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Reproducible results with powerful microarray analysis
Copy number variations (CNVs) are well-recognized genomic structural variants associated with genetic disorders and chromosomal microarray analysis (CMA). CMA can successfully detect submicroscopic CNVs. The American College of Medical Genetics (ACMG) recommends CMA be used as a first-tier test for postnatal research of unexplained intellectual disability, developmental delay, autism spectrum disorders, and congenital abnormalities.
Applied Biosystems CytoScan microarrays enable labs to advance postnatal clinical research with powerful CMA. 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 research solutions are designed to provide reproducible results, save you time and money while delivering quality performance consistent with your laboratory requirements.
Workflow
Thermo Fisher Scientific offers powerful microarray solutions for postnatal 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)
CytoScan HD Array
The benchmark in cytogenetics research with highest genome-wide resolution of CNVs for applications in postnatal 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
- Superior 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
CytoScan XON Array
Sensitive single exon-level copy number analysis with exceptional coverage within exons across the whole genome. Use as a stand-alone test or to confirm CNV findings with alternative technologies like next generation sequencing. With the CytoScan XON array, you can:
- Comprehensively detect single-exon deletions and duplications in a cost-effective manner
- Complement NGS mutation analysis with reliable exon-level deletion and duplication detection
- Confirm CNV findings from alternative technologies
- Simplify and streamline copy number variants analysis
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, which includes both CNVs and SNPs 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
CytoScan 750K Array
High genome-wide resolution for the analysis of copy number gains and losses for postnatal research. 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)
CytoScan HT-CMA Array Plate
A solution for high-throughput, cost-effective genome-wide copy number analysis for constitutional cytogenetics research applications, as well as study of relevant SNP variants. Key features include:
- 1.1 million markers for copy number analysis, including 1 million SNP and 130,000 nonpolymorphic probes
- Comprehensive whole-genome coverage across RefSeq, OMIM®, and DECIPHER constitutional gene regions
CytoScan Optima Array
A low-cost genome-wide research platform to identify aneuploidies and copy number losses and gains at lower resolution. CytoScan Optima offers:
- 18,018 CN and 148,450 SNP markers uniformly spaced over the genome
- Increased coverage density (25 markers/100 kb) in 400 empirically selected regions
Product specifications
 CytoScan HD Accel |
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| 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 |
Sensitive single exon-level copy number analysis with superior coverage within exons across the whole genome. Use as a standalone test or to confirm CNV findings with alternative technologies like next generation sequencing. |
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 | A solution for high-throughput, cost-effective genome-wide copy number analysis for constitutional cytogenetics research applications, as well as study of relevant SNP variants | A low-cost genome-wide platform for detection of aneuploidies and copy number losses and gains at lower resolution, optimized for constitutional cytogenetics research |
| 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 and other sources of DNA can be used upon building a customized reference file | 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. | Blood, buccal swabs, saliva, uncultured or cultured cells, chorionic villi, amniocytes, POC. | Amniocytes, chorionic villi, POC, blood, uncultured or cultured cells |
| 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) |
95% sensitivity for the detection of exon-level CNVs. Design to cover the whole genome, with increased coverage in 7,000 clinically relevant genes |
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/losses (except for OMIM genes): 400 kb Gains/losses (OMIM genes): 100 kb LOH/AOH: 3 Mb Mosaicism” >15%-20% |
Losses: 1 Mb Gains: 2 Mb LOH/AOH: >5Mb Mosaicism: >20% (approximately) 400 genes at 100 kb resolution |
| Input DNA | ||||||
| 100 ng | 10-250 ng** | 100 ng | 100 ng | 10-250 ng** | 100 ng | 10-250 ng** |
| 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 |
6.85 million empirically selected probes for whole-genome coverage including: 6.5 million copy number probes 300,000 SNP probes for LOH analysis, due-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
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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 |
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 SNP probes for 178 variants across 36 genes such as SMN1 and SMN2 |
Whole genome coverage 315,000 features covering control, CNV and SNP probes -148,000 SNP probes for LOH analysis, duo-trio assessment, and sample tracking |
| Protocol | ||||||
| 2 days | 3-4 days | 4 days | 2 days | 3-4 days | 4 days | 2.5 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.
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For Research Use Only. Not for use in diagnostic procedures.