The DNAscope Assay
Copy Number Variation, Gene Deletions, Viral Integration
DNAscopeTM DUPLEX ASSAY SPATIAL IS IN OUR DNA
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Sample 3 (break-apart negative)
Sample 4 (break-apart positive)
Sample 2 (break-apart positive)
Sample 1 (break-apart negative)
BRINGING MOLECULAR CYTOGENETIC ANALYSIS TO YOUR BENCH CHROMOGENIC DETECTION OF DNA FOR EASE OF VISUALIZATION
For accurate and reliable detection of DNA aberrations current commercial FISH techniques fall short on morphological detail due to the use of fluorescent nuclear staining and rely on expensive high-resolution microscopes to visualize gene rearrangement and copy number variation signals. Additionally, use of Bacterial Artificial Chromosome (BAC) clone-based probes that are large and tend to span multiple genes, lack single gene detection specificity limiting the scale and development of DNA research
To overcome these limitations, we are introducing a new chromogenic DNA in situ hybridization (ISH) technology. DNAscopeTM employs the proven “double-Z” probe design and signal amplification system of RNAscope®, enabling rapid and flexible probe development for any DNA target enabling visualization of target in paraffin embedded tissues.
SIMPLIFIED WORKFLOW FOR RAPID RELIABLE DNA DETECTION
The DNAscope chromogenic duplex (red/blue) staining allows researchers to use a standard bright-field microscope to visualize and quantify gene copy number variations (amplifications/deletions) and gene rearrangements/fusions in tissues at with spatial and morphological context at single cell resolution.
Tissue Section
Start with properly prepared tissue sections
and pretreat to allow access to target DNA
Hybridize to target DNA
Hybridize two sets of target specific ZZ probes
to two DNA targets
Amplify Signal
Capture a cascade of signal amplification molecules into each
target via hybridization
Image at 40x
Visualize target DNA using a standard
bright-field microscope
DNA 1 DNA 2
Target DNA-specific aligo probes
Pre-Amp Amp label probe
Sample 2 tumor appeared to be positive for ROS1 gene rearrangement indicated by break-apart event visualized as bright blue dots.
Sample 4 tumor appeared to be positive for ALK gene rearrangement indicated by break-apart event visualized as bright blue dots.
R O
S 1
-C 1
/R O
S 1
-C 2
A LK
-C 1
/A LK
-C 2
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KEY ADVANTAGES
DUPLEX ASSAY ENABLES DETECTION OF ANY DNA COPY NUMBER OR STRUCTURAL ALTERATIONS DETECTION OF COPY NUMBER VARIATION
Brightfield Visualization enabling
Easy data Interpretation and Analysis
Signal Amplification for high sensitivity and
signal to noise ratio
High resolution and Precise target Detection
for small genomic regions/single gene locus
Rapid custom probe design capability and
universal assay conditions
MDAMB231 (negative for ERBB2 amplification)
ERBB2-C1/CEP17q-C2 CDKN2A-C1/CEP9q-C2
BT474 (positive for ERBB2 amplification)
MDA-MB-231 (positive for CDKN2A deletion)
SKBR3 (negative for CDKN2A deletion)
CEN17
CEP17
Chr 17ERBB2
Target
CEN9
CEP9
Chr 9CDKN2A
Target
ERRBB2 unamplified ERRBB2 amplified CDKN2A wildtypeCDKN2A deleted
