N2Jenomics Lab Pvt. Ltd. offers comprehensive and highly flexible genotyping services tailored to projects of all sizes—from small-scale studies to large population-based research—as well as standard and fully customized workflows. Our services support human samples and a wide range of plant, animal, and microbial species.

Leveraging an advanced portfolio of high-density genotyping arrays, premium-quality reagents, automated platforms, and robust bioinformatics pipelines, we deliver accurate and reliable detection of single nucleotide polymorphisms (SNPs), copy number variations (CNVs), insertions/deletions (Indels), and other genetic variants.

Designed to meet the diverse needs of research, agricultural, clinical, and pharmaceutical applications, our scalable genotyping solutions ensure exceptional data quality, rapid turnaround times, and cost-effective performance. Backed by experienced scientists, cutting-edge technologies, and stringent quality standards, N2Jenomics Lab Pvt. Ltd. is a trusted partner for delivering high-confidence genotyping results that accelerate genomic discoveries.

What is Genotyping?

Genotyping is a molecular genetic technique used to identify the specific genetic variants, or alleles, present at particular locations (loci) within an organism's genome. By analyzing DNA sequences, researchers can determine an individual's unique genetic makeup and study how genetic differences contribute to biological traits, disease susceptibility, and phenotypic diversity.

The process involves comparing a DNA sample with a reference genome or another sample to detect genetic variations, including single nucleotide polymorphisms (SNPs), copy number variations (CNVs), insertions/deletions (Indels), and other sequence alterations. These insights help establish relationships between genotype and phenotype, enabling researchers to understand the genetic basis of inherited traits, diseases, and population diversity.

Genotyping has become an indispensable tool across genomics research, precision medicine, agricultural breeding, evolutionary biology, and population genetics, providing valuable information for biomarker discovery, disease association studies, genetic mapping, and personalized healthcare.

Single Nucleotide Polymorphism (SNP) Genotyping

Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genetic variation, representing single base-pair changes within the DNA sequence. Typically occurring once every 1,000 base pairs, SNPs are distributed throughout the genome, including coding, non-coding, regulatory, and intronic regions. These genetic variations can influence gene expression, transcription factor binding, RNA splicing, protein structure, and numerous other biological processes, ultimately contributing to individual diversity, disease susceptibility, and evolutionary adaptation.

As one of the two major sources of genetic variation—alongside Copy Number Variations (CNVs)—SNPs serve as powerful molecular markers for investigating complex traits and diseases. SNP genotyping has become an essential tool in genomics research, enabling applications such as disease association studies, precision medicine, pharmacogenomics, population genetics, agricultural breeding, and personalized healthcare.

Depending on the research objectives, SNP genotyping is generally categorized into two approaches:

• • Genome-Wide SNP Genotyping: A comprehensive strategy that analyzes hundreds of thousands to millions of SNP markers across the entire genome, making it ideal for genome-wide association studies (GWAS), genetic diversity analysis, and large-scale population studies.

• • Targeted SNP Genotyping (Fine Mapping): A focused approach that evaluates a selected set of SNPs within specific genomic regions. Fine mapping is commonly performed following genome-wide studies to validate and refine candidate loci associated with diseases or important biological traits. This method enables high-density analysis of targeted regions while delivering excellent accuracy, high call rates, and efficient processing of large sample cohorts.

Selecting the appropriate genotyping technology is critical for generating reliable, high-quality data while meeting the specific goals of each project. N2Jenomics Lab Pvt. Ltd. provides flexible, high-throughput SNP genotyping solutions that support projects ranging from targeted marker validation to comprehensive genome-wide analysis. Our advanced genotyping platforms enable the analysis of thousands to millions of genetic markers with exceptional accuracy, reproducibility, and scalability.

By integrating state-of-the-art technologies, optimized laboratory workflows, and comprehensive bioinformatics analysis, we deliver high-density genome-wide coverage and the latest scientifically validated marker content. Whether your research focuses on human health, agriculture, animal genetics, or evolutionary biology, our SNP genotyping services provide robust, reliable, and actionable genomic insights to accelerate scientific discovery.

