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The Introduction to SNP Microarray

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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, 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 the various of genotyping services, delivering high-quality data at a low per-sample cost. Microarrays are 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.

HLA Typing

Figure 1. Our workflow of HLA typing.

Service Specifications

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-effective and high-throughput
  • Identifies SNPs in targeted or whole genome scale
  • In addition to SNPs, other genetic differences, such as copy number variations, can be measured
  • Applications 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 for 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 analysis 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 thedetermination 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.

FAQs

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, the number of SNPs per sample, and the number of samples. For different cases, we recommend different genotyping technologies.

    1. For genome-wide SNP genotyping, we recommend Illumina BeadChips, Affymetrix GeneChips or NGS.
    2. For gene-wide SNP genotyping, such as fine mapping or haplotyping of candidate regions we recommend NGS or array-based technologies.
    3. 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
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Tel: 1-631-275-3058
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