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PRODUCT BULLETIN
nCounter® PanCancer Panels Collection
nCounter® PanCancer Panels Collection
Pathway Deregulation • Immune Profiling • Cancer Progression
A COLLECTION OF GENE EXPRESSION PANELS DEVELOPED AROUND THE HALLMARKS OF CANCER
Sustaining
proliferative
signaling
Evading
growth
suppressors
Avoiding
immune
destruction
Deregulating
cellular
energetics
The PanCancer Panels
Collection
• nCounter PanCancer Pathways Panel
Understand basic cancer biology
Resisting
cell death
Hallmarks
of Cancer
Enabling
replacative
immorality
and pathway deregulation.
• nCounter PanCancer Immune Profiling Panel
Explore the immune response to cancer.
• nCounter PanCancer Progression Panel
Genome
instability &
mutation
Tumorpromoting
inflammation
Inducing
angiogenesis
Activating
invasion &
metastasis
REFERENCE The Hallmarks of Cancer. Originally published in Cell, 144,
Hanahan D & Weinberg RA, Hallmarks of Cancer: The Next Generation, 646–674,
Copyright Elsevier 2011.
The Hallmarks of Cancer are one of the most widely
recognized organizing principles for the holistic study of
cancer today. Its profoundly simple framework was first
introduced in 2000 by authors Douglas Hanahan and
Robert Weinberg and defines a distinct set of acquired
capabilities that distinguish cancer from normal tissue.
The Hallmarks help explain the complexities of cancer
by describing a common set of capabilities present in
cancer cells. These processes that, if unstopped, will allow
cancer cells to thrive and proliferate in the unique tumor
environment they create. This framework, represented in
the now famous Hallmarks of Cancer wheel, is often the
first roadmap researchers use to study all types of cancer.
Investigate cancer progression
and metastasis.
NanoString has embraced the Hallmarks of Cancer
philosophy and shares the vision to bring simplicity to
an otherwise extremely complex disease and to enable
productive research. Our collection of three nCounter
PanCancer Panels delivers a family of multiplex gene
expression assays to enable basic and translational research
into pathway deregulation studies, the emerging area of
immune profiling, and cancer progression.
Highlights of the PanCancer
Panel Collection
• Comprehensive coverage of all ten Hallmarks
of Cancer included in three distinct panels.
• >1,850 unique genes included across all panels.
• Customize with up to 30 additional
user-defined genes.
• Compatible with protein panels for
multi-omic assays.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
1
nCounter® PanCancer Panels Collection
PRODUCT BULLETIN
nCounter® PanCancer Panels Collection
Discover Connections • Discover Interactions • Discover Functions
The NanoString PanCancer panels provide researchers with our most highly-multiplexed gene expression panels and represent over 1,850 unique
genes. Designed for universal research of any cancer type.
Overlapping & Unique Content in the PanCancer Panels:
PANCANCER PATHWAYS PANEL
770 cancer pathways genes
PanCancer
Pathways
PanCancer Immune
Profiling
• 606 pathway genes for 13 canonical pathways
• 124 cancer driver genes
• 40 reference genes
PANCANCER IMMUNE PROFILING PANEL
770 cancer immune genes
• 24 different immune cell types
• 30 CT antigens
• > 500 genes covering innate and adaptive
immune response
• 40 reference genes
PANCANCER PROGRESSION PANEL
PanCancer Progression
770 cancer progression genes
ABOVE Human PanCancer Panels Venn diagram with >1,850 unique genes.
The genes shared between these panels are members of the PI3K, JAK-STAT,
and TGF- pathways, as well as normalization genes.
• 277 angiogenesis genes
• 269 epithelial-mesenchymal transition genes
• 254 extracellular matrix genes
• 173 metastasis genes
• 30 references genes
RNA:Protein Analysis
nCounter Panel-Plus
Simultaneous analysis of RNA and protein targets enable you to see
Customize PanCancer panels with the optional Panel-Plus feature,
more from a single sample. Measure both gene expression and cell
and add up to 30 of your preferred genes to create a panel that is
response from as few as 150,000 cells (up to 500,000 cells for PBMCs
uniquely your own.
and primary cells). The nCounter Protein Plus PanCancer Immune
Profiling Panel includes 30 immunology-related protein targets that
can be used with any PanCancer Gene Expression Panel.
