Global-EXT6107-CytoScan Brochure - 112723
Global-EXT6107-CytoScan Brochure - 112723
Global-EXT6107-CytoScan Brochure - 112723
Powerfully efficient
cytogenetics analysis
Whole-genome hybrid-SNP array research solutions
The map reflects the number of labs worldwide using
Applied Biosystems™
Cytoscan™ cytogenetics suite.
Expansive whole-genome
cytogenetics research
Advancements in cytogenetic technologies are providing
clinical researchers with powerful new approaches
to investigate chromosomal aberrations such as
copy number variations (CNVs), chromosomal
imbalances, and allelic imbalances. However, test
methods such as karyotyping, optical genome mapping
(OGM), whole-exome sequencing (WES), whole genome
sequencing (WGS), and low-resolution arrays each
have constraints that can lead to missed aberrations
and delays or increased costs. Microarrays that include
the latest available content for both polymorphic and
nonpolymorphic regions of the entire genome with
fast assays and artificial-intelligence (AI)-enabled variant
identification can overcome some of these limitations and
potentially boost discovery yield.
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Contents
Boost efficiency and productivity in one
complete solution 4
3
Boost efficiency and productivity
in one complete solution
Complete chromosomal microarray (CMA) solution
for genome-wide copy number analysis
Identify aneuploidies, microdeletions, microduplications, and
other types of chromosomal aberrations across the genome
quickly and easily. The Applied Biosystems™ CytoScan™
arrays and Applied Biosystems™ OncoScan™ arrays offer a
highly reliable, consistent, and sensitive genome-wide
approach for high-resolution DNA copy number analysis.
Quickly detect gains and losses that may indicate loss of
heterozygosity (LOH), absence of heterozygosity (AOH),
copy-neutral loss of heterozygosity (cnLOH), uniparental
disomy (UPD), regions identical by descent, and mosaicism.
Flexible throughput DNA Automated array Fully integrated, automated Genome-wide view and
Flexible throughput Automated array Fully integrated, automated Genome-wide view and
amplification, fragmentation, hybridization, washing, array scanning analysis of chromosomal
DNA amplification, hybridization, washing, array scanning analysis of chromosomal
and labeling and staining aberrations, SNP variants,
fragmentation, a nd and staining aberrations, SNP variants,
and copy number
labeling and copy number
determinations
determinations
Figure 1. The robust workflow is aligned with your research laboratory workflow requirements, with intuitive processes to
streamline data analysis and reporting.
CytoScan 750K
CytoScan HD
CytoScan HD Accel
OncoScan
CytoScan HT-CMA
CytoScan XON
Figure 2. Applied BioSystems microarrays enable a wide range of cytogenetics research application areas.
SNP analyses are also used for: • Postnatal genetic testing helps clinical researchers study
• Breakpoint determination congenital anomalies, diseases, and developmental delays
following birth.
• Mendelian consistency checking
• Product of conception (POC) genetic testing of fetal tissue
• Confirmation of CNV events after the loss of a pregnancy helps clinical researchers study
chromosomal anomalies associated with miscarriage.
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Boost productivity with tailored
cytogenetic analysis
Constitutional applications
Select a CytoScan hybrid-SNP array that is tailored to your application
and detection sensitivity requirements. CytoScan assays feature Scientific spotlight:
Applied Biosystems GeneChip cartridge microarrays designed
™ ®
Learn why GeneDx, a leader
specifically for prenatal and postnatal research applications.
in testing for rare genetic
CytoScan arrays are manufactured using photolithography disorders, switched to high-resolution
technology, which produces arrays with very high batch-to-batch
whole-genome CMAs for prenatal
reproducibility without probe dropouts that are inherent in some
other array manufacturing techniques. and postnatal research applications.
• CMA is the recommended first line test by ACMG guidelines
and is used by the cytogenetics community worldwide[2,3]. “The hybrid SNP microarray
Detect chromosomal aberrations at high resolution with a
•
genome-wide, gene-centric design containing high density requires less DNA. This is
SNP and CNV probes.
especially good for buccal
• Analyze your data with the powerful and intuitive ChAS software
with enhanced analysis features, included free-of-charge. and uncultured prenatal
• Boost your discovery yield with the evidence-based CytoScan
AIR solution.
samples. We have been able
to reduce the amount of
Hybrid-SNP array: A practical approach to sample necessary by 40%.
complex problems in era of NGS
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Table 1. CytoScan Suite specifications
Research
applications
Fast turnaround High genome-wide High genome- Low-cost genome- High-throughput, Sensitive, high
with latest available resolution of CNVs wide resolution wide platform to cost-effective, coverage, whole
content for prenatal, for applications to analyze copy detect aneuploidies genome-wide copy genome, single
postnatal, and in prenatal and number gains and and copy number number analysis exon-level copy
oncology research postnatal research losses for prenatal losses and gains for constitutional number analysis.
