Targeted/Custom Genotyping

Data from genome-wide association studies, next-generation sequencing and other research approaches produce a large number of candidate genetic associations for a variety of diseases and phenotypes.  Confirmation, fine-mapping and screening these genetic markers requires approaches that allow you to focus on just the genetic regions or variants of interest.  AGRF offers a range of options to meet this challenge, allowing you to genotype anywhere from 1 to 1 million SNPs, on a few to thousands of samples.  Whatever it is that you need we have a solution for you.

Agena Bioscience MassARRAY

Illumina GoldenGate

Illumina iSelect HD Custom Genotyping

Qiagen Pyrosequencing

Sanger Sequencing

Agena Bioscience MassARRAY

Agena Bioscience MassARRAY is a mass spectrometry based system (MALDI-TOF) for rapid and cost effective custom genotyping.  Typically projects between 1-500 SNPS are run on this platform. 

The application of mass spectrometry to genotyping provides several benefits:

  • Very high sensitivity.  The high resolution possible from mass spectra permits clear separation of non-specific background from signal.
  • High throughput and Low Cost.  A broad mass window allows inclusion of many analytes into a single multiplexed well.   Up to 50 SNPs can be tested in a single reaction.  When used in combination with 384 well sample configurations the system is capable of genotyping projects with thousands of samples.
  • No requirement for florescent dyes.  Genotype detection is based on mass so unlabelled primers are used in all chemistry steps.  The use of unlabelled probes yields more robust chemistry and greater flexibility to create and modify customized assay panels.

The Agena Bioscience MassARRAY system is compatible with a range of applications:

  • SNP Genotyping.  This is the primarily application for this platform.  SNPs can be bi-allelic, tri-allelic or tetra-allelic.  SNPs can be from any diploid or haploid organism (for higher ploidy levels please enquire).
  • Insertion and Deletions:  Assays for small indels and some large indels can be developed depending on sequence limitations.
  • Somatic mutation profiling.  A number of pre-designed panels are available for human somatic mutation analysis.
  • Sample ID barcoding.  Your samples are valuable and the manipulations of downstream processes can sometimes lead to sample mix-ups.  Sample ID allows you to determine a genetic barcode for all your samples, so that these mix-ups can be quickly solved and rectified when they occur.
  • CpG methylation.   The EpiTYPER application on the Agena allows for quantitative measurement of CpG methylation in regions 200-500bp in length.
  • and more..

To use the service you select the variants in whatever organism you are working on, and we run these through design pipelines to ensure capability with the system. This is provided free of charge so there is no risk.  Design outlines are provided and when a SNP panel is agreed on we quote you for the project. 

Illumina GoldenGate

Our Illumina GoldenGate service utilises the high throughput Illumina iScan system to deliver custom SNP panels with mid-to high numbers of SNPs.  The GoldenGate Genotyping Assay is flexible and cost effective for interrogating either 96 loci or between 384-1536 SNPs (in multiples of 96), simultaneously making it ideal for large scale association studies. GoldenGate panels can be processed on 12-, and 32-sample Universal BeadChips.

Using the GoldenGate Assay technology, the AGRF provides the following services:
Custom GoldenGate Panels: These panels can be custom designed to meet the researchers’ needs, providing flexibility with user defined content across a wide range of genomes. For GoldenGate Custom Panels, AGRF can assist and facilitate in the selection of markers based on your region and density requirements. The final conversion success rate is influenced by:

  • Stringent QC criteria adhered to by illumina during manufacture of GoldenGate custom panels
  • The sequence nature of the chosen loci
  • Analysis criteria

GoldenGate Focused Content Panels encompass a variety of BeadChips that have been optimised for screening specific interest areas. Also available using the GoldenGate assay are standard panels for mouse and human linkage:
Cancer SNP Panel
DNA Panel

Please note that AGRF recommend selecting validated loci and/or loci with high design scores.

Illumina iSelect HD Custom Genotyping

For even higher numbers of SNPs custom iSelect can be developed. 

The Infinium iSelect HD Genotyping BeadChip is extremely flexible, allowing researchers to select practically any SNP in the genome for any species of interest. With iSelects high throughput capabilities, it offers the ability to simultaneously process up to 24-samples and screen between 3,000 and 1,000,000 custom SNPs. The iSelect BeadChips utilise Infinium chemistry for performing large scale custom genotyping, such as fine mapping.

The Infinium iSelect HD Genotyping BeadChips can be used to additionally include up to 60,800 custom SNPs per sample for both the semi-custom HumanHap1M-Duo+ and the HumanHap550+ BeadChips or up to 200,000 markers on the HumanOmniExpress+.

Please note that the minimum order for iSelect BeadChips is for 1,152 samples.

Qiagen Pyrosequencing

Pyrosequencing allows for real-time, sequence-based detection and quantitation of sequence variants.  The approach is suitable for a range of applications including:

  • SNP validation
  • Allelotyping
  • Quantitation of differential allelic gene expression
  • Insertion/Deletion genotyping
  • STR analysis
  • Variable gene copy number
  • CpG Methylation – Probably the most extensively used application.  Further details can be found here.

Sanger Sequencing

For routine, validation or ad hoc genotyping on small numbers of samples, Sanger sequencing still provides the gold standard many genotyping applications.

Details on how to use our Sanger service can be found here.

News

Aboriginal mitogenome analysis shows 50,000 years of connection to country

16 March 2017

Genomic analysis of hair samples collected from Australian Aboriginals across the nation have indicated that cultural connection to country has existed for as many as 50,000 years. 

The Aboriginal Heritage Project, led by the University of Adelaide’s Australian Centre for Ancient DNA recently published their findings in the journal Nature (online 8th March 2017).  AGRF is proud to be associated with the work as part of an ARC linkage grant, with the AGRF’s Operations Manager Dr John Stephen as a Partner Investigator.

Read more ›