Genomics facilities

  • Life Technologies Ion Torrent ™ Personal Genome Machine ® System
This benchtop sequencer can yield up to 5 million reads per run and up to 400bp sequence lengths.

We can multiplex up to 64 samples per run, effectively lowering your sequencing cost per sample.

Suitable for RNA or DNA sequencing using targeted panels or PCR products and microbial genome sequencing or 16S analysis.

  • Life Technologies QuantStudio ™ 12K Flex Real Time PCR System
This system has interchangeable blocks and we can run Fast 96-well plates, 384-well plates, Taqman array cards or QuantStudio 12K Flex OpenArray plates (3,072-well).

Capable of detection of FAM, VIC, ROX, SYBR, NED and TAMRA dyes.

  • Bio-Rad Life Sciences QX100 ™ Droplet Digital ™ PCR System
This system provides an absolute quantification of target DNA molecules and enables the detection of rare DNA target copies with high sensitivity and the measurement of small fold differences with the highest precision.

  • Agilent 2100 Bioanalyzer
The industry standard for RNA sample quality control, yielding the essential RNA integrity number (RIN) required by most sequencing services.

Also useful for accurate DNA size and quantity analyses with minimal sample consumption (1ul).

  • Pippin Prep DNA Size Selection System

Guide to sample submission for the Ion Torrent ™ Personal Genome Machine ® (PGM™) System

In the case of customer-prepared libraries, at least 25 µl of 26pM library is required. We recommend using a qPCR method for accurately quantifying your libraries and Agilent Bioanalyzer analysis, to ensure that your insert sizes are within the sequencing capacity of the type of sequencing you would like to carry out (i.e. 200bp or 400bp sequencing). If you need your libraries to be prepared for you, then please get in touch to discuss your project. As a rough guide, for 16S amplicon sequencing we would need at least 50ng of purified PCR products, measured by a Qubit® Fluorometer.

The largest chip size available for the PGM™ is the 318 chip, which can yield up to five million reads. Therefore you might decide to use target enrichment to get good coverage of your regions of interest.

Targeted enrichment technology enables NGS platform users to sequence specific regions, instead of the entire genome, thereby achieving more sensitive mutation detection. Target enrichment solutions allow you to quickly answer specific biological questions and use valuable resources more effectively. There are several different target enrichment methods available for the PGM™, these include off-the-shelf panels from Life Technologies (Ion AmpliSeq™ Panels) and Qiagen (GeneRead DNAseq Gene Panels). Both of these options use a PCR-based method of enrichment:

Alternatively, you can enrich for your sequences of interest by capturing them with probes, e.g. CATCH-seq from Ubiquity Genomics, xGen Lockdown Probes and Panels from Integrated DNA Technologies and the Haloplex Target Enrichment System from Agilent Technologies.

Guide to data obtained from the Ion Torrent ™ Personal Genome Machine ® (PGM™) System

After sequencing and analysis is complete, a folder is provided which contains the raw data, a summary report of the run and any variant analysis carried out. The PGM™ sequencing reads are provided as FASTQ files, which contain the associated quality values. Alignments are provided in BAM format with an associated BAM index file and variants are provided as vcf files. Variants can also be listed in an Excel table (if preferred) and detailed annotation can be carried out using Ion Reporter™ software.