Faculty of Science - Leading creativity and innovation in the sciences


Genomics Centre


The Genomics Centre, in conjunction with New Zealand Genomics Ltd (NZGL), offers a number of sequencing facilities as a service through ASAS.

Prices for these platforms are set in conjunction with NZGL. For price information, please submit an NZGL enquiry.

 

Comparison of sequencing platforms

Platform Illumina MiSeq Life Technologies Ion Torrent PGM
Application

Metagenomics and amplicon sequencing

Bacterial whole genome sequencing

Small RNA sequencing

Targeted sequencing of selected genes

Custom and amplicon panels

Whole genome sequencing of small genomes

Length of Reads 2 x 25 bp to 2 x 300 bp 200 bp to 400 bp
Number of Reads Up to 20 - 30 million paired end reads / run >6 million paired end reads / run

Illumina MiSeq Genome Sequencer


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The Illumina MiSeq is a next generation desktop DNA sequencer using industry standard genomics workflows, with high accuracy, sensitivity and specificity.

Services

  • DNA and RNA samples can be submitted for sequencing on the MiSeq using applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.

Techniques

  • New MiSeq reagents enable up to 15 Gb of output with 25 M sequencing reads and 2x300 bp read lengths.
  • The MiSeq uses the same protocols to make DNA libraries as used on the high-throughput HiSeq machines, but offers longer read lengths.
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Life Technologies Ion Torrent Personal Genome Machine (PGM)


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The PGM is a desktop next generation DNA sequencer which harnesses the power of the Life Technologies AmpliSeq oligo design website and database to create pools of primers capable of large targeted resequencing projects, creating ready-made libraries for sequencing on the PGM.

Services

The PGM is used for sequencing PCR amplicons at low cost and with high speed turnaround. PCR amplicon samples produced using predesigned or custom primer panels can be submitted for sequencing on the PGM.

  • PGM reagents enable a choice of chips (400,000 to 5,000,000 reads), and up to 400 bp read lengths

The following pre-designed panels are single pools of primers used to target and sequence genomic ‘hotspot’ regions. Lists of targeted genes and mutations are available from the Life Technologies website.

Ion AmpliSeq™ Cancer Hotspot Panel v2

Ion AmpliSeq™ Comprehensive Cancer Panel

Ion AmpliSeq™ Inherited Disease Panel

Ion AmpliSeq™ Sample ID Panel

Ion AmpliSeq™ Community Panels Flyer

Ion AmpliSeq™ Colon and Lung Panel Flyer

Ion AmpliSeq™ BRCA1 and BRCA2 Panel Flyer

Custom amplicon libraries can also be easily designed using the AmpliSeq website to target other regions of interest.

Techniques

  • When used in conjunction with Ion Reporter Software, the PGM allows the rapid and cost effective detection of sequence variation in PCR amplicons.
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Affymetrix GeneChip Instrument System


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The Affymetrix GeneChip® Instrument System is a fully integrated platform for conducting gene expression research using GeneChip® brand probe arrays. Affymetrix experiments can be very quick to design and complete. The data can also be analysed extremely rapidly, yielding widely understood and verifiable data to speed experimental progress.

Our Services include

  • The Affymetrix GeneChip® Instrument System offers cost-efficient gene expression analysis per sample
  • Due to the simplicity of analysis, projects can attract lower bioinformatics costs than RNAseq experiments.

Techniques

  • RNA or DNA samples can be submitted for gene/miRNA expression analysis or SNP detection, on GeneChip® brand probe arrays.
  • We offer a variety of labelling methods for gene expression using either 3’ or whole transcript labelling.
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Our people


Liam Williams and Tim Lawrence are technicians in the Genomics Centre. Contact Liam Williams for more information or assistance.

See, Selected Publications