Genotyping Methods

Genotyping encompasses a range of molecular techniques used to identify and characterize genetic variations within an individual's genome. The choice of method depends on factors such as the number of genetic markers to be analyzed, sample throughput, required resolution, and the objectives of the study. Below are the key methodologies commonly employed in modern genotyping workflows.

• DNA Preparation

The first step in any genotyping workflow is the extraction of high-quality genomic DNA. DNA is isolated from biological samples such as whole blood, saliva, tissue, buccal swabs, cultured cells, or formalin-fixed paraffin-embedded (FFPE) tissues. During extraction, cellular components, proteins, and contaminants are removed to obtain purified DNA suitable for downstream molecular analysis. Depending on the sample type and application, extraction can be performed using conventional organic methods or automated column- and magnetic bead-based purification systems.

• DNA Hybridization

Hybridization is a fundamental principle underlying many genotyping technologies, including microarrays, PCR-based assays, and next-generation sequencing (NGS). It involves the specific binding of complementary single-stranded DNA molecules through base-pair matching. This highly specific interaction enables accurate detection and identification of genetic variants across the genome.

• PCR-Based Genotyping

Polymerase Chain Reaction (PCR) is one of the most widely used methods for genotyping due to its speed, sensitivity, and accuracy. PCR selectively amplifies target DNA regions, allowing the detection of specific genetic variants. Common PCR-based genotyping approaches include:

• - Allele-Specific PCR (AS-PCR): Detects known genetic variants using allele-specific primers.
• - PCR-Restriction Fragment Length Polymorphism (PCR-RFLP): Differentiates alleles based on restriction enzyme digestion patterns.
• - TaqMan® SNP Genotyping Assays: Utilizes fluorescent allele-specific probes for rapid, highly accurate, and high-throughput SNP detection.

These techniques are extensively applied in clinical research, disease association studies, and molecular diagnostics.

• MassARRAY® iPLEX Genotyping

The MassARRAY® iPLEX platform combines multiplex PCR with single-base extension chemistry and MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization–Time of Flight) mass spectrometry for precise SNP genotyping. This technology enables simultaneous analysis of multiple genetic markers with high accuracy, making it well suited for medium- to high-throughput validation studies, pharmacogenomics, and targeted genetic screening.

• Pyrosequencing

Pyrosequencing is a sequencing-by-synthesis technology designed for accurate analysis of short DNA fragments. During DNA synthesis, the incorporation of each nucleotide generates a measurable light signal, allowing real-time determination of DNA sequences. This method is particularly useful for SNP genotyping, mutation detection, methylation analysis, and validation of sequence variants.

• Microarray-Based Genotyping

Microarray technology enables high-throughput analysis of hundreds of thousands to millions of genetic variants in a single experiment. Platforms such as Illumina Infinium® and Affymetrix GeneChip® use allele-specific probes immobilized on a solid surface to detect SNPs and other genomic variations through DNA hybridization. Following hybridization, fluorescent signal intensities are measured to accurately determine genotypes.

Microarray-based genotyping is widely used for:

• • Genome-Wide Association Studies (GWAS)
• • Population genetics and diversity studies
• • Copy Number Variation (CNV) analysis
• • Agricultural and livestock genomics
• • Precision medicine and pharmacogenomics

Next-Generation Sequencing (NGS)-Based Genotyping

Next-Generation Sequencing (NGS) has revolutionized genotyping by enabling comprehensive detection of genetic variants across targeted regions, exomes, or entire genomes. Unlike traditional genotyping methods that focus on predefined markers, NGS can identify both known and novel variants, including SNPs, insertions/deletions (Indels), structural variants, and copy number changes.

NGS-based genotyping offers exceptional sensitivity, scalability, and genome-wide coverage, making it the preferred approach for precision medicine, rare disease research, cancer genomics, and large-scale population studies.

Our Genotyping services

Our genotyping service portfolio includes:

• Whole Genome SNP Genotyping

High-density genome-wide SNP profiling for Genome-Wide Association Studies (GWAS), population genetics, genomic selection, trait mapping, and genetic diversity analysis.

