In this presentation we showcase the latest advancements in myeloid genomic profiling: The Ion Torrent Oncomine Myeloid Assay GX. Learn how this solution addresses key challenges in myeloid molecular testing and see recent data from the University of Pennsylvania. Learn more at www.oncomine.com/myeloid

1. The world leader in serving science
A New Day for Myeloid Genomic Profiling
How NGS Advancements Are Providing Deeper Insight
with Faster Time to Results
For Research Use Only. Not for use in diagnostic procedures.

2. 2 For Research Use Only. Not for use in diagnostic procedures.
Welcome
Dr. Andy Felton Dr. Kojo Elenitoba-Johnson
Vice President of Product Management
Clinical Next-Generation Sequencing
Thermo Fisher Scientific
Peter C. Nowell, M.D., Professor, University of Pennsylvania
Perelman School of Medicine
Director, Center for Personalized Diagnostics
Director, Division of Precision and Computational Diagnostics

3. 3 For Research Use Only. Not for use in diagnostic procedures.
Myeloid Testing Challenges
Genetically
complex
Heterogeneous cell
populations
Potential for rapid
proliferation
Rapidly growing list
of biomarkers
Myeloid samples can be challenging for molecular analysis
Labs need:
A streamlined approach for profiling a
growing list of relevant biomarkers
Results to be available at rapid speeds
(1–2 days)

4. 4 For Research Use Only. Not for use in diagnostic procedures.
Current Research Testing Paradigm
This approach is becoming infeasible as the number of relevant biomarkers continually increases
Sanger
sequencing/
qPCR
qPCR
FISH
NGS
outsourcing
• FLT3
• NPM1
• IDH1/2
• BCR-ABL
• JAK
• Multi-gene DNA
and RNA panels
• PML-RARA
• BCR-ABL
Laborious
Inefficient
Time-consuming workflows
Losing control of samples
to NGS outsourcing
Multiple weeks for all test results
Current methodology: serial testing with multiple assays and methods

5. 5 For Research Use Only. Not for use in diagnostic procedures.
A Disruptive Technology: Next-Generation Sequencing (NGS)
Rapid Efficient High sensitivity High specificity Novel variants
One test All key biomarkers Multiple samples
for across
PML-RARA
FLT3-ITD
CALR
KIT
TP53
NPM1
RUNX1
BCR-ABL
JAK2
IDH1
IDH2
MPL
ASXL1 + more

6. 6 For Research Use Only. Not for use in diagnostic procedures.
Traditional Challenges with Implementing NGS in Many Laboratories
Too slow Too complex Too costly
High level of user expertise required
to run NGS
Modular workflows requiring multiple
instruments and touchpoints
Requires many days and often
weeks to get the results
Cost of hiring and training staff
Cost penalty for running small
sample batches

7. 7
Welcome to a New Day for Myeloid Genomic Profiling

8. 8 For Research Use Only. Not for use in diagnostic procedures.
* Specimen-to-report workflow will be available after the Ion Torrent™ Genexus™ Purification System
and integrated reporting capabilities are added in 2021.
Ion Torrent™ Oncomine™ Myeloid Assay GX on the Ion Torrent™ Genexus™ System*
1-day turnaround time
Flexible sample batching
Automated workflow from specimen to report*
Integrated reporting
Simultaneously profiling of DNA mutations + RNA fusion transcripts

9. 9 For Research Use Only. Not for use in diagnostic procedures.
Oncomine Myeloid Assay GX
* Specimen-to-report workflow will be available after the Genexus Purification System and integrated reporting capabilities are added in 2021.
Get rapid results for FLT3-ITD, TP53, NPM1, IDH1, IDH2
PML-RARA, and other biomarkers in 1 day*
1
Simultaneously interrogate all relevant DNA mutations and RNA fusion
transcripts for research on myeloid malignancies
2
Cover biomarkers for all major myeloid disorders, including AML,
MDS, MPN, CML, CMML, and JMML
3
Detect challenging targets with confidence with the dedicated
FLT3-ITD detection software
4
Get clear and concise reports that link biomarkers to relevant evidence
from public data sources
5
Simplify and accelerate myeloid profiling with 1-day NGS

10. 10 For Research Use Only. Not for use in diagnostic procedures.
Integrated Specimen-to-Report Workflow
* Specimen-to-report workflow will be available after the Genexus Purification System and integrated reporting capabilities are added in 2021.
All common specimen types
• Whole blood
• Peripheral blood leukocytes (PBLs)
• Bone marrow
Automated workflow*
• Nucleic acid extraction and quantitation
• Library preparation
• Sequencing
• Reporting and analysis
Annotated variant report
• Biomarkers linked to relevant
evidence from public data sources
1-day, automated specimen-to-report workflow*

11. 11 For Research Use Only. Not for use in diagnostic procedures.
Summary of Genes Covered by the Oncomine Myeloid Assay GX
Comprehensive gene content
for myeloid disorders research
40 DNA genes
• 23 hotspot genes
• 17 full genes
29 RNA fusion driver genes
• ~700 fusion isotypes
5 expression genes
5 expression control genes

