Microarrays for Prenatal Genetic Research

Make confident decisions with trusted microarray solutions, from samples to insights

Microarrays are an ideal platform for copy number variation (CNV) analysis and molecular cytogenetic research. American College of Obstetricians and Gynecologists (ACOG) proposes that CMA be used as the primary prenatal genetic analysis method of choice. This is based on the major advantage of CMA over standard karyotyping in terms of discovery yield.

 

Applied Biosystems CytoScan microarrays offer a reliable genome-wide approach for high-resolution DNA copy number analysis to study 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, help 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 time and money, while delivering quality performance consistent with your laboratory requirements. 

Workflow

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

 

Our complete microarray research 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 prenatal 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

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 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 study 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

Product specifications


CytoScan HD Accel

CytoScan HD

CytoScan XON
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 exceptional coverage within exons across the whole genome. Use as a standalone research tool or to confirm CNV findings with alternative technologies like next generation sequencing
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
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 relevant genes
Input DNA
100 ng 10-250 ng** 100 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
Protocol
2 days 3-4 days 4 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.

Ordering information

For Research Use Only. Not for use in diagnostic procedures.