• Targeted SNP Genotyping (Fine Mapping)

Accurate validation and characterization of candidate SNPs identified through genome-wide studies, providing high call rates and robust performance for medium- and large-scale sample cohorts.

• Copy Number Variation (CNV) Genotyping

Comprehensive detection and analysis of genomic copy number gains and losses to support disease research, cancer genomics, and structural variation studies.

• DNA Fragment Analysis Services

High-resolution fragment analysis for applications such as microsatellite (SSR) genotyping, STR analysis, mutation detection, indel analysis, and quality assessment using capillary electrophoresis.

Sample requirements

Analysis Pipeline

The fundamental input data can comprise diverse types of microarray chip data and next-generation sequencing data such as whole genome sequencing or whole exome sequencing data. Ordinarily, genotyping results from microarray chip data are furnished by the chip manufacturer. The subsequent pipeline delineates the systematic approach to analyzing genotyping by utilizing whole genome sequencing data.

Advantages of Our Genotyping Services

At N2Jenomics Lab Pvt. Ltd., we are committed to delivering accurate, reliable, and high-quality genotyping solutions that support diverse research and clinical applications. Our comprehensive services combine advanced technologies, rigorous quality standards, and scientific expertise to provide dependable results tailored to your research objectives.

Why Choose Our Genotyping Services?

• • Comprehensive Genotyping Solutions: We offer end-to-end genotyping services supported by internationally recognized quality standards, ensuring consistent, accurate, and reproducible results.
• • Experienced Scientific Team: Our multidisciplinary experts specialize in assay design, laboratory processing, data analysis, and bioinformatics, delivering meaningful insights from complex genomic datasets.
• • Fast Turnaround with High Accuracy: Optimized laboratory workflows and automated analytical pipelines enable rapid project completion without compromising data quality or reliability.
• • Multi-Species Expertise: We support a wide range of sample types, including human, animal, plant, and microbial genomes, making our services suitable for diverse research disciplines.
• • Advanced Genotyping Technologies: Our laboratory utilizes industry-leading platforms and continuously adopts the latest genotyping innovations to deliver high-resolution, high-throughput genetic analysis.
• • Customized Project Solutions: Every project is designed around your specific research goals, sample size, species, and budget, ensuring the most effective and economical genotyping strategy.
• • Dedicated Scientific Consultation: Our experts work closely with researchers to recommend the optimal platform, experimental design, and analytical workflow, maximizing project success while minimizing costs.

Our End-to-End Genotyping Workflow

• Scalable Genotyping Platforms

We provide flexible genotyping solutions capable of handling projects ranging from a few samples to large-scale population studies. Our diverse portfolio of SNP genotyping platforms enables efficient analysis of hundreds to millions of genetic markers across varying project sizes.

• Stringent Quality Assurance

Every project undergoes comprehensive quality control throughout sample processing, genotyping, and data analysis. Our rigorous QC procedures ensure exceptional data accuracy, reproducibility, and confidence in every result.

• Optimized Experimental Design

Our scientists assist in selecting the most informative SNP markers and the most appropriate genotyping platform based on your research objectives, sample volume, species, and study design.

• High-Precision Genotyping

We offer both validation of known genetic variants and discovery of novel SNPs using advanced molecular technologies, providing reliable genotyping results for a broad range of research applications.

• Comprehensive Data Delivery

Results are delivered in user-friendly formats, including Microsoft Excel and standard genotype files. Depending on the project, we also provide:

• • SNP genotype datasets
• • Raw data files
• • Variant annotations
• • Linkage Disequilibrium (LD) analysis
• • Quality control metrics
• • Statistical summaries
• • Bioinformatics reports and data interpretation (optional)

Results Display

Our advanced bioinformatics pipelines transform complex genotyping data into clear, accurate, and biologically meaningful results. By integrating sophisticated analytical tools, we enable comprehensive analysis of Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) across datasets containing thousands to millions of genetic markers.

Our analysis workflows facilitate:

• •  Comprehensive evaluation of genome-wide SNP and CNV data
• • Identification of sample outliers and quality control assessment
• • Detection and annotation of genetic variants
• • Functional interpretation of genomic variations and their biological significance
• • Generation of publication-ready visualizations and analytical reports