Back to top

Whole Exome Sequencing

Whole Exome Sequencing
Use whole exome sequencing to:
  • Focus on selected regions and small variations within a genome
  • Confine observations to the protein coding regions of a genome in a diagnostic related setting
  • Reduce costs and turnover time for recurrent detection in a long term study



Considerations before starting a whole exome sequencing project:

  • Which organism and reference genome?
  • Aim of the study?
  • Required coverage?

Let us guide you – from design to analysis

Example projects using whole exome sequencing:

  • Single nucleotide variations (SNVs) and small insertions and deletions (InDels) observations for cancer samples
  • Comparing SNV profiles
  • Time series observation of mutagen treatment consequences on protein modification

Applications related to whole exome sequencing:

  • Eukaryotic resequencing
  • Microsatellite marker development


A typical workflow for a whole exome sequencing project is shown in the graphic below. Please note that our highly-modular processes allow you various entry and opting out options. If you outsource your entire NGS project to Microsynth or only parts of it is up to you.


For further reading and a detailed technical description, please download our Application Note Illumina Whole Exome Sequencing (see related downloads).


The results produced by our analysis module help answer two main questions of a resequencing of a eukaryotic exome aiming at detecting variations to a pre-annotated reference exome.

  1. How well was the target exome covered? (see Table 1)
  2. Which are the single nucleotide variations and small insertions/deletions in comparison to the reference genome and which are the effects of these detected variations on the protein level? (see Tables 2A and 2B)
  3. Which of the detected variations are also known and listed in public databases (e.g., ClinVar - NCBI - NIH)? (see Table 3)
Table 1: This is a cutout of the full table detailing read coverage for every target in the sequenced exome.
Table 2A: This detail of a results table shows the detected variations and their annotation.
Table 2B: This detail of a results table shows the detected variations and their effect on the respective protein sequence.
Table 3: This detail of a results table shows detected variations that are also listed in public databases such as ClinVar - NCBI - NIH.

Turnaround Time

  • Delivery of data within x working days upon sample receipt (includes library preparation and sequencing)
  • Additional x working days for data analysis (bioinformatics)
  • Express service possible on request

x= on request