FFPE Samples

Formalin-fixed paraffin-embedded, or FFPE, samples are the most common and available world-wide specimen type for human disease diagnosis. As such, they represent a very rich and valuable reservoir of relevant DNA and RNA sequence information. However, the process used to create these samples results in highly fragmented and chemically damaged nucleic acid that present unique challenges for NGS applicants.

Omega Bioservices has extensive expertise in the successful extraction and nucleic acid purification of FFPE samples and even manufactures an extraction kit specifically optimized for this very difficult sample type. Omega Bioservices translates this expertise into on-site service capability and consistently provides this extraction method for many customers, specifically on FFPE samples for NGS applications.

FFPE sample sequencing is performed on an Illumina HiSeq 2500 utilizing V4 chemistry or the MiSeq with V3 chemistry. These chemistries allow you to receive the maximum value for your samples. Results delivered via secure cloud drive or external hard drives are available.

  • Fast turnaround time
  • Highly experienced personnel
  • Data quality analysis report provided
  • Customized bioinformatics solutions available
  • Dedication to quality


request-quote extraction-service equipment sample-submission

Quality of data

At Omega Bioservices, we understand that the quality of the DNA going into next generation sequencing is directly related to the quality of the sequence data coming out. That is why quality metrics are captured at vital points during our process:

  • Post extraction: DNA is analyzed to ensure it is of sufficient fragment size and quantity for optimal library preparation chemistries.
  • Post library preparation: Fragment size and quantity is again checked to ensure optimal loading onto the Illumina flow cell.
  • Post capture: For exome sequencing service, the fragment size and quantity of the capture pool is again checked for optimal flow cell loading.
  • NGS run: Careful monitoring of the quality (Q) scores along with cluster densities, percentage of reads passing filter, number of reads generated, and average length of reads.

This constant and consistent quality monitoring effort result in the very best product possible delivered to the customer.


As next generation sequencing methodologies continue to improve and evolve, they can generate expansive datasets that address complex biological questions. Existing bioinformatics programs may not be able to adequately address the nuanced aspects of your problem set or simply do not offer the level of analysis that you need.

If you need analysis advice on your NGS dataset, or need direct analysis assistance, Omega Bioservices has a network of specialized bioinformatics providers with the expert knowledge and computational resources to help you achieve your data analysis objectives. We can also help in the experimental design at the very beginning of your project to maximize the value of your data. Contact us and let us connect you with the very best bioinformatics capabilities available.

Sample extraction services

Our understanding and commitment to quality includes our offer to take full control of the quality of your sequence data by offering a complete suite of sample extraction services. Omega Bio-tek has a full product line of manual and automated extraction technologies for most any type of sample that you want to extract and purify both DNA and RNA for next generation sequencing. These sample types include:

  • Whole blood, serum, tissue, stool, urine, fungi, bacteria, virus, plant, soil, water, air filter