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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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Next-generation Sequencing

Next-generation Sequencing

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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Sanger Sequencing

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-seq

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...

Maxam-Gilbert Sequencing

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Related Experiment Video

Updated: Oct 11, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Sequencing-based genome-wide association studies reporting standards.

Aoife McMahon^1,2, Elizabeth Lewis¹, Annalisa Buniello¹

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.

|December 6, 2021

Summary

This summary is machine-generated.

Genome sequencing advances genome-wide association studies (GWASs) by enabling rare variant analysis. However, inconsistent reporting and limited data sharing hinder data accessibility and reusability.

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Last Updated: Oct 11, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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Published on: August 21, 2016

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Statistical Genetics
Bioinformatics

Background:

Genome sequencing is increasingly used for genome-wide association studies (GWASs), offering comprehensive variation analysis, including rare variants.
Existing GWASs predominantly utilize array-based genotyping, with established reporting standards.

Purpose of the Study:

To evaluate the reporting quality and data sharing practices of sequencing-based GWAS (seqGWAS) publications from 2014-2020.
To identify areas for improvement in standardization and data accessibility for seqGWAS.

Main Methods:

Systematic review of 167 exome- or genome-wide sequencing-based GWAS publications.
Assessment of statistical methods, analysis reporting, results presentation, and dataset availability.
Comparison of reporting practices with array-based GWASs.

Main Results:

81% of publications employed aggregate association tests, often using multiple models.
Inconsistent terminology and incomplete dataset reporting were observed, especially for aggregate tests.
Sequencing-based GWASs showed lower summary statistics sharing compared to array-based GWASs.

Conclusions:

Standardized reporting and increased data sharing are crucial for FAIR (findable, interoperable, accessible, reusable) seqGWAS data.
Recommendations include adopting standard seqGWAS terminology and aligning single-variant analysis reporting with array-based GWAS standards.
Proposed initial standards for aggregate analysis metadata and summary statistics are provided to enhance data utility.