Rising Popularity of Whole Exome Sequencing and Whole Genome Sequencing
Whole exome sequencing and whole genome sequencing (and the Bioinformatics to go along with them) seem to be the “It” topics. They were a major focus at many of the large Genomic and Biotechnology shows this year (including BIO International 2017 and The Festival of Genomics). Application of these methods to drug development, personalized therapeutics and a host of other real world applications were major points of topic during the talks and presentations.
Since the concept of high throughput genomics was first introduced, the per sample price for next-generation sequencing has dropped significantly. Re-sequencing experiments are now an affordable option. This is especially true of whole exome sequencing, which presents itself as a lucrative option since it targets the most interesting 1% of the genome, the protein coding regions.
Whole exome sequencing is the targeted sequencing of the coding regions of the genome (the exons). This type of targeted sequencing can be used to determine how the protein coding regions of the genome are affected due to applied conditions. For instance, locus-specific targets of selection or cancer/disease causing mutations may be identified through the careful use of this protocol.
Whole Exome Sequencing Applied in a Clinical Setting
A recent study in Genetics in Medicine (Ghazani et al. 2017) highlighted the potential clinical utility of whole exome sequencing in cancer research by employing a streamlined method to uncover clinically relevant somatic mutations.
In this study, researchers sampled 165 patients with colorectal or lung carcinoma and carried out whole exome sequencing on tumor and peripheral blood samples. Somatic mutations were identified and clinically relevant variants were called using PHIAL, Precision Heuristics for Interpreting the Alteration Landscape. The resultant group of mutations was then clinically classified based on three levels of information. The first level took into account the functional consequence of the variant. The second level included information about the frequency with which a variant was associated with a given cancer type. Finally, therapeutic evidence was accumulated for each variant of interest.
This is an example of how the combination of information across all levels may lead to a framework that can be used to provide a clinical plan of action.
Why Use Whole Exome Sequencing?
To date, whole exome sequencing is a popular approach that enables a cost effective method to gain an appreciable amount of information about the genome. Below, I provide some of the advantages of using whole exome sequencing in relation to whole transcriptome (RNA-Seq) or whole genome sequencing methods.
Aspects that make whole exome sequencing advantageous over whole genome sequencing:
- Data can be sequenced at greater depths for more affordable prices.
- The amount of data returned, though various, is typically at a more manageable scale than whole genome sequencing data.
Aspects that make whole exome sequencing advantageous over whole transcriptome sequencing:
- The data includes all genes that are expressed within the genome. Identification of genes, variants or regions of interest is not restricted due to low or no expression.
- Unlike RNA-Seq, whole exome sequencing data includes information about chromosomal rearrangements and copy number variants.
We Can Help You With Whole Exome Sequencing Service!
One of the challenges to carrying out whole exome sequencing experiments is determining the appropriate sample size and depth of coverage for your experiment.
Here at Phalanx Biotech, we provide complimentary initial in-depth experimental design consultation with Ph.D. level Specialists.
We also offer competitive prices and advanced bioinformatics analysis to provide you with your desired data output from Whole Exome Sequencing.
Our basic bioinformatics package includes:
- Data filtering and quality control
- Mapping/Alignment of reads to a reference genome
- SNP & Indel calling
- Variant & Indel annotation
- Functional analysis of SNPs
Contact us to setup a consultation and get a quote for service!
Read other great blog entries from our scientists about NGS:
Gene Expression Analysis: RNA-Seq vs. Microarray
Transcriptome Sequencing – Applications and Preparation