Info Sheet: Whole Exome Sequencing


  1. QC: DNA quantification using the TapeStation Genomic Screen Tape
  2. Library construction from total DNA and subsequent enrichment of the human or mouse exome
  3. Library QC
  4. Illumina Short-Read Sequencing (paired end, sequencing, mode depends on protocol)
  5. Bioinformatics data analysis (optional)
Expected turnaround time: 6 weeks after passing QC

Supported protocols

Agilent SureSelect Human/Mouse Exome
Link to Agilent
  • low to standard input, compatible with FFPE DNA samples
  • SureSelectXT Low Input Target Enrichment Kit with UDI's added during library preparation
We offer Agilent's V6 + UTR panel (90Mb) as a service, also for small sample sizes (cost effective n > 4, 70-fold coverage).
For larger sample cohorts (n > 16) different Agilent panels can be requested.

IDT xGen Exome Research Panel v2
Link to IDT
  • standard input, high quality DNA (DIN > 8)
  • IDT Exome Research Panel (45 Mb)
  • multiplexed enrichment in a set of 6 samples
  • recommended for large sample cohorts
The sequencing library is prepared with the Trused DNA Nano library kit (Illumina) and the IDT enrichment process can be carried out in a multiplex of 6 samples

Input Requirements

  • Agilent 10-200 ng high-quality, RNA-free genomic DNA
  • IDT 100 ng high-quality, RNA-free genomic DNA
  • Fresh frozen tissue, FFPE, blood samples as source, others on request
  • Somatic mutations require control samples from corresponding healthy tissue of the same individual

Note for FFPE samples: The degradation state of a DNA sample has a high impact on the coverage of the exome after sequencing. For degraded DNA samples (DIN < 8) we recommend an increase of 2-fold on sequencing reads to ensure a good coverage.

Submit samples in 1.5 ml tubes labeled with B-Fabric Tube ID
How to submit samples for Illumina/Short Read Sequencing.pdf

Standard Sequencing Recommendations

  • 150bp paired-end reads
  • Units of 200M reads

For larger sample sizes (n>16) a entire NovaSeq6000 Flowcell can be requested with 100PE run mode (SP, S1, S2 Flowcell)

NextSeq 500
For flexible run times
Mid out put (130M reads, 75PE)
High Output (350M reads)

Recommended sequencing depth
germline mutations: 70-fold coverage
somatic mutations: 150-fold coverage

Costs for UZH und ETH research group

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