Introduction to Whole-Exome Sequencing
Whole exome sequencing (WES) is targeted to protein coding regions (exome) only. The exome represents less than 2% of the genetic code, but contains ~85% of known disease-related variants, which allows you to interrogate single-nucleotide variants (SNVs), indels, structural variants (SVs) and copy number variants (CNVs) in both the ~1% part of the genome that encodes protein sequences and the ~99% of remaining non-coding sequences. Exome sequencing is a transitional technology that has an excellent chance of finding variants responsible for inherited conditions at a significantly lower cost than whole-genome sequencing.
Exome sequencing can efficiently identify coding variants across a wide range of applications, including population genetics, genetic disease, and cancer studies. Also, transition of new exome sequencing methodologies to the clinical laboratory is under way and is likely to have a major impact on all areas of medicine.
Advantage of Whole-Exome Sequencing
-Identifies variants across a wide range of applications
-Achieves comprehensive coverage of coding regions
-Provides a cost-effective alternative to whole-genome sequencing (allow to sequence target regions at a higher depth at the same cost)
-Produces a smaller, more manageable data set for faster, easier analysis compared to whole-genome approaches
Exome sequencing is targeting exon regions of the genome. Entire exome is captured using specific kits prior to the sequencing process. Even though sequencing process is essentially the same, it is possible to increase sequencing depth while spending same cost because exome is only a fraction of whole genome.
The table below compares specifications of Whole Exome Sequencing and Target Region Sequencing.
|Whole Exome Sequencing||Target Region Sequencing|
|Objective||Accurate variants detection within exon region||Accurate variant detection within specific targets|
|Cf.||There are only a few readily available exome capture kits. If you wish to proceed no matter what. it is possible to order a custom exome capture kit.||The economic upper threshold of target sequencing is~2.5Mb. If the total size of your targets of interest is greater than 2.5Mb. exome sequencing would be a better choice|
|Sample Requirements||Minimum Quantity = 1μg Minimum Concentration = 50ng/μl OD260/280 = 1.6~2.2|
|Note||The “Sufficient depth” above is based on human sample.|
|WES Basic Analysis Criteria|
|1. Summary of data production|
|2. Histogram of depth distribution in target region|
|3. Evenness of exome capture|
|4. Mapping statistics|
|5. Annotation of the resulting SNVs|
|6. Annotation of the resulting Indels|
|7. Multiple Variants Calling|
|8. Trio(Family-based) Analysis (if applicable)|
Illumina HiSeq Capture Kit
Agilent SureSelectXT Human All Exon V4+UTRs (71M)
Agilent SureSelectXT Human All Exon V5 (50M)
Agilent SureSelectXT Human All Exon V5+UTRs (75M)
Agilent SureSelectXT2 Human All Exon V4+UTRs (71M)
Agilent SureSelectXT2 Human All Exon V5 (50M)
Agilent SureSelectXT2 Human All Exon V5+UTRs (75M)
Life Technologies Ion Proton Capture Kit
The Ion AmpliSeq™ Exome Kit (50M)