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. AGRF also offers a customised SNP linkage marker set which contains informative markers for crosses of many common mouse strains. Genome-Wide SNP applications include:
Affymetrix GeneChip Human Mapping
illumina BeadChip Human Mapping
Genome-Wide SNP: Sample Submission Requirements
Affymetrix GeneChip Human Mapping
The AGRF offers a NATA accredited service with full service processing on all catalogue Affymetrix Human GeneChip arrays. The Affymetrix genotyping technology is designed for whole-genome SNP analyses. The reaction consists of reproducibly amplifying a subset of the human genome through a single primer amplification reaction using restriction enzyme digested, adapro-ligated human genomic DNA. This DNA is then fragmented, labelled and hybridised to a GeneChip array.
Whole genome SNP scans can be performed at varying densities by utilising the following Affymetrix products:
- Affymetrix 10K SNP Chip
- ideal for identifying and refining linkage regions
- covers entire genome with 10 204 SNPs
- Affymetrix 50K (Xba or HindIII) SNP Chip
- mainly utilised for linkage analysis studies as well as association studies and copy number analysis
- covers entire genome with ~50 000 SNPs
- Affymetrix 100K (Xba and Hind III) SNP Chip
- mainly utilised for linkage analysis studies as well as association studies and copy number
- covers entire genome with 116 204 SNPs
- Affymetrix 250K (Nsp or Sty) SNP Chip
- enables high powered whole genome association studies in addition to copy number applications
- covers entire genome with ~250 000 SNPs (Nsp I ~262 000 SNPs and Sty I ~238 000 SNPs)
- Compatible with whole-genome amplified DNA
- Affymetrix 500K (Nsp and Sty) SNP Chip
- enables high powered whole genome association studies in addition to copy number applications
- comprises two arrays, enabling genotyping of 500 000 SNPs
- compatible with whole-genome amplified DNA
- Affymetrix 5.0 SNP Chip
- enables high powered whole genome association studies in addition to copy number applications
- A single array featuring all SNPs for the original 500K array as well as 420 000 additional non-polymorphic probes that can measure genetic differences, such as copy number variation
- compatible with whole-genome amplified DNA
- Affymetrix 6.0 SNP Chip
- enables high powered whole genome association studies in addition to copy number applications
- features 1.8 million markers for genetic variation, including 906 600 SNPs and 946 000 probes for the detection of copy number variation
- compatible with whole-genome amplified DNA
Click here to access annotation files for each of the Affymetrix Human Genechip arrays.
Affymetrix GeneChip Human Mapping Service Process
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 single or 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. Hich 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:
- Human 1M-Duo
- more than 1 million SNPs for genotyping with median density down to ~1.5kb and less large gaps for high-resolution Copy Number Variance
- Human 610-Quad
- High-throughput format of genome-wide SNP and CNV markers with more than 620 000 markers
- Humanexon510S-Duo
- Gene-centric coverage density of ~5kb
- Compliments the Human610-Quad BeadChip for emphasis of genes and other high-value functional regions
- HumanCNV370-Quad
- More than 370 000 markers with a median marker spacing of 5.0kb
illumina BeadChip Human Mapping Service Process
Bovine Genotyping
For agricultural whole-genome SNP applications AGRF offers full service processing on Affymetrix and illumina arrays.
Affymetrix 10K SNP Bovine array: The Affymetrix GeneChip® Bovine Genome Array is specifically designed to monitor expression of approximately 23,000 bovine transcripts. The array is representative of all publicly known, high quality, bovine gene sequences, enabling researchers to conduct whole-genome expression profiling of cattle for agricultural applications. Bovine targeted genotyping arrays are run on the Affymetrix GeneChip Scanner 3000 7G MegAllele system, which utilizes molecular inversion probe (MIP) technology. The 10K SNP bovine arrays have been designed for high resolution linkage and association studies in beef and dairy breeds. The 10K SNP chip has been validated against six breeds (Angus, Brahmin, Hereford, Holstein, Jersey and Limousin). Genotyping data is generated and analysed in batches using the GeneChip Targeted Genotyping System (GTGS) software.
illumina Bovine SNP50 BeadChip: The illumina Bovine SNP50 BeadChip features more than 54 000 evenly spaced probes that target common SNPs described in publicly available sources for interrogation of genetic variation in virtually any cattle breed. These chips utilise illumina's BeadArray System, a microarray system which is based on the use of 3-micron silica beads. The Bovine SNP50 BeadChip presents an average SNP spacing of 51.5 Kb across the entire genome, offering more than sufficient SNP density for applications including whole-genome association studies, genome-wide selection, determination of genetic merit and comparative genetic studies.
The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Affymetrix Bovine Genotyping Service Process
illumina Bovine Genotyping Service Process
Mouse Genotyping
AGRF offers full service processing for the Mouse 5K targeted genotyping array, which utilizes molecular inversion probe (MIP) technology. These arrays are run on the Affymetrix GeneChip Scanner 3000 7G MegAllele system. AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis. The 5K SNP array consists of one universal panel allowing rapid high throughput and high resolution linkage mapping for genotyping crosses of the most common mouse strains. This panel features approximately 5,500 SNPs, with a median of 1500 informative markers across any two of the 20 most commonly studies strains. Genotyping data is generated and analysed in batches using the GeneChip Targeted Genotyping System (GTGS) software.
Mouse Genotyping Service Process
Canine Genotyping
The illumina Canine SNP20 BeadChip enables the genome-wide interrogation of genetic variation within any domestic dog breed. The illumina chip features more than 22 000 evenly distributed SNPs with a uniform coverage across the bovine genome. The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Canine Genotyping Service Process
Equine Genotyping
The illumina Equine SNP50 BeadChip features 54 602 highly informative SNPs uniformly distributed across the entire genomes of fifteen breeds of horses. The content is derived from data generated by the Broad Institute's Equine Genome Sequencing Project. Genotyping applications utilising this chip include whole-genome association studies and quantitative trait loci identification. The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Equine Genotyping Service Process
Mouse SNP Linkage Marker Set
The mouse SNP linkage marker set is a panel of over 550 SNPs spaced at an average distance of 3-5cM across the mouse genome. The AGRF provides a comprehensive SNP genotyping service for this panel, which has been specifically designed as a low cost solution for speed cogenics strain development. This service is provided on the Sequenom MassARRAY system, and utilises the homogenous MassExtend (hME - single base extension) reaction, termed iPLEX GOLD, allowing for the analysis of up to 36 SNPs in a single multiplex. The table below indicates the mouse strains that have been characterised on this marker set so far. For those crosses that are not listed on the table below, statistics relating to the number of informative SNPs can be obtained on enquiry to AGRF.
Sequenom iPLEX GOLD Brochure (PDF)
Characterised Mouse Strains
Mouse SNP Linkage Marker Set Service Process
