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)

Datasheet

Learn about CytoScan HD Accel Array

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

Learn about CytoScan HD Array

Datasheet

Learn about microarrays for in vitro diagnostic use

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

Learn about CytoScan XON Array

Download datasheet

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.