Waikato DNA Sequencing Facility (WDSF)

Services

• Sequencing services
• Genotyping services
• GS Junior services
• Results
• Archiving
• Fast turnaround
• International service

Sequencing Services

Each DNA template that meets the requirements for sequencing is reacted using a commercial dye terminator chemistry and a specified single primer per reaction, including several common primers the WDSF provides free of charge or using any custom primer suitable for sequencing. DNA sequences are then resolved using an ABI 3130XL fitted with 50 cm capillary arrays. Resulting trace and sequence information is then made available according to individual customer requirements.

• Dye Terminator Chemistries
  Sequencing reactions are performed using Applied Biosystems Big Dye v3.1.
• Primers
  Sequencing requires only a single primer for each reaction. The sequencing reaction has linear reaction kinetics due to this single primer, rather than exponential PCR reaction kinetics.  Residual primers or DNA fragments which could initiate DNA replication can often cause trouble and we advise that all practicable steps are taken to ensure template and primer purity.

Genotyping Services

The Waikato DNA sequencing facility operates a Genotyping service based on the 3130 Genetic Analyser and GeneMapper 4 series software. The DNA template requirements for genotyping match those of the sequencing service in terms of required concentrations and template purity. Genotyping requires one primer from each pair to be labelled with a suitable reporter.

• Genotyping Ranges
  The fragment profiling system is capable of accurately differentiating genotypic fragments up to 1200bp in length in two distinct ranges according to the standard. The WDSF can supply standards for 600 or 1200 bp runs.
• Fluorescent Reporters
  Each primer pair requires that one primer of the pair is labelled with a fluorescent reporter, the availability of certain reporters may depend on your chosen primer supplier. The WDSF can accept and utilises the following reporters.
• Results
  Results are available as either a Fragment List (listing of all fragments) or a called List with results sorted and counted (binned) according to customer specified product lengths.
• Availability
  Due to the array nature of the genotyping service, we prefer to run at least 16 samples at a time.

GS Junior Services

An optimized solution for a wide variety of sequencing applications.

• De Novo Sequencing
  Sequence complete bacterial, viral, small fungal and other small genomes or multiple BACs and plasmids on the GS Junior System. Use long single reads alone, or in combination with paired end reads to generate high-quality de novo assemblies with few contigs. Perform comparative analysis of multiple whole genomes and identify differences between samples.
• Targeted Resequencing
  Perform ultra-deep sequencing of amplicons (PCR products) with the GS Junior System. Generating an average of 100,000 high quality reads per run, the system is ideally suited for detecting low level variants (<1% frequency) in pooled amplicon samples, such as viral or human DNA. For many targeted sequencing projects, dozens or hundreds of amplicons can be tiled across genomic regions of interest (i.e. disease-associated regions) and sequenced together.
• Targeted sequencing using sample-enrichment technologies
  Sequence capture technologies allow researchers to target and sequence only the regions of interest in the genome and assess the genetic variation within the captured DNA regions. The GS Junior System is ideal for small sequence capture projects that require sequencing of 40 million bases or less.
• Metagenomic Characterization
  The GS Junior System enables a comprehensive view into the diversity and metabolic profile of an complex environmental samples. Analysis of 100,000 reads can yield a high percentage of species identification in complex metagenomes and even higher in less complex samples. The long reads provide the enormous specificity needed to compare sequenced reads against DNA or protein databases and give unambiguous assignment of even closely related species.