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. The 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 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

Datasheet

Learn about CytoScan 750K Accel Array

CytoScan 750K Array

High genome-wide resolution for the analysis of copy number gains and losses for prenatal 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)

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Datasheet

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

Learn about CytoScan HT-CMA Array Plate

Datasheet

CytoScan Optima

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

Learn more about CytoScan Optima

Datasheet

Product specifications

CytoScan HD Accel	CytoScan HD	CytoScan 750K Accel	CytoScan 750K	CytoScan HT-CMA	CytoScan Optima
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 cytogenetics 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	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; 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)	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	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	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	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	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.