Related Experiment Video
Updated: Nov 15, 2025
10:34
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
23.4K
Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the
Ghausia Begum1, Ammar Albanna1,2, Asma Bankapur1
1College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates.
International Journal of Molecular Sciences
|March 6, 2021
Summary
Long-read sequencing effectively detects more genomic structural variations (SVs) in autism spectrum disorder (ASD) families. This technology is crucial for identifying non-coding SVs, offering new insights into rare genetic diseases.
Area of Science:
- Genomics
- Medical Genetics
- Bioinformatics
Background:
- Genomic structural variations (SVs) are implicated in rare genetic diseases, including autism spectrum disorders (ASD).
- Identifying pathogenic variants in non-coding regions remains challenging with traditional sequencing methods.
- Long-read sequencing offers enhanced capabilities for detecting complex genomic alterations.
Purpose of the Study:
- To develop and apply a scalable workflow for characterizing SVs impacting non-coding elements in ASD.
- To compare the efficacy of long-read versus short-read sequencing in detecting SVs in an ASD family.
- To assess the utility of long-read sequencing for identifying novel genetic risk factors in rare diseases.
Main Methods:
- Whole-genome sequencing was performed on an Emirati family with three children diagnosed with ASD, utilizing both long-read and short-read technologies.
- Multiple analytical pipelines were employed to identify SVs with high sensitivity and specificity.
- Comparative analysis of SVs detected by both sequencing technologies was conducted.
Main Results:
- Long-read sequencing detected a significantly higher number of SVs (987) compared to short-read sequencing (509) at 15-fold coverage (p < 1.1020 × 10^-57).
- The majority of long-read sequencing variants (97.9%) were within the 1-100 kb size range (p < 9.080 × 10^-67), impacting over 5000 genes.
- Long-read sequencing identified 604 non-coding RNAs (p < 9.02 × 10^-9), including microRNAs, lncRNAs, and snoRNAs.
Conclusions:
- Long-read sequencing is a reliable and sensitive technology for detecting SVs, particularly those impacting non-coding genomic elements.
- This approach provides a valuable tool for investigating the genetic basis of ASD and other rare genetic diseases.
- The workflow enables comprehensive characterization of SVs, advancing the understanding of complex genomic variations.
Related Concept Videos
03:21RNA-seq
11.0K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.0K
03:00Next-generation Sequencing
95.7K
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....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
95.7K
01:57Sanger Sequencing
766.0K
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...
766.0K
03:36Genome Annotation and Assembly
19.8K
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.
19.8K
01:05Maxam-Gilbert Sequencing
11.9K
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.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
11.9K
02:54Evolutionary Relationships through Genome Comparisons
6.6K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.6K