Introduction to 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 disease susceptibility. Illumina offers a variety of array and next-generation sequencing (NGS) solutions for high-resolution copy number analysis.
Array-Based CNV 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.
CNV Array Products
Illumina offers both human and non-human genotyping arrays for CNV analysis. Illumina scientists strategically select the markers on the arrays to provide maximum genome coverage for optimal copy number analysis.
Cytogenomic research arrays
Arrays for cytogenomic research, which are specifically validated for CNV analysis as part of the manufacturing process.
Learn MoreHuman genotyping arrays
Unbiased, non-targeted approach for human variant detection, providing high coverage across the human genome.
Learn MoreNon-human genotyping arrays
Comprehensive suite of array-based kits for genotyping non-human species such as crops, livestock, and model organisms.
Learn MoreCustom genotyping arrays
Design custom or semi-custom arrays for any species, with convenient online tools and Illumina expert assistance.
Learn MoreCopy Number Analysis with NGS
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.
Featured NGS Products and Software for CNV Analysis
TruSeq PCR-Free Library Prep Kit
Identify the greatest number of variants and sequence challenging regions.
View ProductTruSeq Nano Library Prep Kit
Efficiently interrogate samples with limited available DNA, with high coverage quality and reduced bias.
View ProductBaseSpace Whole-Genome Sequencing App
Analyze whole-genome sequencing data using fast, accurate Isaac algorithms for alignment and calling of variants, including CNVs.
View AppStudying Downstream Effects of CNVs
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. Learn more about targeted RNA-Seq.
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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Cytogenomics
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.
Cancer Chromosome Abnormalities
Sequencing- and array-based technologies offer complementary approaches for studying chromosomal rearrangements, CNVs, and other abnormalities in cancer samples. Learn more about cancer chromosomal abnormality studies.
Complex Disease Variant Discovery
Array and NGS solutions can help researchers identify causative variants, including CNVs, associated with complex diseases. Learn more about complex disease research.
Preimplantation Genetic Diagnosis
Illumina offers solutions for rapid preimplantation genetic diagnosis (PGD) of single-gene disorders and balanced chromosomal translocations in IVF embryos. Learn more about PGD.
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Additional Resources
System for NGS and Cytogenomic Arrays
Perform sequencing and high-quality cytogenomic array scanning all on a single platform, the NextSeq 550 System.
Chromosomal Genetics Studies
Researchers adopt NGS and array technologies to analyze chromosomal abnormalities and their connection to disease.
CNV Array Data Analysis Training
Learn how to analyze CNV data from Infinium genotyping arrays using GenomeStudio Software.
Gene Panel and Array Finder
Identify sequencing panels or microarrays that target your genes of interest.