What is a SNP Microarray Test?

A Single Nucleotide Polymorphism (SNP) Microarray is a high-throughput genomic technology used to identify and analyze genetic variations across the genome. It detects single nucleotide polymorphisms (SNPs)—the most common type of genetic variation—where a single DNA base differs between individuals. These genetic differences play an important role in disease susceptibility, drug response, inherited traits, population genetics, and precision medicine.

Using thousands to millions of genomic markers simultaneously, SNP microarrays enable rapid, accurate, and cost-effective analysis for large-scale genetic studies, biomarker discovery, and clinical research.

How Does a SNP Microarray Work?

SNP microarrays use specially designed chips containing millions of DNA probes that target known genetic variants.

• • High-Density Microarray Chips: Each chip contains thousands to millions of oligonucleotide probes attached to a solid surface using advanced bead-based or photolithography technologies.
• • DNA Hybridization: Fluorescently labelled DNA from the sample binds to complementary probes on the array.
• • Signal Detection: The hybridization signals are captured and analyzed to determine the genotype of each SNP with high accuracy and reproducibility.

This technology enables simultaneous analysis of a vast number of genetic markers within a single experiment.

SNP Microarray Services at N2Jenomics Lab Pvt. Ltd.

N2Jenomics Lab Pvt. Ltd. provides comprehensive SNP microarray services using industry-leading Illumina and Affymetrix (Thermo Fisher Scientific) platforms. Our high-density genotyping solutions deliver reliable, reproducible, and high-quality genomic data for a broad range of research and clinical applications.

Our services support:

• • Genome-wide SNP genotyping

• • Copy Number Variation (CNV) analysis
• • Genome-wide association studies (GWAS)
• • Population and evolutionary genetics
• • Pharmacogenomics research
• • Precision medicine and biomarker discovery
• • Agricultural and animal genomics
• • Custom SNP array-based projects

With robust laboratory workflows and expert bioinformatics support, we help researchers identify genetic variants associated with disease risk, therapeutic response, and important biological traits.

SNP Microarray Services for Diverse Research Applications

N2Jenomics Lab Pvt. Ltd. offers scalable and cost-effective SNP genotyping solutions for projects ranging from small validation studies to large population-scale research. Our services are designed to generate high-quality genomic data while maintaining rapid turnaround times and competitive per-sample costs.

We support both Illumina and Affymetrix microarray platforms, enabling researchers to select the most appropriate technology based on their species, study objectives, sample size, and marker requirements.

Our SNP microarray services are widely used in:

• • Precision medicine research
• • Clinical and translational genomics
• • Pharmacogenomics
• • Disease association studies
• • Consumer genomics
• • Agricultural and livestock breeding
• • Plant genetics and crop improvement
• • Population and evolutionary genomics

Whether your project involves human, animal, or plant genomics, our team provides end-to-end support—from array selection and laboratory processing to data analysis and biological interpretation.

Machine	Platform	Applications
	GeneChip Scanner 3000 7G System together with Affymetrix GeneChip	Precision Medicine Research The detection of all known microorganisms ADME

Advantages of Our SNP Microarray Service

At N2Jenomics Lab Pvt. Ltd., we provide reliable, high-quality SNP microarray solutions designed to support a wide range of genomic research applications.

• • Customizable and Scalable Solutions – Choose from standard or custom SNP arrays tailored to your research objectives.
• • Exceptional Accuracy – High genotype call rates (>99%) with excellent reproducibility and data quality.
• • Cost-Effective High-Throughput Genotyping – Process large numbers of samples efficiently while reducing per-sample costs.
• • High-Density Genome Coverage – Analyze thousands to millions of SNP markers across the genome.
• • Comprehensive Variant Detection – Detect both single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in a single assay.
• • Broad Species Support – Available for human, animal, and plant genomics research.
• • Rapid Turnaround Times – Optimized laboratory workflows ensure timely project completion.
• • Expert Data Analysis – End-to-end support, from sample processing to bioinformatics analysis and biological interpretation.
• • Flexible Research Applications – Suitable for genome-wide studies, targeted genotyping, validation studies, and custom research projects.

Applications of SNP Microarray

SNP microarrays are widely used across biomedical, agricultural, and translational research due to their ability to rapidly analyze genetic variation at scale.

• Genetic Research - Identify genetic variants associated with inherited traits, complex diseases, and biological pathways to advance genomic research.

• Genome-Wide Association Studies (GWAS) - Discover SNPs linked to diseases, quantitative traits, and complex phenotypes through large-scale association studies.

• Precision and Personalized Medicine - Support precision healthcare by identifying genetic markers that influence disease risk, drug efficacy, and treatment response.

• Pharmacogenomics -  Understand how genetic variation affects drug metabolism and therapeutic outcomes, enabling more personalized treatment strategies.

• Clinical and Translational Research -  Investigate genetic risk factors, validate biomarkers, and support studies focused on disease diagnosis and prognosis.

• Population Genetics and Evolutionary Biology -  Explore genetic diversity, ancestry, population structure, and evolutionary relationships across different populations and species.

