CytoScan™ HT-CMA 96F Assay Kit
CytoScan™ HT-CMA 96F Assay Kit
Applied Biosystems™

CytoScan™ HT-CMA 96F Assay Kit

The Applied Biosystems CytoScan HT-CMA 96F Assay Kit enables the detection of chromosomal abnormalities such as deletions, duplications, and uniparentalRead more
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Catalog NumberQuantity
90602596 reactions
Catalog number 906025
Price (CNY)
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Quantity:
96 reactions
The Applied Biosystems CytoScan HT-CMA 96F Assay Kit enables the detection of chromosomal abnormalities such as deletions, duplications, and uniparental disomy (UPD), and does so in a high-throughput, automated format. The assay is designed for use with genomic DNA from blood or amniotic fluid samples. Please see the CytoScan HT-CMA Assay Training Kit for arrays, reagents, and sample plates sufficient for the FAS led training week as well as the following proficiency run.

Features of the CytoScan HT-CMA 96F Assay Kit include:
• Consolidated testing with a dual CNV and SNV design
• Increased sample throughput with a fully automated assay protocol
• Fast and easy high-resolution genome-wide copy number analysis with the free Chromosome Analysis Suite software

High-resolution genome-wide copy number and SNV analysis in one
The CytoScan HT-CMA assay enables cytogenetic researchers to detect and analyze relevant chromosomal aberrations with confidence. The assay provides high-resolution coverage of OMIM and DECIPHER genes, along with high-density SNP coverage for loss of heterozygosity (LOH) and UPD detection. The CytoScan HT-CMA assay also includes up to 178 relevant single nucleotide variants (SNV) and content for analysis of SMN1, which allows for consolidation of testing.

High-throughput array format and full automation
Bring consistency to your cytogenetic analysis and free up technician time with the fully automated CytoScan HT-CMA assay. Preparation of gDNA for hybridization onto the arrays is automated on the NIMBUS Target Preparation Instrument, with automated array processing occurring on the GeneTitan MC Instrument.

Chromosome Analysis Suite-designed for cytogenetic applications
The popular Chromosome Analysis Suite (ChAS) software is available free of charge as part of the CytoScan HT-CMA assay. ChAS software is tailored to cytogenetic research analysis and reporting with:
• Streamlined analysis and reporting workflow
• Ability to apply customized filters to analyze the genome at different levels of resolution
• Options to create, modify, and upload annotation files and flag regions for focused analysis
• A database for storage, query, and visualization of samples
• Direct access to external databases such as NCBI, UCSC Genome Browser, Ensembl, and OMIM
• Trio consistency checking for parental studies

The new standard in high-throughput cytogenetic analysis
The combined high resolution DNA copy number data and the ability to screen a panel of SNVs on a single array makes the CytoScan HT-CMA assay the new standard for high throughput cytogenetics analysis.

For Research Use Only. Not for use in diagnostic procedures.
Specifications
For Use With (Application)Microarray Analysis
Number of Markers1162042
Product LineApplied Biosystems™
Quantity96 reactions
Shipping ConditionApproved for shipment at Room Temperature or on Wet or Dry Ice
TypeHT-CMA 96F Assay Kit
ArrayTissue
FormatArray Plate
Number of Arrays96 arrays
SpeciesHuman
Unit SizeEach
Contents & Storage
• 1 MOD 1, store at -20°C
• 1 MOD 2-1, store at -20°C
• 1 MOD 2-2, store at 4°C
• 1 MOD 3-1, store at -20°C
• 1 MOD 3-2, store at 4°C
• 2 Wash A, store at room temp
• 1 Wash B, store at room temp
• 1 Water, store at room temp
• 1 96F HT-CMA array plate, store at 4°C
• 1 GTMC consumable kit, store at room temp

Frequently asked questions (FAQs)

What are the QC metrics for the CytoScan HT-CMA assay and what does each metric indicate?

Copy Number QC Metrics:
a. SNPQC ≥ 10 - SNPQC is a measure of how well genotype alleles are resolved in the microarray data.
b. MAPD ≤ 0.28 - A global measure of the variation of all microarray probes across the genome. It represents the median of the distribution of changes in Log2 Ratio between adjacent probes. Since it measures differences between adjacent probes, it is a measure of short range noise in the microarray data.
c. Waviness SD ≤ 0.07 - A global measure of variation of microarray probes that is insensitive to short-range variation and focuses on long-range variation.

Genotyping QC Metrics:
a. DQC ≥ 0.88 - DQC is a single-sample measure of "interference" between foreground and background signal distributions. It is independent of other samples in the analysis run. Values range from 0 to 1, with higher values being better. Water is ~0.05 and 'bad' sample or assay problems center around 0.5.
b. QC Call Rate ≥ 98.5% - A metric computed over a representative set of well-behaved probe sets. Low QC call rate over well-behaved probe sets suggest problems with sample quality. Samples with low QC call rate but high DQC values are consistent with sample contamination. Monitor DQC values by plate and time to detect problem trends and problem plates.

SMN metrics:
a. MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.
b.MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Does the CytoScan HT-CMA assay have 100% concordance with CytoScan 750k?

No, HTCMA and 750k have different array designs. Some regions have higher probe coverage on HTCMA than on 750k and vice versa, so some aberrations may be called differently (such as different break points).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

With the CytoScan HT-CMA assay, how can I feel confident in reporting variants that have not been verified?

For unverified content, the reporting on variants is a user's decision. Users can do cross-platform testing, for example TaqMan assay/Sanger sequencing to verify the mutation.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

In the CytoScan HT-CMA assay, why are not all 181 variants verified?

While the Cytoscan HT-CMA assay covers >180 structural and sequence variants, some of the mutations are extremely rare. Therefore, it is extremely challenging to get the positive clinical samples to verify the content of all the variants.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

For the CytoScan HT-CMA assay, what control should I add to the plate?

The CytoScan HT-CMA 96F Assay Kit does not include a control. A positive control should be identified by the user and used during training and proficiency runs to generate a baseline for the control's performance. Ref103 can be purchased separately if desired (Cat. No. 951957).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.