SNP Microarray - CD Genomics

CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost.

The Introduction to SNP Microarray

Powered by state-of-the-art variant detection and SNP genotyping technologies, CD genomics provides various genotyping services, delivering high-quality data at a low per-sample cost. Microarray is a valuable tool to enable researchers to explore genetic variants such as single nucleotide polymorphisms (SNPs) and large structural changes, from discovery applications to routine screening.

Affymetrix and Illumina genotyping microarrays both provide trusted performance with respect to precision medicine initiatives, clinical and translational research, pharmacology, consumer screening, and agricultural applications. Based on the species and the selection of SNPs, multiple genotyping strategies are available.

Table 1. Our available automated SNP genotyping platforms.

	Platform	Applications
	GeneTitan instrument together with Axiom array plates	The model organism studies Agricultural genotyping CarrierScan Assay Mouse Diversity Genotyping
	GeneChip Scanner 3000 7G System together with Affymetrix GeneChip	Precision medicine research The detection of all known microorganisms ADME
	Illumina iScan system together with Illumina BeadChips	GWAS Exonic content studies Population-scale studies CNV and LOH Agricultural genotyping

Advantages of SNP Microarray

Custom, flexible, and scalable;
High call rates (> 99%) and high accuracy;
Cost-effectiveness and high-throughput;
Identifies SNPs in a targeted or whole genome scale;
In addition to SNPs, other genetic differences, such as copy number variations, can be measured
Applied in biomarker discovery and validation, clinical testing, GWAS, pharmacogenomics, forensics, and breed discrimination.

SNP Microarray Workflow

The general workflow for SNP Microarray is outlined below. We have three well-recognized genotyping platforms (Table 1) for genome-wide or targeted identification of SNPs and copy number variations in a high-throughput and affordable manner. Our highly experienced expert team executes quality management, following every procedure to ensure confident and unbiased results.

SNP Microarray

Service Specifications

	Sample Requirements Sample source: humans, plants or animals High-quality genomic DNA with minimal fragmentation DNA amount ≥ 100 ng (DNA concentration ≥ 100 ng/µl) Sample purity: OD260/280 = 1.8~2.0 All DNA samples are validated on purity and quantity
	SNP Genotyping A wide range of arrays are available for humans, plants and animals, or custom genotyping arrays panels can be created to fully meet your specific needs GeneTitan instrument GeneChip Scanner Illumina iScan Accuracy and reliability for the assays are usually above 99.5%
	Bioinformatics Analysis We provide customized bioinformatics analyses including: SNP identification GWAS Linkage map construction Genomic selection Population structure analysis

Our Full Service covers the complete process, from quality control of genomic DNA to the determination of genotypes. Besides, CD Genomics can also help create your own custom microarray which can be tailored to meet specific project requirements. If you have additional requirements or questions, please feel free to contact us.

1.The introduction of Illumina and Affymetrix genotyping platforms.

Table 1. Affymetrix and Illumina genotyping solutions.

Affymetrix genotyping solutions	The Affymetrix SNP microarray applies a combination of photolithography and combinatorial chemistry to directly synthesize oligonucleotides on a glass surface. Affymetrix arrays can achieve very high density to accommodate millions of probes on a single chip.
Illumina genotyping solutions	Illumina's unique BeadArray technology is based on 3-micron silica beads that self-assemble in micro-wells on planar silica slides. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide, which acts as the capture sequence. Accuracy and reliability of the assays are usually above 99.5%.

2.How to choose the most suitable genotyping platform for my specific needs?

The choice of genotyping strategies depends on the species, the purpose and the number of SNPs per sample, as well as the number of samples. For different cases, we recommend different genotyping technologies.

For genome-wide SNP genotyping, we recommend Illumina BeadChips, Affymetrix GeneChips or NGS.
For gene-wide SNP genotyping, such as fine mapping or haplotyping of candidate regions, we recommend NGS or array-based technologies.
For the analysis of individual SNPs, we recommend Real-time PCR assays, Sanger Sequencing, Illumina BeadChips, Affymetrix technology or NGS.

3.What arrays are available at CD Genomics?

At CD Genomics, we have both ready-made and custom arrays for your SNP genotyping projects.

Table 2. Our available arrays for SNP genotyping.

Humans	Animals	Plants
Infinium Global Screening Array-24 Kit Infinium Multi-Ethnic Array Infinium CoreExome v1.1 BeadChip Axiom Biobank Genotyping 610k SNP Array Genome-wide SNP 6.0 Array (900k SNPs and 950k CNV) Axiom™ Precision Medicine Research Array CarrierScan™ Assay Kit	Infinium BovineSNP50 v3.0 BeadChip Kit Infinium PorcineSNP60 v2 BeadChip CanineHD DNA Analysis BeadChip Kit Axiom Buffalo 90k SNP Array Axiom Chicken 580k SNP Array Mouse Diversity 623k SNP Array CanineHD BeadChip (highly polymorphic SNP content for breed association and CNV studies) OvineSNP50 BeadChip (for genome-wide association studies of sheep) PorcineSNP60 v2 BeadChip (for genome-wide association studies of multiple porcine breeds)	MaizeSNP50 DNA Analysis BeadChip Axiom Strawberry 95k SNP Array Axiom™ Soybean Genotyping Array Axiom™ Wheat Breeder's Genotyping Array atSNPtilx520433 Arabidopsis Cartridge Array