and postnatal at lower resolution, cytogenetics Use as a stand-
research optimized for research and alone research
constitutional testing of relevant tool or to confirm
cytogenetics SNP variants CNV findings
research with alternative
technologies like
next generation
sequencing
Sample types Blood, buccal Blood, buccal Blood, buccal Blood, uncultured Blood, buccal Blood (Custom-
swabs, saliva, swabs, saliva, swabs, saliva, or cultured cells, swabs, saliva, built reference
uncultured or uncultured or uncultured or chorionic villi, uncultured file enables other
cultured cells, cultured cells, cultured cells, amniocytes, and or cultured cells, sources of DNA)
chorionic villi, chorionic villi, chorionic villi, POC chorionic villi,
amniocytes, POC, amniocytes, amniocytes, amniocytes,
and fresh, frozen, and POC and POC and POC
or FFPE tissue
Input DNA 100 ng 10–250 ng** 10–250 ng** 10–250 ng** 100 ng 100 ng
Probe 2.8 million markers 2.67 million markers 750,000 markers Whole genome 750,000 markers 6.85 million
structure for whole genome for whole genome for whole genome coverage for whole genome empirically selected
coverage coverage coverage coverage probes for whole-
315,000 markers
genome coverage
2 million 1.95 million 550,000 covering control, 550,000
including:
nonpolymorphic nonpolymorphic nonpolymorphic CNV and SNP nonpolymorphic
markers markers markers probes markers 6.5 million copy
number probes
~750,000 SNP ~743,000 SNP ~200,000 SNP ~148,000 SNP ~200,000 SNP
probes for LOH/ probes for LOH/ probes for LOH probes for LOH probes for LOH ~300,000 SNP
AOH analysis, duo- AOH analysis, duo- analysis, duo-trio analysis, duo-trio analysis, duo-trio probes for LOH
trio assessment, trio assessment, assessment, and assessment, and assessment, and analysis, duo-trio
and sample and sample sample tracking sample tracking sample tracking. assessment, and
tracking tracking sample tracking
SNP probes for 178
variants across 36
genes
Protocol 2 days 3–4 days 3–4 days As little as 2.5 days 4 days 4 days
Click on
each icon to
download
datasheets
*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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Oncology applications The new Applied Biosystems™ CytoScan™ HD Accel Array
Unlike constitutional applications of microarray analysis, which incorporates updated coverage in more than 5000 regions
are performed on whole blood samples, microarray analysis of as categorized by industry databases. The two-day assay
solid tumors is challenging because tumor tissues are typically workflow and lower input sample requirement help boost
formalin fixed and paraffin embedded (FFPE). laboratory efficiency.
CytoScan HD Suite for hematologic OncoScan assays for solid tumors research
malignancies research OncoScan assays are whole-genome copy number assays
Capture chromosomal abnormalities and genomic instability, designed to detect structural variants that are not well
which can be some of the most important aberrations in characterized by short-read sequencing or targeted sequencing.
tumors. The CytoScan HD Suite assay is designed with
Detect deletions, duplications, LOH, cnLOH, breakpoint
2.67 million markers for copy number analysis, facilitating
determination, ploidy, mosaicism, and unbalanced translocations
comprehensive coverage at the exceptional resolution so you
with Applied Biosystems™ OncoScan™ CNV assay and Applied
do not miss important aberrations.
Biosystems™ OncoScan™ CNV Plus Assay (previously known as
Applied Biosystems™ OncoScan™ FFPE Assay).
Allele difference
CytoScan HD Suite:
a comprehensive solution Smooth signal
for analyzing karyotypes in
hematological malignancies
Figure 4.
Chromothripsis
detected on
Log2 ratio chromosome 18
Watch now using CytoScan HD
arrays (top) and on
Allele difference chromosome 19
Webinar: Exploring the using OncoScan
genetic landscape of solid B allele frequency
arrays (bottom),
revealed by the
tumors using whole-genome sequential copy
number changes
copy number analysis and the multiple
breakpoints seen in
the different tracks.
