Microarrays for Oncology Research

Trusted microarray analysis for uncompromised results

Microarrays are an ideal platform for copy number variation (CNV) analysis and molecular cytogenetic research for solid and liquid tumors. Applied Biosystems CytoScan microarrays offer a reliable genome-wide approach for high-resolution DNA copy number analysis to detect gains, losses, loss of heterozygosity (LOH)/absence of heterozygosity (AOH), copy-neutral loss of heterozygosity (cnLOH), regions identical-by-descent, and mosaicism.

All CytoScan arrays are hybrid-SNP chromosomal microarrays that contain large numbers of both SNP probes and non-polymorphic probes. Hybrid-SNP arrays, with more than 99% genotype accuracy, boost confidence in breakpoint determination and provide independent confirmation of copy number events throughout the entire genome.

Our robust microarray solutions are designed to provide reproducible results, save you time and money, reduce error, and deliver quality performance consistent with your laboratory requirements.

Workflow

Thermo Fisher Scientific offers powerful microarray solutions for oncology clinical research that are powered with robust workflows that make it easy to obtain consistent, reliable, and high-quality results.

Our complete microarray platform, the CytoScan Cytogenetics Suite, includes hybrid-SNP arrays, automated and manual target preparation options, fully kitted reagents, the GeneChip System 3000 instrument for array processing, and Chromosome Analysis Suite (ChAS) software for data interpretation and reporting. These tools support laboratories to help maximize operational time.

Product overview

CytoScan HD Accel Array

With enhanced speed, improved coverage, and lesser sample input requirement, the CytoScan HD Accel Array can help maximize lab productivity by 100%, enabling you to reach a new level of efficiency.

Two-day assay workflow
100 ng of genomic DNA input—50% less than other commercially available chromosomal microarrays
Consistent target generated by the assay that is hybridized to the array for reproducible and reliable results
Challenging sample types (e.g., buccal swabs, saliva, products of conception, amniotic fluid, and chorionic villus sampling (CVS)) included in reference model file to help enable generation of higher-quality results
Improved coverage in more than 5,000 regions across entries in OMIM® database, RefSeq, ClinGen, DECIPHER/DDD constitutional regions, and the COSMIC Cancer Gene Census (CGC)

Datasheet

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CytoScan HD Array

The benchmark in cytogenetics research with highest genome-wide resolution of CNVs for applications in oncology research. Key highlights of CytoScan HD array are:

2.67 million markers for copy number analysis, including 750,000 SNPs and 1.9 million nonpolymorphic probes.
Exceptional coverage across entries in OMIM database, RefSeq, ClinGen, DECIPHER/DDD constitutional regions, and the COSMIC Cancer Gene Census (CGC)
Advanced, proprietary manufacturing technology that produces highly reproducible arrays between batches, with no risk of probe dropout that occurs with bead array technology

Datasheet

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CytoScan 750K Accel Array

The CytoScan 750K Accel Suite enables comprehensive whole-genome coverage and superb performance for detecting chromosomal aberrations in a broad range of sample types for constitutional and oncology research applications.

Two-day assay workflow
Highly flexible and hybrid probe design that includes both CNVs and SNP arrays with standardized testing for all samples
Fewer re-runs with as little as 100 ng of genomic DNA sample
Whole-genome coverage for a broad range of sample types and applications

Datasheet

Learn about CytoScan 750K Accel Array

CytoScan 750K Array

High genome-wide resolution for the analysis of copy number gains and losses for oncology testing. CytoScan 750K offers:

750,000 markers for copy number analysis, including 200,000 SNPs and 550,000 nonpolymorphic probes
Comprehensive whole-genome coverage across entries in OMIM database, RefSeq, ClinGen, DECIPHER/DDD constitutional regions, and the COSMIC Cancer Gene Census (CGC)

Datasheet

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OncoScan Assay

Catch critical copy number changes with OncoScan CNV Assay. If you work with highly degraded DNA, such as that derived from FFPE tumor samples of various ages or product of conception (POC), and with low amounts of DNA starting material, common in cell-free DNA (cfDNA), learn more why this assay is a natural choice for clinical research and beyond.

Learn more about OncoScan Assay

Product specifications

CytoScan HD Accel	CytoScan HD	CytoScan 750K Accel	CytoScan 750K	OncoScan Assay
Research applications	Research applications
Fastest turnaround time in the industry with improved coverage for highest genome-wide resolution of CNVs for applications in prenatal and postnatal	The benchmark in cryogenics research with highest genome-wide resolution of CNVs for applications in prenatal and postnatal research	Faster turnaround time with improved coverage for highest genome-wide resolution of CNVs for applications in prenatal, postnatal, and oncology research	High genome-wide resolution for the analysis of copy number gains and losses for prenatal and postnatal research	High resolution analysis, up to 50 kb in top cancer genes and 300 kb across whole genome in FFPE and fresh frozen tissues
Sample types	Sample types
Blood; buccal swabs; saliva; bone marrow; uncultured or cultured cells; chorionic villi; amniocytes; POC	Blood, buccal swabs, saliva, uncultured or cultured cells, chorionic villi, amniocytes, POC.	Blood; buccal swabs; saliva; bone marrow; uncultured or cultured cells; chorionic villi; amniocytes; POC; and fresh, frozen tissue	Blood, buccal swabs, saliva, uncultured or cultured cells, chorionic villi, amniocytes, POC.	FFPE, fresh and frozen tissue
Size of aberration*	Size of aberration*
Losses: 25 kb Gains: 50 kb LOH/AOH: 3 Mb Mosaicism: >15% (approximately)	Losses: 25 kb Gains: 50 kb LOH/AOH: 3Mb Mosaicism: >15% (approximately)	Losses: 100 kb Gains: 400 kb LOH/AOH: 5 Mb Mosaicism: >20%	Losses: 100 kb Gains: 400 kb LOH/AOH: 5Mb Mosaicism: >15%-20% (approximately)	Gains: 50 kb Losses: 50 kb LOH/AOH: 10 Mb Mosaicism (% aberrant cells): 15%
Input DNA	Input DNA
100 ng	10-250 ng**	100 ng	10-250 ng**	80 ng**
Probe structure	Probe structure
2.8 million markers for whole genome coverage 2 million nonpolymorphic markers 750,000 SNP probes for LOH/AOH analysis, duo-trio assessment, and sample tracking	2.67 million markers for whole genome coverage 1.95 million nonpolymorphic markers -743,000 SNP probes for LOH/AOH analysis, duo-trio assessment, and sample tracking	960,755 markers for whole genome coverage 706,054 nonpolymorphic markers 254,701 SNP probes for LOH/AOH analysis, duo-trio assessment, and sample tracking Balanced hybrid dual-probe design: Yes Balanced Whole-genome coverage: Yes	750,000 markers for whole genome coverage 550,000 nonpolymorphic markers -200,000 SNP probes for LOH/AOH analysis, duo-trio assessment, and sample tracking	220,000 molecular inversion probes (MIPs), whole genome coverage 5,700 non-polymorphic probes 216,000 SNP probes
Protocol	Protocol
2 days	3-4 days	2 days	3-4 days	2-3 days

*Size of aberration—The size of the segment call depends on the average marker spacing in the region. Best performance can be achieved in regions with higher marker coverage. Mosaicism detection may depend on the size of the altered segment and the type of aberration involved.

**250 ng is optimal but users have reported success using as little as 10 ng starting DNA.