Performance comparison of exome DNA sequencing technologies.
Michael J Clark1, Rui Chen, Hugo Y K Lam
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Nature Biotechnology
|September 28, 2011
Summary
Comparing three exome sequencing platforms, Nimblegen requires less sequencing for small variant detection. Agilent and Illumina capture more variants, with Illumina also targeting untranslated regions, revealing variants missed by whole genome sequencing.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
Background:
- Whole exome sequencing (WXS) is a cost-effective method for analyzing the protein-coding regions of the human genome.
- WXS is widely used in basic and translational research for genetic variant discovery.
Purpose of the Study:
- To compare the performance of three major commercial exome sequencing platforms: Agilent, Illumina, and Nimblegen.
- To evaluate the platforms' ability to detect small genetic variants and their coverage of genomic regions.
- To compare exome sequencing with whole genome sequencing (WGS) for variant detection.
Main Methods:
- Application of three commercial exome sequencing platforms (Agilent, Illumina, Nimblegen) to the same human blood sample.
- Analysis of sequencing data to assess variant detection sensitivity, coverage, and targeted regions.
- Comparison of exome sequencing results with whole genome sequencing data from the same sample.
Main Results:
- Nimblegen platform, utilizing high-density overlapping baits, required the least sequencing for sensitive small variant detection, despite covering fewer genomic regions.
- Agilent and Illumina platforms detected a higher total number of variants with increased sequencing depth.
- The Illumina platform uniquely captured untranslated regions, and exome sequencing identified variants missed by whole genome sequencing.
Conclusions:
- Platform choice in exome sequencing impacts variant detection sensitivity, coverage, and cost-effectiveness.
- Exome sequencing offers complementary variant detection to whole genome sequencing, particularly for small variants.
- Illumina's platform provides broader coverage, including untranslated regions, enhancing comprehensive variant analysis.
More Related Videos
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
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...
03:00Next-generation Sequencing
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.
01:57Sanger 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...
03:21RNA-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 microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:05Maxam-Gilbert Sequencing
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...
02:26Comparing 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%...
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%...