Table 2. Suite specification for oncological clinical research sample profiling solutions
Research application High resolution analysis of genome High resolution analysis, up to 50 kb in top Fast turnaround with latest
wide CNVs in liquid and solid tumors cancer genes and 300 kb across the whole available content for prenatal,
genome in FFPE and fresh frozen tissues postnatal, and oncology research
Sample types Blood, bone marrow, and fresh and FFPE, fresh and frozen tissue Blood, bone marrow, and fresh,
frozen tissue frozen, or FFPE tissue
Probe structure 2.67 million markers for whole 220,000 molecular inversion probes (MIPs) 2.8 million markers for whole
genome coverage for whole genome coverage genome coverage
1.95 million nonpolymorphic markers 5,700 non-polymorphic probes 2 million nonpolymorphic markers
~743,000 SNP probes for LOH/AOH 216,000 SNP probes ~750,000 SNP probes for
analysis and sample tracking LOH/AOH analysis, duo-trio
assessment, and sample tracking
Click on each
icon to download
product literature
*OncoScan CNV Plus Assay includes somatic mutation panel covering 64 mutations in 9 genes (BRAF, EGFR, IDH1 and 2, KRAS, NRAS, PIK3CA, PTEN, and TP53)
**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.
†Mosaicism in cancer is classified by % aberrant cells in the sample and is called in ChAS software.
‡250 ng is optimal but users have reported success using as little as 10 ng starting DNA.
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Enhance efficiency with fully integrated
array processing
Streamline analysis,
interpretation, and reporting
for challenging genes
View and analyze chromosomal aberrations across the
genome, including copy number gain or loss, LOH, and
mosaicism. Developed with input from our customers and
leading experts, Applied BiosystemsTM Chromosome
The Applied Biosystems™ GeneChip™ System 3000 is a fully Analysis Suite (ChAS) software is designed
integrated platform to boost your research productivity using specifically for analysis and reporting in chromosomal
CytoScan or OncoScan arrays. aberration research. Enhanced, intuitive features simplify
cytogenetics investigation.
The GeneChip System 3000 combines advanced design and
automation to deliver high resolution scanning with minimized
Key features
hands-on time. This comprehensive system includes the Applied
• Whole-genome support for CytoScan Suite
Biosystems™ GeneChip™ Scanner 3000 7G, Applied Biosystems™
GeneChip™ Fluidics Station 450, Applied Biosystems™ GeneChip™ • CN state for CytoScan Suite
Hybridization Oven 645, and a powerful computer workstation • LIMS APIs
installed with instrument control software.
• Analyze data at different levels of resolution
The pre-assembled internal autoloader helps enable complete
• Automatically prioritize segmented data using scoring
walk-away freedom for scanning your arrays and supports more
inspired by the ACMG
efficient installation. The GeneChip Scanner 3000 7G uses a
solid-state laser so it needs no external laser power supply or • Customize and load your own annotations and regions for
focused analysis
special cooling system and fits easily into a laboratory benchtop.
Accurate gridding improves data integrity. Highly consistent • Store, query, and display historic sample data and
scanner-to-scanner performance facilitates data sharing annotations for streamlined analysis
among collaborators. • Directly access NCBI, UCSC Genome Browser, DECIPHER,
ClinVar, ClinGen, Ensembl, and OMIM databases and others
Highlights • Export user-selected data in formats like browser extensible
• Higher-resolution scanning from 0.51 to 2.5 μm pixels data (BED), Applied Biosystems™ Affymetrix™ extensible data
automatically selected by array type (AED), and variant call format (VCF) files
• Optimal image uniformity and collection efficiency • APIs to push and pull segment coordinates in and out of
across the entire scan area with proprietary Applied ChAS software
Biosystems™ Flying Objective™ Lens technology
• Automatic results file generation with zero manual
• Complete walk-away scanning of up to 48 arrays at set-up required
a time with pre-assembled autoloader
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Routine-use
Laboratory Assay training Software
Planning Installation service
preparation and proficiency training
and support
Maximize your CytoScan expertise for greater at Thermo Fisher Scientific, including technical sales specialists,
laboratory efficiency field service engineers, field application scientists, and clinical
Our commitment to your success in cytogenetics research application consultants, support you with comprehensive
goes beyond tools and technologies. Leverage our support from initial planning to routine implementation.
