Service summary

• DNA extractions with Qiagen kits on QIAsymphony*
• QC check with Victor Nivo Multimode Microplate Reader and Agilent Bioanalyzer
• Library preparation and sample indexing with Illumina kits
• Full automated library preparation on Hamilton NGS STAR
• Sequencing with NovaSeq 6000, 8Gb (100X) output per Sample
• Turnover time approx. 4 to 5 weeks**

(*) For unextracted samples.
(**) Turnover times are not guaranteed, may change according to your project.

Sample requirements

Accepted Sample Type	Recommended Amount	Shipment method
Whole Blood (Fresh or Frozen)	650μL -1mL	Blue ice for fresh blood Dry ice for frozen blood
Buccal Swab	Follow the kit manufacturer's instructions
Tissue	30 - 50 mg	Dry ice
FFPE Tissue	4-6 slices for 10µm, 8-10 slices for 5µm	Room temprature
Cell Pellet	≥10^6 cells (eukaryotic) ≥10^8 cells (microorganism)	Dry ice
Saliva	650μL-1mL	Dry ice or blue ice
Genomic DNA (RNA-free)	50μL, >20 ng/μL	Dry ice

How to evaluate the sample quality

We check your samples upon arrival, however we still require our users to do their own QC steps before sending samples.

Checking the concentration

Please use fluorometric measurements (e.g. Qubit, Quant-it), not absorbance measurements (Nanodrop, spectrophotometer).

Checking the quality and purity

The DNA should be in water or EB buffer, of high quality, and ideally have an A260/280: 1.8- 2.0 and A260/230: 2.0 – 2.2. Please use non-EDTA based buffers or low EDTA-buffers.
If your samples are below the required thresholds, please get in touch.

What we do with your samples

Once your samples arrive at SZAOMICS, we start by performing a reception control step in which we make sure the samples meet our requirements.

If the samples fail this quality control step, we will contact you to discuss possible options. Should you choose to proceed with samples not fulfilling the criteria it will be at your own risk, NGI will only make one attempt at library preparation and if the library preparation does not work you will be charged to the for the library preparation regardless.

If the samples pass reception control, the samples will be queued for library preparation.

Library preparation

At SZAOMICS, we offer whole exome sequencing including library preparation and enrichment using the Illumina DNA Prep with Enrichment Kit.

The protocol for library preparation involves DNA fragmentation and ligation of Illumina adapters with sample-specific barcodes. After sample and library preparation, a hybridization-based target enrichment step is performed using probes that contain specific sequences that are designed to bind complementary to the exome DNA sequences.

Library QC and sequencing

We evaluate the concentration of the libraries using qPCR and look at the fragment size distribution of the library molecules using Bioanalyzer. Once the libraries have passed this QC step, they are normalized, pooled, and queued for sequencing.

Expected results

In general, we have been successfully generating libraries that provide enough good quality reads for sequencing of genomic DNA. However, the sequencing results from each library prep will d¬epend on the characteristics of the sample:

• The yield of the library preparation could be insufficient when the input is below our input criteria or if the DNA is degraded.
• When the library concentration is too low, generating an even pooling is more difficult, so you can expect uneven reads yields.