Quality control

The Ramaciotti Centre for Genomics is committed to providing high quality genomics services. We do this through:

Sample quality control

All samples submitted to the Ramaciotti Centre must first undergo initial quality control (QC) checks. These checks are subject to established thresholds to ensure the delivery of high-quality data. Based on our experience, samples that fall below these thresholds often yield suboptimal results; therefore, we strongly encourage clients to meet or exceed them whenever possible. If a sample does not pass QC, the client will be notified and provided with recommended next steps and potential solutions.

Quantification and purity assessment

Samples are read on a spectrophotomer to assess concentration and purity. Samples can fail this QC step for several reasons:

• Sample too diluted
• Sample too concentrated
• Sample contaminated with protein, 260:280 ratio <1.8
• Samples contaminated with reagents used during the extraction protocol, 260:230 ratio <1.8 or >2.3

Pure RNA should have a A260:A280 ratio between 1.8–2.1 and a A260:A230 ratio of 1.8–2.3. Ratios of less than 1.8 indicate contamination with proteins or chemicals used in the extraction procedure, or dilution of your samples in full strength TE. In most cases samples with a 260:230 ratio of less than 1.0 are OK if they are column purified. However as we cannot determine the nature of the contaminant, we cannot guarantee it will not interfere with the labeling or library preparation procedure.

Quantification assessment by fluorescent assay

Some samples are quantified using fluorescence-based assays such as PicoGreen or Qubit. Client-prepared library concentrations are verified using Qubit, while DNA samples submitted for genotyping by array are quantified using the PicoGreen assay.

Integrity or size check

Total RNA 
Total RNA samples are assessed for integrity using either the Agilent Bioanalyzer or TapeStation. RNA that is degraded or contaminated with DNA is not suitable for gene expression or transcriptome analysis and should be excluded. The final decision to proceed with such samples rests with the client. 

Genomic DNA 
The integrity of genomic DNA is assessed using the Agilent TapeStation or Perkin Elmer LabChip GX. This provides a DNA Intergrity Number (DIN) or Genomic DNA Quality Score (GQS), respectively.  This is calculated from the size distribution of the sample.

Amplicons
Amplicon products submitted for next-generation sequencing are run on the TapeStation or Bioanalyzer to check their size. 

Client prepared libraries
Client prepared libraries submitted for next-generation sequencing are run on the TapeStation or Bioanalyzer to accurately check the insert size.

For further information on interpreting QC data, please download our RAMAC Quality Control Datasheet.

Quality control of final data

Before data is released, its quality and output are reviewed to ensure they meet required specifications. Any analysis that fails to meet the manufacturer's QC metrics will be repeated at no additional cost. The only exception is when a client has instructed us to proceed with a sample that failed QC or has requested a deviation from the standard protocol.