comprehensive onboarding service and support offerings
for the CytoScan Suite solution to maximize your expertise
and minimize the time needed to ramp up your cytogenetics
Contact a Chromosome
research investigations. The team of experienced professionals
Microarray specialist
Ordering information
Product Description Cat. No
CytoScan HD Accel
CytoScan HD Accel Kit Plus 24 Arrays and reagents for 24 reactions with amplification kit 952465
CytoScan HD Accel Kit Plus 96 Arrays and reagents for 96 reactions with amplification kit 952466
CytoScan HD Accel Array Kit and Arrays and reagents sufficient for 24 reactions 952460
Reagent Kit Bundle
CytoScan HD Accel Training Kit Arrays and reagents sufficient for 24 reactions to perform 952461
assay training
CytoScan HD
CytoScan HD Kit Plus 24 Arrays and reagents sufficient for 24 reactions and CytoScan 905824
Amplification Kit sufficient for 96 reactions
CytoScan HD Kit Plus 96 Arrays and reagents sufficient for 96 reactions and CytoScan 905896
Amplification Kit sufficient for 96 reactions
CytoScan HD Array Kit and Reagent Arrays and reagent sufficient for 24 reactions plus training materials 901835
Kit Bundle
CytoScan HD Training Kit Arrays and reagent sufficient for 24 reactions plus training materials 901834
CytoScan 750K
CytoScan 750K Kit Plus 24 Arrays and reagents sufficient for 24 reactions and CytoScan 905924
Amplification Kit sufficient for 96 reactions
CytoScan 750K Kit Plus 96 Arrays and reagents sufficient for 96 reactions and CytoScan 905996
Amplification Kit sufficient for 96 reactions
CytoScan 750K Array and Reagent Arrays and reagent sufficient for 24 reactions 901859
Kit Bundle
CytoScan 750K Training Kit Arrays and reagent sufficient for 24 reactions plus training materials 901860
CytoScan Optima
CytoScan Optima Kit Arrays and reagent sufficient for 24 reactions 902533
CytoScan Optima Training Kit Arrays and reagent sufficient for 24 reactions plus training materials 902534
CytoScan HT-CMA
CytoScan HT-CMA 96F Assay Kit Arrays and reagent sufficient for 96 reactions 906025
CytoScan HT-CMA 96F Assay Training Kit Arrays and reagent sufficient for 96 reactions plus training materials 906027
CytoScan XON
CytoScan XON Assay Kit Arrays and reagent sufficient for 24 reactions 931311
CytoScan XON Assay Training Kit Arrays and reagent sufficient for 24 reactions plus training materials 931312
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Ordering information continued
Product Description Cat. No
OncoScan
OncoScan CNV Plus Assay Arrays and reagent sufficient for 24 reactions 902293
OncoScan CNV Plus Training Kit Arrays and reagent sufficient for 18 reactions plus training materials 902305
OncoScan CNV Assay Arrays and reagent sufficient for 24 reactions 902695
OncoScan CNV Training Kit Arrays and reagent sufficient for 18 reactions plus training materials 902693
Analysis software
Chromosome Analysis Suite (ChAS) Available as a free download from thermofisher.com/chas NA
24 tokens 00.1001
CytoScan Automated Interpretation and
96 tokens 00.1003
Reporting (AIR) Tokens
384 tokens 00.1004
Support products
Reproductive Health Research Analysis Available as a free download from thermofisher.com/chas NA
Suite (RHAS)
GeneChip System 3000 Includes: 00-0218
GeneChip Scanner 3000 with AutoLoader
GeneChip Fluidics Station 450
GeneChip Hybridization Oven 645i
Workstation with GeneChip Data Collection Software
GeneChip Fluidics Station 450 Single station available for purchase separately from 00-0079
the GeneChip System 3000
GeneChip Hybridization Oven 645i Single unit available for purchase separately from 00-0331
the GeneChip System 3000
GeneTitan MC Fast Scan Instrument Automated array-processing instrument required to hybridize, 00-0373
wash, stain, and scan arrays
NIMBUS Target Preparation Instrument Robotics workstation and laptop 00-401
NIMBUS CytoScan Training Kit
™ ™
Sample preparation reagents to be used with robotics workstation 902169
References
1. Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril. 2018 Feb;109(2):201-212.
doi: 10.1016/j.fertnstert.2018.01.005. PMID: 29447663; PMCID: PMC5856154.
2. Manning M, Hudgins L; American College of Medical Genetics and Genomics (ACMG) Professional Practice and
Guidelines Committee. Addendum: Array-based technology and recommendations for utilization in medical genetics
practice for detection of chromosomal abnormalities. Genet Med. 2020 Dec;22(12):2126. doi: 10.1038/s41436-
020-0848-8. Epub 2020 Jun 8. Erratum for: Genet Med. 2010 Nov;12(11):742-5. PMID: 32514088.
3. Shao L, Akkari Y, Cooley LD, Miller DT, Seifert BA, Wolff DJ, Mikhail FM; ACMG Laboratory Quality Assurance
Committee. Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021
revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021
Oct;23(10):1818-1829. doi: 10.1038/s41436-021-01214-w. Epub 2021 Jun 15. PMID: 34131312.
For Research Use Only. Not for use in diagnostic procedures. © 2023 Thermo Fisher Scientific Inc. All rights reserved. All
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