Single Cell Analysis
All PanCancer panels are also available in a single cell format. These
Protein Panels
nCounter Protein Plus
PanCancer Immune Profiling Panel
2
Number of Protein Targets
kits include validated primer pools for multi-target enrichment. Primer
pools are provided at no additional charge for the study of single cells
30
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
or for studies using low input samples.
NanoString Technologies
PRODUCT BULLETIN
Subtype
Binding.Density
Scanned.Date
OR13443
OR13457
OR13458
OR13452
OR11024
OR12918
OR11014
OR13231
OR13242
OR13567
OR13005
OR13014
OR12969
OR12968
OR13550
OR12881
OR1007
OR1004
OR1017
OR1020
OR1003
OR1013
OR1010
OR1006
OR1002
OR13465
OR13420
OR13379
OR13466
OR13392
OR13398
OR12892
OR13220
OR13247
OR12899
OR13542
OR12975
OR11012
OR13249
OR12858
OR13183
OR12917
OR13273
OR12890
OR12862
OR13208
OR12868
OR11013
OR13243
OR13241
OR12976
OR12878
OR13184
OR12686
OR12700
OR13397
OR13470
OR12707
OR12705
OR12721
OR13004
OR13449
OR13468
OR12908
OR13236
OR13380
OR13435
OR13440
OR13471
OR12952
OR12955
OR12888
OR13437
OR1107
OR12925
OR12971
OR12961
OR12963
OR12965
OR12854
OR13422
OR13462
OR12973
OR12911
OR13387
OR13476
OR12859
OR12967
OR13478
OR12872
OR12856
OR13229
OR11015
OR13412
OR1106
OR13414
OR12893
OR13228
OR13441
OR13403
OR12897
OR12895
OR12853
OR13258
OR13022
OR12712
OR13383
OR13381
OR13453
OR12903
OR12910
OR13489
OR13425
OR13444
OR13411
OR13385
OR12861
OR13275
OR1108
OR13433
OR13408
OR13442
OR12905
OR13199
OR12962
OR13233
OR13269
OR12879
OR13226
OR12974
OR13268
OR12870
OR13186
OR12904
OR12877
OR13187
OR12693
OR13061
OR13456
OR13430
OR11021
OR1109
OR13464
OR13009
OR12682
OR13212
OR12923
OR12921
OR13190
OR13544
OR13244
OR12715
OR13076
OR12866
OR12958
OR13215
OR12865
OR11023
OR12863
OR12914
OR13209
OR12966
OR13224
OR12884
OR13197
OR13245
OR12959
OR12696
OR13013
OR13206
OR12915
OR12889
OR13276
OR13399
OR13434
OR12902
OR12864
OR13054
OR13025
OR12926
OR13230
OR13402
OR12857
OR12694
OR13026
OR13203
OR12894
OR13223
OR12907
OR12852
OR13545
OR13390
OR13482
OR13211
OR12876
OR12887
OR13219
OR13388
OR13473
OR12916
OR13506
OR12855
OR13222
OR13432
OR11010
OR13188
OR12871
OR12954
OR12957
OR13416
OR13393
OR13474
OR13436
OR12882
OR12873
NanoString offers advanced software tools that address the continuous
demands of data analysis and help answer the specific biological
questions encompassed in our most popular PanCancer Panels.
PANCANCER PATHWAYS ADVANCED ANALYSIS
MODULE
• Score pathway deregulation with end-to-end analysis.
