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 catalogue Affymetrix products. Please contact us for all available products.
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. 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:
Group |
Infinium BeadChip |
SNP/Markers(per sample) |
Samples (per BeadChip) |
Median Marker Spacing |
Comment |
Standard Content |
301,232 |
12 |
6.2 kb |
Efficient coverage for cost-effective genome-wide association studies (GWAS) and for cytogenetic screening. |
|
733,202 |
12 |
2 kb |
Genome-wide SNPS coverage and CNV regions with content derived from all 3 HapMap Project phases. |
||
1,140,419 |
4 |
1.2 kb |
Comprehensive genome-wide coverage and additional high-value regions, including new content from 1,000 Genomes Project. |
||
2,450,000 |
4 |
1.2 kb |
Comprehensive genome-wide coverage, including common and rare SNP content from the 1,000 Genomes Project. |
||
Custom Content |
iSelect-24 Custom Panel |
~3,000 - 60,800 |
24 |
- |
Your own selection of markers |
iSelect-12 Custom Panel |
~60,801 - 200,000 |
12 |
- |
Your own selection of markers |
- HumanCytoSNP-12
The HumanCytoSNP-12 BeadChip includes markers that have been hand-selected by Illumina scientists to target specific regions of cytogenetic importance. Researchers have access to more than 3.6 million genetic markers on one BeadChip, and can be deployed on a 12-sample format.The HumanCytoSNP-12 BeadChip contains nearly 300,000 genetic markers per sample that target all known cytogenetic abnormalities found in genes and disease pathways linked to mental retardation, autism, and other common chromosome anomalies.
- HumanOmniExpress
A powerful genotyping BeadChip encompassing strategically selected optimised tag SNP content, providing the highest data quality. OmniExpress assists researchers in the discovery of novel assoications with traits and diseases via a high degree of common SNP variation.
- HumanOmni1-Quad
High-throughput format with more than 1 million SNPs and probes. High marker density and the fewest large gaps ensure precise CNV detection - more than 6,000 common and 5,000 rare CNV regions with 10-15 markers per region. Dense marker spacing with 1.5 kb median marker spacing for CNV discovery, content from the 1,000 Genomes Project and confirmed disease associations.
- HumanOmni2.5-Quad
High-throughput format with more newly discovered genome-wide common and rare variants from the 1,000 Genomes Project (1kGP). The Omni2.5 delivers unprecedented genome coverage for both SNP and copy number variation (CNV) analysis, in a 4-sample format for a total of approximately 10 million markers per array.
illumina BeadChip Human Mapping Service Process
Bovine Genotyping
For agricultural whole-genome SNP applications AGRF offers full service processing on illumina arrays.
illumina BovineHD BeadChip: The illumina BovineHD BeadChip features more than 770,000 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 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 characterization for evaluating biodiversity.
The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
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.
illumina Bovine Genotyping Service Process
Canine Genotyping
The illuminaCanineHD BeadChip features more than 170,000 evenly spaced probes that target common SNPs described in publicly available sources for interrogation of genetic variation within any domestic dog breed. The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Canine Genotyping Service Process
Ovine Genotyping
The illumina Ovine SNP50 BeadChip was developed in collaboration with International Sheep Genomics Consortium and contains more than 50,000 SNPs, providing uniform genome-wide coverage with an estimated one marker per 46kb on average. The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Ovine Genotyping Service Process
Porcine Genotyping
The illuminaPorcine SNP60 BeadChip features more than 60 000 highly informative SNPs providing even spacing with an estimated one marker per 40kb across the pig genome. The content is ideal for interrogating genetic variation in multiple porcine breeds including Duroc, Landrace, Pietran, and Large White. The AGRF service includes all reagents and consumables, extensive quality monitoring and options for customised analysis.
Porcine 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