• Biomarker Discovery and Validation -  Identify and validate genomic biomarkers for disease prediction, diagnosis, prognosis, and therapeutic monitoring.

• Agriculture and Animal Breeding -  Accelerate crop improvement and livestock breeding by identifying genetic markers associated with productivity, quality, and disease resistance.

• Forensic and Identity Testing - Support applications requiring genetic identification, ancestry analysis, and breed or lineage discrimination.

SNP Microarray Workflow

Our SNP microarray workflow is designed to deliver accurate, reproducible, and high-quality genotyping results through rigorous laboratory and quality control processes.

Typical Workflow

• Sample Submission – Collection and quality assessment of DNA samples.

• DNA Quality Control – Quantification and integrity evaluation before processing.

• Microarray Processing – DNA amplification, fragmentation, labeling, hybridization, staining, and scanning using Illumina or Affymetrix platforms.

• Data Acquisition – Generation of high-quality genotype data with stringent quality metrics.

• Bioinformatics Analysis – SNP genotyping, CNV detection, quality filtering, and downstream statistical analysis.

• Interpretation and Reporting – Comprehensive data analysis, visualization, and delivery of project-specific reports.

Using industry-leading genotyping platforms and standardized quality management procedures, our experienced scientists ensure reliable, unbiased, and reproducible results for both genome-wide and targeted SNP analysis

	Sample Requirements Genomic DNA≥300 ng, Minimum Quantity: 100 ng, concentration≥8 ng/µL DNA samples require an OD260/280 as close to 1.8~2.0 as possible. All DNA should be RNase-treated and should show no degradation or contamination. Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
	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 multiple customized bioinformatics analyses: SNP identification GWAS Linkage map construction Genomic selection Population structure analysis Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

Deliverables

• The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in SNP Microarray for your writing (customization)

Q1. What SNP microarray genotyping platforms are available?

N2Jenomics Lab Pvt. Ltd. offers SNP genotyping services using industry-leading Illumina and Affymetrix (Thermo Fisher Scientific) microarray platforms. Both technologies provide high-throughput, reliable, and reproducible SNP analysis for a wide range of research applications.

•  Illumina Genotyping Platform

• Uses proprietary BeadArray® technology with high-density bead-based arrays.
• Delivers exceptional accuracy and reproducibility, typically exceeding 99.5%.
• Well suited for genome-wide association studies (GWAS), population genetics, pharmacogenomics, and large-scale genetic screening.

• Affymetrix Genotyping Platform

• Utilizes advanced photolithography-based microarray technology to synthesize millions of oligonucleotide probes directly on glass chips.
• Supports ultra-high-density SNP analysis with excellent genomic coverage.
• Ideal for genome-wide genotyping, copy number variation (CNV) analysis, and precision medicine research.

Q2. How do I choose the right SNP genotyping platform?

The ideal platform depends on your research objectives, sample type, number of samples, and required marker density.

• Genome-wide SNP Analysis

• Recommended for GWAS, population genetics, and genomic screening.
• Suitable platforms: Illumina BeadChips, Affymetrix GeneChips, or Next-Generation Sequencing (NGS).

• Targeted or Gene-Specific SNP Analysis

• Best for fine mapping, haplotype analysis, and candidate gene studies.
• Suitable platforms: Targeted NGS or SNP microarrays.

• Single or Limited SNP Analysis

• Ideal for validating specific genetic variants.
• Suitable technologies include Real-Time PCR, Sanger Sequencing, SNP Microarrays, or NGS, depending on project scale.

Our experts help you select the most appropriate technology based on your study design, species, throughput requirements, and budget.

Q3. Which SNP microarrays are available at N2Jenomics Lab Pvt. Ltd.?

We provide access to a comprehensive portfolio of commercial and custom SNP microarrays for human, animal, and plant genomics research.

Human Genotyping Arrays

• • Infinium Global Screening Array-24 (GSA-24)
• • Infinium Multi-Ethnic Array
• • Infinium CoreExome v1.1 BeadChip
• • Axiom Biobank Genotyping 610K SNP Array
• • Genome-Wide SNP 6.0 Array
• • Axiom Precision Medicine Research Array
• • CarrierScan Assay Kit

Animal Genotyping Arrays

• • Infinium BovineSNP50 v3.0 BeadChip
• • Infinium PorcineSNP60 v2 BeadChip
• • CanineHD DNA Analysis BeadChip
• • Axiom Buffalo 90K SNP Array
• • Axiom Chicken 580K SNP Array
• • Mouse Diversity 623K SNP Array
• • OvineSNP50 BeadChip
• • Additional custom livestock and companion animal SNP arrays

Plant Genotyping Arrays

• • MaizeSNP50 DNA Analysis BeadChip
• • Axiom Strawberry 95K SNP Array
• • Axiom Soybean Genotyping Array
• • Axiom Wheat Breeder's Genotyping Array
• • Arabidopsis atSNPtilx520433 Cartridge Array
• • Additional crop-specific and custom plant SNP arrays

We also support custom SNP array design, enabling researchers to develop panels tailored to specific species, traits, populations, or research objectives. Our team can recommend the most suitable array based on your experimental requirements.