High Density/Genome-wide SNP

Single nucleotide polymorphisms (SNPs) represent the most frequent type of DNA variation.  For those projects which require a better understanding of the genetics of phenotypic variation,  AGRF offers a variety of technology platforms for genome-wide SNP scans covering a broad range of species.  Common goals of SNP research are to understand the genetics of phenotypic variation in human and agricultural populations.  SNP genotyping services offered by the AGRF include numerous whole genome chip based SNP assays at varying densities providing powerful tools to cater for a range of applications.

Illumina BeadChip Human Mapping

Illumina Model Organism BeadChips

Illumina BeadChip Human Mapping

The AGRF offers a full service processing on all catalogue Illumina Human BeadChip arrays. Illumina's Infinium whole-genome genotyping BeadArray solution offers multi-sample BeadChip formats and high-density design with the flexibility to add additional custom SNP assays. A key feature of the Infinium Assay protocols, is the single-tube sample preparation without PCR or ligation. High call rates and accuracy are achieved via an enzymatic discrimination step.

Whole genome SNP scans can be performed at varying densities by utilising the following Illumina products.

 

  Array Array Details Array Format
Infinium HD
BeadChip
contents

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HumanOmni5-Quad ~4.3m SNP loci 4 samples/chip
HumanOmni2.5-8 ~2.5m SNP loci 8 samples/chip
HumanCytoSNP-12 ~300k SNP loci 12 samples/chip
HumanCytoSNP-850K ~850k SNP loci 8 samples/chip
HumanCore >250k SNP loci 12 samples/chip
Infinium
focused chip
contents

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HumanExome >250k exonic markers 12 samples/chip
Human OmniExpressExome >700k SNP loci
>250k exonic markers
8 samples/chip
HumanOmni5Exome >4.3m SNP loci
>250k exonic markers
4 samples/chip
Semi-custom
Infinium

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HumanOmni5-Quad+ ~4.3 million (fixed)
up to 500k (custom)
4 samples/chip
HumanOmniExpress+ ~700,000 (fixed)
up to 500k (custom)
12 samples/chip
Infinium
HTS-24

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HumanOmniExpress - 24 ~700k SNP loci 24 samples/chip
HumanCoreExome - 24 >550,000 SNP loci 24 samples/chip
OncoArray-500K ~500k SNP loci 24 samples/chip
PsychArray ~265k SNP loci 24 samples/chip
Whole Human
Methylation

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 Human Meth450
 ~450K SNP loci

12 samples/chip

       

Infinium iSelect HD Custom Genotyping

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 3,072 and 1,000,000 custom SNPs. The iSelect BeadChips utilise Infinium chemistry for performing large scale custom genotyping, such as fine mapping.

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

Illumina Model Organism BeadChips

Bovine Genotyping

BovineHD BeadChip: The BovineHD BeadChip enables a broad range of applications such as genome-wide selection, identification of quantitative trait loci, evaluation of genetic merit, cross-breed mapping, linkage disequilibrium studies, comparative genetic studies, and breed characterisation for evaluating biodiversity.

Bovine SNP50 BeadChip: The Bovine SNP50 BeadChip target common SNPs described in publicly available sources for interrogation of genetic variation in virtually any cattle breed. 

BovineLD BeadChip: The BovineLD BeadChip enables genotyping to understand the impact of genetics on milk production, reproduction, health, and more. 

Canine Genotyping
The CanineHD BeadChip for interrogation of genetic variation within any domestic dog breed.

Ovine Genotyping
The Ovine SNP50 BeadChip was developed in collaboration with International Sheep Genomics Consortium.

Porcine Genotyping
The Porcine SNP60 BeadChip content is ideal for interrogating genetic variation in multiple porcine breeds including Duroc, Landrace, Pietran, and Large White. 

Maize Genotyping
The Maize SNP50 BeadChip features more than 50 000 highly informative SNPs were subjected to rigorous functional testing across over 30 diverse maize lines to ensure strong performance. 

News

NovaSeq 6000 Service now available!

15 May 2017

An exciting addition to the AGRF technology portfolio has arrived and is currently undergoing rigorous validation testing.

AGRF’s NovaSeq 6000 sequencing hardware is the first of its kind that is operational in Australia and opens the door to broader, more comprehensive genome studies.

Read more ›