• Measure gene expression with 730 essential genes
representing all major cancer pathways including: Wnt,
OR13443
OR13457
OR13458
OR13452
OR11024
OR12918
OR11014
OR13231
OR13242
OR13567
OR13005
OR13014
OR12969
OR12968
OR13550
OR12881
OR1007
OR1004
OR1017
OR1020
OR1003
OR1013
OR1010
OR1006
OR1002
OR13465
OR13420
OR13379
OR13466
OR13392
OR13398
OR12892
OR13220
OR13247
OR12899
OR13542
OR12975
OR11012
OR13249
OR12858
OR13183
OR12917
OR13273
OR12890
OR12862
OR13208
OR12868
OR11013
OR13243
OR13241
OR12976
OR12878
OR13184
OR12686
OR12700
OR13397
OR13470
OR12707
OR12705
OR12721
OR13004
OR13449
OR13468
OR12908
OR13236
OR13380
OR13435
OR13440
OR13471
OR12952
OR12955
OR12888
OR13437
OR1107
OR12925
OR12971
OR12961
OR12963
OR12965
OR12854
OR13422
OR13462
OR12973
OR12911
OR13387
OR13476
OR12859
OR12967
OR13478
OR12872
OR12856
OR13229
OR11015
OR13412
OR1106
OR13414
OR12893
OR13228
OR13441
OR13403
OR12897
OR12895
OR12853
OR13258
OR13022
OR12712
OR13383
OR13381
OR13453
OR12903
OR12910
OR13489
OR13425
OR13444
OR13411
OR13385
OR12861
OR13275
OR1108
OR13433
OR13408
OR13442
OR12905
OR13199
OR12962
OR13233
OR13269
OR12879
OR13226
OR12974
OR13268
OR12870
OR13186
OR12904
OR12877
OR13187
OR12693
OR13061
OR13456
OR13430
OR11021
OR1109
OR13464
OR13009
OR12682
OR13212
OR12923
OR12921
OR13190
OR13544
OR13244
OR12715
OR13076
OR12866
OR12958
OR13215
OR12865
OR11023
OR12863
OR12914
OR13209
OR12966
OR13224
OR12884
OR13197
OR13245
OR12959
OR12696
OR13013
OR13206
OR12915
OR12889
OR13276
OR13399
OR13434
OR12902
OR12864
OR13054
OR13025
OR12926
OR13230
OR13402
OR12857
OR12694
OR13026
OR13203
OR12894
OR13223
OR12907
OR12852
OR13545
OR13390
OR13482
OR13211
OR12876
OR12887
OR13219
OR13388
OR13473
OR12916
OR13506
OR12855
OR13222
OR13432
OR11010
OR13188
OR12871
OR12954
OR12957
OR13416
OR13393
OR13474
OR13436
OR12882
OR12873
Subtype
Scanned.Date
pathway visualizations.
Binding.Density
• Generate follow-on research hypotheses using
EXAMPLE 1 Heatmap of the samples’ correlation matrix. Blue indicates low
correlation and red indicates high correlation
Hedgehog, Apoptosis, Cell Cycle, RAS, P13K, STAT, MAPK,
SubtypeD
Notch, TGF-, Chromatin Modification, Transcriptional
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Regulation and DNA Damage Control.
30
●
KIT
PANCANCER IMMUNE PROFILING ADVANCED
ANALYSIS MODULE
antigens and differential expression testing in minutes
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●UBE2T
PKMYT1
25
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H2AFX
●
MAML2
●
ERBB2
20
●
ITGA7
●
CCNB1
●
HIST1H3H
●
EZH2
●
INHBA
●
TTK
●
E2F1
●
HIST1H3B
IGF1
●
IL11RA
●
PDGFD
●
PPARG
LEPR
●●
RUNX1T1
●
CDKN1C
●
JUN
●
CDKN2C
●
ID4
●
●
SFRP1
15
estimation of immune cell abundance, detection of CT
●
LIFR
●
NTRK2
−log10(p−value)
• Set up wide-ranging exploratory analyses, including
●
CCNA2
●
SPRY2
with a simple wizard.
●
XPA
● ● ● ●
●
representing 16 different cancer immune cell types and
●
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5
• Measure gene expression with 730 essential genes
10
●
populations, major immune response categories, and 30
• Intuitive step-by-step wizard allows gene sets and cell
abundance analysis to be customized.
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common cancer testis antigens.
