Genomic tools for CNV detection

Perform high-resolution copy number analysis with arrays and NGS

Copy Number Variation (CNV) Analysis

Copy number variations (CNVs) are genomic alterations that result in an abnormal number of copies of one or more genes. Structural genomic rearrangements such as duplications, deletions, translocations, and inversions can cause CNVs.

Like single-nucleotide polymorphisms (SNPs), certain CNVs have been associated with susceptibility to diseases such as cancer, autoimmune diseases, inherited genetic disorders, and more. Illumina offers a variety of microarray and next-generation sequencing (NGS) solutions for high-resolution copy number analysis.


Genome-wide genotyping arrays are commonly used to detect genetic variants, including CNVs that contribute to diseases and phenotypes. Array-based approaches for copy number analysis offer reliable, efficient methods for large-scale analysis.

Researchers can process multiple samples on a single microarray for broad surveys of genomic structural variation, and accurately profile chromosomal aberrations such as amplifications, deletions, rearrangements, and copy-neutral loss of heterozygosity.

Array-Based CNV Analysis
Cytogenomic Arrays

Arrays for cytogenomics research, which are specifically validated for CNV analysis as part of the manufacturing process.

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Human Genotyping

Unbiased, non-targeted arrays for human variant detection, providing high coverage across the human genome.

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Custom Genotyping

Design custom or semi-custom arrays for any species, with convenient online tools and Illumina expert assistance.

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All Microarray Kits

Find ready-to-use microarrays for a wide variety of genotyping and epigenetics studies.

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While efficient for large CNV detection, genotyping arrays are less sensitive for detecting CNVs smaller than 50 kilobases. By providing a base-by-base view of the genome, NGS detects small or novel copy number variants that arrays often miss.

NGS can also map the exact location of a CNV. The high resolution of sequencing complements the high throughput of arrays, enabling a comprehensive view of the genome.

Unmasking Autoimmune Diseases Using Genomics

Researchers initially used genome-wide arrays to identify copy number variations associated with lupus. To gain further insights, they adopted NGS (whole-genome and exome sequencing) to interrogate large numbers of genes for rare mutations.

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Illumina DNA PCR-Free Prep

A high-performing, fast, and integrated library prep workflow for sensitive applications such as human whole-genome sequencing.

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DRAGEN Bio-IT Platform 

Perform accurate, ultra-rapid analysis of genomic data, including CNV analysis for insights into genomic structural variation.

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BaseSpace Whole-Genome Sequencing App

Analyze WGS data using fast, accurate Isaac algorithms for alignment and calling of variants, including CNVs.

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TruSight Software Suite

Simplify rare disease variant analysis by calling and reporting on variants (including small variants, CNVs, mitochondrial variants, and more) from one software interface.

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Copy number variation often alters gene expression. Targeted RNA sequencing (RNA-Seq) is an unbiased approach for analyzing and quantifying transcripts of interest. RNA-Seq can capture subtle gene expression changes, measure allele-specific expression, and detect fusion genes. By characterizing the downstream effects of variants, researchers can better understand the molecular mechanisms of disease.

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NGS Shows CNV Impact on Gene Expression

Researchers use targeted RNA-Seq to uncover how a CNV linked to schizophrenia affects gene expression in the brain.

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SMN1 & SMN2 Copy Number Analysis from WGS Data

Scientists developed a bioinformatics tool that detects SMN1 and SMN2 gene copy number based on whole-genome sequencing data, to help advance spinal muscular atrophy research.

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Accurate CYP2D6 Genotyping Using WGS Data

Compared with traditional genotyping assays, whole-genome sequencing provides a promising option for building accurate allele frequency databases for pharmacogenomics applications because it assays CNVs as well as other variants.

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Illumina offers microarrays designed to detect chromosome aberrations and provide accurate cytogenomic data. NGS may be used to confirm copy number variants detected by arrays. Learn more about cytogenomics.

Whole-Genome Sequencing
Scientist Sequencing in Lab

Get a high-resolution, base-by-base view of the genome and identify potential causative disease variants. Learn more about WGS.

Disease Variant Discovery
Causal Variant Discovery

Array and NGS solutions can help researchers identify causative variants, including CNVs, associated with complex diseases. Learn more about causal variant discovery.


This technique creates a map of embryo chromosomes, giving researchers valuable insight into the role that genomics plays in the inheritance of single-gene defects. Learn more about karyomapping.

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System for NGS and Cytogenomic Arrays
System for NGS and Cytogenomic Arrays

Perform sequencing and high-quality cytogenomic array scanning all on a single platform, the NextSeq 550 System.

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Chromosomal Genetics Studies with Arrays & NGS
Chromosomal Genetics Studies

Researchers adopt NGS and array technologies to analyze chromosomal abnormalities and their connection to disease.

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CNV Array Data Analysis Basics
CNV Array Data Analysis Training

Learn how to analyze CNV data from Infinium genotyping arrays using GenomeStudio Software.

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Gene Panel and Array Finder
Gene Panel and Array Finder

Identify sequencing panels or microarrays that target your genes of interest.

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