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DETECTION OF BREAK-APART EVENTS
Control Wild type ALK (fused signals)
ALK Rearrangements
(Break-apart signals)
BREAK-APART EVENTS ARE DETECTED THROUGH APPEARANCE OF PURE BLUE DOTS
EML4 Chr2ALK
5’ probe 5’ probe3’ Probe
Break point Break point
ALK EML4 ALK EML4
3’ Probe
Break point Break point
KEY ADVANTAGES • High resolution
Detect small genomic regions/single gene locus
• Unparalleled performance Much larger dot size as compared to both FISH & CISH signal
• Easy Interpretation and Data Analysis Permanent chromogenic signal and superior morphological context
APPLICATIONS- think of better title here
DETECTION OF COPY NUMBER VARIATION
DETECTION OF BREAK-APART EVENTS
KEY ADVANTAGES • High resolution
Detect small genomic regions/single gene locus
• Unparalleled performance Much larger dot size as compared to both FISH & CISH signal
• Easy Interpretation and Data Analysis Permanent chromogenic signal and superior morphological context
APPLICATIONS- think of better title here
DETECTION OF COPY NUMBER VARIATION
DETECTION OF BREAK-APART EVENTS
ALK WT BREAK-APART NEGATIVE CELL LINE HS-ALK-BA-5’ / HS-ALK-BA-3’
ALK BREAK-APART POSITIVE CELL LINE HS-ALK-BA-5’ / HS-ALK-BA-3’
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PRODUCT INFORMATION
TARGET PROBES
GENE NAME PROBE NAME CATALOG NUMBER
ERBB2 (HER2) DS-Hs-ERBB2-C1 1080031-C1
EGFR DS-Hs-EGFR-C1 1080041-C1
MET DS-Hs-MET-C1 1080051-C1
TP53 DS-Hs-TP53-C1 1080061-C1
CDKN2A DS-Hs-CDKN2A-C1 1080071-C1
ALK DS-Hs-ALK-BA5-C1 1080081-C1
ALK DS-Hs-ALK-BA3-C2 1080091-C2
ROS1 DS-Hs-ROS1-BA5-C1 1080101-C1
ROS1 DS-Hs-ROS1-BA3-C2 1080111-C2
NTRK1 DS-Hs-NTRK1-BA5-C1 1080151-C1
NTRK1 DS-Hs-NTRK1-BA3-C2 1080161-C2
NTRK2 DS-Hs-NTRK2-BA5-C1 1080171-C1
NTRK2 DS-Hs-NTRK2-BA3-C2 1080181-C2
NTRK3 DS-Hs-NTRK3-BA5-C1 1080191-C1
NTRK3 DS-Hs-NTRK3-BA3-C2 1080201-C2
CONTROL PROBES
GENE NAME PROBE NAME CATALOG NUMBER
CEP3q DS-Hs-CEP3q-C2 1080211-C2
CEP7q DS-Hs-CEP7q-C2 1080221-C2
CEP9q DS-Hs-CEP9p-C2 1080231-C2
CEP12p DS-Hs-CEP12p-C2 1080241-C2
CEP17q DS-Hs-CEP17q-C2 1080251-C2
PRODUCT NAME DESCRIPTION CATALOG NUMBER
DNAscope™ HD Duplex Reagent Kit
• Contains DNAscope™ HD Duplex Detection- Reagents
• DNAscope Pretreatment Reagents Kit
• 50x wash buffer
324700
• mRNA or lncRNA target (>300nt)
• 1-plex or Duplex chromogenic: Automated and Manual
• Up to 4-plex fluorescence: Automated and Manual
• Up to 48-plex fluorescence: Manual
• Splice variants, short/ highly homologous sequences, and point mutations (50-300nt)
• 1-plex chromogenic: Automated and Manual
• Duplex chromogenic: Manual
• New probe design strategy
• ASOs, miRNAs, siRNAs, and other smaller RNA sequences (17-50nt)
• 1-plex chromogenic: Automated and Manual
• Leverage the ZZ design strategy
• Utilize 2 orthogonal signal amplification systems to detect 2 RNA targets
• Application focus on break-apart and copy number variation
• Validated menu of probes
• Duplex chromogenic assay
DNAscopemiRNAscopeBaseScopeRNAscope
BIO-TECHNE SPATIAL ANALYSIS PORTFOLIO
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NOTES
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NOTES
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