The Ramaciotti Centre for Genomics is committed to providing high quality genomics services. We do this through:
- Performing rigorous quality control on submitted samples.
- Consistently providing quality analytical services to our clients through data that meets or exceeds manufacturer’s specifications.
- Ensuring that all personnel are competent and qualified for the tasks they perform.
- Developing and applying a quality management system according to the ISO/IEC17025 Standard.
Sample Quality Control
All samples submitted to the Ramaciotti Centre must first pass initial quality control (QC) checks. A threshold for these checks has been put in place to ensure you receive data of the highest quality. We know from experience that samples below these thresholds may not perform well so advise clients to where possible meet or exceed them. Clients are notified if their samples do not pass QC and are advised of the next steps and possible 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 dilute
- 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 a fluorescence-based assay such as PicoGreen or Qubit. Client prepared library concentrations are verified by Qubit and DNA samples submitted for genotyping by array and quantified by picogreen assay.
Integrity or Size Check
Total RNA
Total RNA samples are run on either the Agilent Bioanalyzer or TapeStation to assess the integrity of the total RNA. RNA that has degraded during extraction or is contaminated with DNA is a poor candidate for gene expression or transcriptome analysis and should not be used. The final decision on whether to process a sample 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
Prior to releasing data the quality and output is reviewed to ensure it passes specifications. Any analysis that fail to meet the QC metrics set by the manufacturer will be repeated free of charge. The only exception being if the client has advised us to proceed with a sample that has failed QC or requested a deviation from standard protocol.