Overview

N2Jenomics Lab Pvt. Ltd. provides high-quality Comparative Genomic Hybridization (CGH) Microarray services for a wide range of species, including human, mouse, rat, and chicken, with custom CGH array solutions available for additional organisms.

Our CGH microarray platform enables high-resolution, genome-wide detection of copy number variations (CNVs), including chromosomal deletions and duplications that may not be detectable using conventional cytogenetic methods. Supported by validated laboratory workflows, optimized protocols, high-resolution microarray scanners, and advanced bioinformatics analysis, we deliver accurate, reproducible, and rapid results for both research and clinical applications.

Introduction to CGH Microarray

Comparative Genomic Hybridization (CGH) Microarray is an advanced molecular cytogenetic technology used to identify DNA copy number changes across the entire genome. It provides a comprehensive assessment of chromosomal gains and losses associated with genetic disorders, developmental abnormalities, congenital diseases, and cancer.

Compared with traditional cytogenetic techniques, CGH microarray offers significantly higher resolution, enabling the detection of both large chromosomal abnormalities and submicroscopic genomic alterations that are often missed by conventional karyotyping.

How Does CGH Microarray Work?

CGH microarray is based on the principle of comparative genomic hybridization, where genomic DNA from a test sample is compared directly with DNA from a reference sample.

The workflow includes:

• • Extraction of high-quality genomic DNA from both test and reference samples.

• • Fluorescent labeling of DNA using different dyes (commonly Cy3 and Cy5).
• • Co-hybridization of the labeled DNA onto a high-density microarray containing thousands of genomic probes.
• • High-resolution scanning to measure fluorescence intensity across the array.
• • Bioinformatic analysis to compare signal ratios and identify chromosomal gains or losses.

• Differences in fluorescence intensity reveal regions of DNA amplification or deletion, allowing precise genome-wide copy number analysis.

What Can CGH Microarray Detect?

CGH Microarray is designed to detect a broad spectrum of genomic copy number abnormalities, including:

• • Copy Number Variations (CNVs), including deletions and duplications
• • Microdeletions and microduplications associated with genetic syndromes
• • Chromosomal gains and losses across the genome
• • Genomic imbalances linked to developmental disorders, congenital anomalies, and cancer
• • Complex copy number alterations involving multiple chromosomal regions

Note: CGH Microarray cannot detect balanced chromosomal rearrangements such as balanced translocations or inversions because these abnormalities do not involve changes in DNA copy number.

Advantages of Our CGH Microarray Service

• • High Resolution and Sensitivity for detecting small genomic copy number changes.
• • Genome-Wide Coverage for comprehensive chromosomal analysis.
• • Accurate Detection of CNVs, including microdeletions and microduplications.
• • Rapid Turnaround Time through high-throughput microarray processing.
• • Validated Laboratory Workflows ensuring reliable and reproducible results.
• • Advanced Data Analysis using robust bioinformatics pipelines.
• • Applicable Across Multiple Species with custom array design options available.
• • Supports Both Clinical Research and Translational Studies.

CGH Microarray Workflow

Our streamlined CGH Microarray workflow ensures high-quality and reproducible results at every stage.

1. Sample Preparation -  High-quality genomic DNA is extracted from the submitted biological samples.

2. DNA Labeling - Test and reference DNA samples are fluorescently labeled using different dyes.

3. Hybridization -  Equal amounts of labeled DNA are hybridized onto a high-density CGH microarray containing genome-wide probes.

4. Washing and Scanning -  Following hybridization, the array is washed to remove non-specific binding and scanned using a high-resolution microarray scanner.

5. Data Analysis -  Specialized bioinformatics software analyzes fluorescence intensity ratios to identify chromosomal gains, losses, and copy number variations.

6. Results and Reporting -  Comprehensive reports are generated, highlighting detected genomic imbalances along with detailed interpretation to support downstream research or clinical investigations.

Service Specifications

	Sample Requirements Genomic DNA: Volume 3-5μg, concentration≥50 ng/µL Blood: 2~3ml 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.
	Sequencing Strategy Various Chips: 1×1M, 2 x 105K, 8x60K, et Custom Services
	Bioinformatics Analysis We provide multiple customized bioinformatics analyses: Normalization Background correction Segmenting data Identification of CNVs Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Recommendations and Custom Service

Analysis Pipeline

Deliverables

• • Raw data

• • Segmentation analysis based on the DNA copy package
• • Segmentation GFF file
• • Genome annotation GFF file

N2Jenomics Lab Pvt. Ltd.  can also help create your own custom CGH microarray. We are ready to help you with your custom array needs, whether it's a standard design or something more creative. CGH microarray services offered by N2Jenomics Lab Pvt. Ltd. provide a state-of-the-art approach to genomic analysis, combining high resolution, comprehensive coverage, and fast turnaround times to meet the needs of research applications.

Q1. What is the difference between CGH Microarray and SNP Microarray?

Answer:  CGH (Comparative Genomic Hybridization) Microarray is primarily designed to detect copy number variations (CNVs), including genomic gains and losses, by comparing DNA from a test sample with a reference sample. In contrast, SNP (Single Nucleotide Polymorphism) Microarray identifies SNPs while also detecting CNVs, regions of loss of heterozygosity (LOH), uniparental disomy (UPD), and other allele-specific genomic alterations.

Q2. Can a CGH Microarray detect balanced chromosomal rearrangements?

Answer:  No. CGH Microarray cannot detect balanced chromosomal abnormalities, such as balanced translocations or inversions, because these rearrangements do not involve changes in DNA copy number. Techniques such as karyotyping, fluorescence in situ hybridization (FISH), or other cytogenetic methods are required to identify these abnormalities.

Q3. How accurate is CGH Microarray for clinical and research applications?

Answer:  CGH Microarray is a highly accurate and reliable technology for detecting genomic copy number changes. Its high-resolution genome-wide coverage enables the identification of clinically relevant chromosomal imbalances, making it a widely adopted tool for genetic research, constitutional disorder analysis, and clinical diagnostics.

Q4. What are the limitations of CGH Microarray?

Answer:  While CGH Microarray offers excellent sensitivity for detecting copy number variations, it has certain limitations. It cannot identify balanced chromosomal rearrangements, single nucleotide variants (SNVs), or low-level mosaicism below the platform's detection threshold. Additionally, some detected CNVs may be classified as variants of uncertain significance (VUS), requiring further clinical interpretation or confirmatory testing.