate for routine application in trio dataset analysis.