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Genome-wide Association Studies-GWAS

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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...

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A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

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Optical Genome Mapping for Applications in Repeat Expansion Disorders.

Bart van der Sanden¹, Kornelia Neveling¹, Andy Wing Chun Pang²

¹Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands.

Current Protocols

|July 5, 2024

Summary

Optical genome mapping (OGM) offers a precise method for detecting long short tandem repeat (STR) expansions, crucial for diagnosing over 60 genetic disorders. This technique provides accurate length and stability analysis for repeat expansions exceeding 500 bp.

Keywords:

optical genome mapping repeat expansion disorders somatic instability structural variant analysis whole genome analysis

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Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Area of Science:

Genomics
Molecular Biology
Genetic Diagnostics

Background:

Short tandem repeat (STR) expansions are linked to over 60 genetic disorders, with their size and stability correlating to disease severity and onset.
Current diagnostic methods like repeat-primed PCR and Southern blotting struggle to accurately determine the exact length of very long STR expansions.

Purpose of the Study:

To provide methodological guidance for using Optical Genome Mapping (OGM) to accurately determine the length and stability of STR expansions.
To establish OGM as a cost-effective and comprehensive alternative to traditional cytogenetic techniques for analyzing large structural variants and repeat expansions.

Main Methods:

Detailed protocols for sample preparation, including ultra-high-molecular-weight DNA isolation, labeling, and staining.
Procedures for data generation and genome mapping using the Bionano Saphyr® System.
Workflows for data analysis, including manual de novo assembly, local guided assembly, and specific repeat expansion analysis (e.g., EnFocus Fragile X).

Main Results:

Demonstrated the capability of OGM to detect and precisely measure STR expansions greater than 500 bp.
Provided comprehensive protocols covering the entire OGM process, from DNA preparation to specialized repeat expansion analysis.
Established OGM as a viable method for analyzing the length and stability of repeat expansions with size differences exceeding 500 bp from wild-type alleles.

Conclusions:

OGM is a powerful and accessible tool for the accurate diagnosis and characterization of genetic disorders caused by STR expansions.
The provided protocols enable researchers and clinicians to reliably analyze STR repeat lengths and stability, improving diagnostic capabilities.
OGM offers a significant advancement over traditional methods for detecting large structural variants and complex repeat expansions.