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COL11A1
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COMP
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PTTG2
FANCA
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RAD51
CDC25C
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● CDC6
CCNE2
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CDC25A
●
MYD88
●
−4
−2
0
2
p < 0.01
p < 0.001
4
Log(fold change)
EXAMPLE 2 Volcano plot of the comparison between two sets of samples
(shows fold change vs. log 10 p-value)
Advanced Analysis Capabilities:
• Normalization
• Single Gene Select
gene descriptions
• QC
(Immune Profiling)
• Pathway scoring
(Pathways)
• CT Antigen Expression
(Immune Profiling)
• Differential Expression
• Gene Set Analysis
• Built-in compatibility
• Pathview Plot Analysis
for Panel Plus analysis
• Cell type profiling
(Immune Profiling)
Advanced analysis modules provide an interactive .html report with
multiple layers of information along with pathway visualization maps
for generating follow-on hypotheses.
To access annotated demo data sets and details on how to use the
advanced analysis software please visit:
www.nanostring.com/products/nSolver
EXAMPLE 3 Pathview plot of differential expression between two sets of
samples in the TGF-Beta Pathway. Green indicates down-regulated genes,
red indicates up-regulated genes, and grey indicate genes that do not meet
the p-value threshold.
3
PRODUCT BULLETIN
nCounter PanCancer Panels Collection
®
Selecting Your Panel
Fully-annotated gene lists in Excel format are available online for each of the PanCancer panels. All gene lists include the official gene name, accession
number, alias, target sequence, and sortable annotations. The table lists some of the major gene categories or pathways along with the panel in which
they are best represented.
Category/Pathway
Number of Genes
Panel Name
Representative Hallmarks
Adaptive immunity
104
PanCancer Immune Profiling
Avoiding immune destruction
Angiogenesis
277
PanCancer Progression
Inducing angiogenesis
Cancer driver genes
124
PanCancer Pathways
—
Cell cycle and apoptosis
137
PanCancer Pathways
Resisting cell death
Chromatin modification
22
PanCancer Pathways
Genome instability and mutation
DNA repair
50
PanCancer Pathways
Genome instability and mutation
Epithelial-mesenchymal transition
269
PanCancer Progression
Activating invasion and metastasis
Extracellular matrix
254
PanCancer Progression
Activating invasion and metastasis
Hedgehog pathway
28
PanCancer Pathways
Resisting cell death
Humoral immunity
41
PanCancer Immune Profiling
Avoiding immune destruction
Inflammation
66
PanCancer Immune Profiling
Tumor-promoting inflammation
Innate immunity
200
PanCancer Immune Profiling
Tumor-promoting inflammation
JAK-STAT pathway
86
PanCancer Pathways
Sustaining proliferative signaling
MAPK pathway
157
PanCancer Pathways
Sustaining proliferative signaling
Metastasis
173
PanCancer Progression
Activating invasion and metastasis
Notch pathway
24
PanCancer Pathways
Enabling replicative immortality
PI3K pathway
201
PanCancer Pathways
Deregulating cellular energetics
RAS pathway
142
PanCancer Pathways
Sustaining proliferative signaling
TGF-pathway
51
PanCancer Pathways
Evading growth suppressors
Transcriptional misregulation
101
PanCancer Pathways
Genome instability and mutation
Wnt pathway
78
PanCancer Pathways
Enabling replicative immortality
For gene lists describing the content of each of our PanCancer panels, please visit: www.nanostring.com/products
NanoString Technologies, Inc.
CONTACT US
530 Fairview Ave N
Seattle, Washington 98109
[email protected]
United States: [email protected]
Tel: (888) 358-6266
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Fax: (206) 378-6288
Asia Pacific & Japan:[email protected]
www.nanostring.com
Other Regions:
SALES CONTACTS
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© 2016 NanoString Technologies, Inc. All rights reserved. NanoString, NanoString Technologies, the NanoString logo, nCounter, and nSolver are trademarks or registered trademarks
of NanoString Technologies, Inc., in the United States and/or other countries. The manufacture, use and or sale of NanoString product(s) may be subject to one or more patents or
pending patent applications owned by NanoString or licensed to NanoString from Life Technologies Corporation and other third parties.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures. April 2016 USSC_PM0025-v1g