12. 12 For Research Use Only. Not for use in diagnostic procedures.
Oncomine Myeloid Assay GX Gene Content
Hotspot Full gene Fusion Expression
Control
ABL1
BRAF
CBL
CSF3R
DNMT3A
FLT3
GATA2
HRAS
IDH1
IDH2
JAK2
KIT
KRAS
WT1
MPL
MYD88
NPM1
NRAS
PTPN11
SETBP1
SF3B1
SRSF2
U2AF1
ASXL1
BCOR
CALR
CEBPA
ETV6
EZH2
IKZF1
NF1
PHF6
PRPF8
RB1
RUNX1
SH2B3
STAG2
TET2
TP53
ZRSR2
ABL1
ALK
BCL2
BRAF
CCND1
CREBBP
EGFR
ETV6
FGFR1
FGFR2
FUS
HMGA2
JAK2
KMT2A
(MLL)
MECOM
MET
MLLT10
MLLT3
MYBL1
MYH11
NTRK3
NUP214
PDGFRA
PDGFRB
RARA
RBM15
RUNX1
TCF3
TFE3
BAALC
MECOM
MYC
SMC1A
WT1
EIF2B1
FBXW2
PSMB2
PUM1
TRIM27
~700 isotypes

13. 13 For Research Use Only. Not for use in diagnostic procedures.
Oncomine Myeloid Assay GX Content: Number of Assays—RNA
RNA
fusion
target
isoforms
198
52
39
15 12
3 2 2 2 1 1 1 1
KMT2A ETV6 RUNX1 TCF3 NUP214 FGFR1 BRAF RBM15 TFE3 CCND1 EGFR FGFR2 FUS
98
61
45 40 36 31 28 24 20 16 13
5 4 4 3 2 1 1 1 1 1 1
BRAF ABL1 RARA PDGFRB JAK2 MLLT10 PDGFRA FGFR1 MYH11 MLLT3 CREBBP NTRK3 MECOM RUNX1 HMGA2 NUP214 ALK BCL2 EGFR KMT2A MET MYBL1
5′ driver
3′ driver
MLL
Type Assay count
RNAExonVariant 3
ExpressionControl 5
GeneExpression 5
Fusion 687
Total 700
Fusion
RNAExonVariant
Color by type

14. 14 For Research Use Only. Not for use in diagnostic procedures.
Oncomine Myeloid Assay GX on the Genexus Integrated Sequencer
The content provided herein may relate to products that have not been officially released and is subject to change without notice​.
Up to 8 samples per day
prepared and sequenced
simultaneously in a single run
Rapid myeloid testing results
obtained in a single day, from
specimen to report*
32-reaction kit: profiling of 32
complete samples; DNA (two pools)
and RNA (single pool)
2 weeks of on-instrument chip and
reagent stability
Minimized consumables footprint
reduces required storage space
32 DNA and RNA samples
8 8 8 8
* Specimen-to-report workflow will be available after the Genexus Purification System and integrated reporting capabilities are added in 2021.

15. 15 For Research Use Only. Not for use in diagnostic procedures.
Genexus System—Specimen-to-Report NGS Workflow
* Specimen-to-report workflow will be available after the Genexus Purification System and integrated reporting capabilities are added in 2021.
Lysate from
• Bone marrow
• Whole blood
• PBLs
Nucleic acid purification
and quantitation*
Library preparation to
variant interpretation
Report*
Genexus Purification System
(available 2021)
Up to 12 samples
with DNA and/or RNA
DNA and RNA: 5-hour turnaround time
From start to analysis completion:
4 DNA/RNA samples—17 hours
8 DNA/RNA samples—21 hours
Genexus Integrated Sequencer
Ion Torrent™
GX5™ Chip:
12–15M reads/lane

16. 16 For Research Use Only. Not for use in diagnostic procedures.
Genexus Software—End-to-End Integration from Specimen to Report
* Specimen-to-report workflow will be available after the Genexus Purification System and integrated reporting capabilities are
added in 2021.
The content provided herein may relate to products that have not been fully validated by Thermo Fisher Scientific and is subject
to change without notice.
Integrated
Fully integrated solution enabling
specimen-to-report workflow; no
Ion Reporter™ server required
Easy to use
New, simplified user experience helps
minimize the learning curve and human error
Robust
Benchmarks on variant calling accuracy
Flexible
Option to choose either integrated analysis on
instrument, or analysis on Ion Reporter server
or cloud

17. 17 For Research Use Only. Not for use in diagnostic procedures.
Summary of Performance Verification
Flexibility in multiplexing while maintaining high average coverage depth across instruments and workflows
Excellent uniformity (>95%) in clinical research (blood, bone marrow) and control samples
Demonstrated ability to call SNV variants down to 5%, indel variants down to 10%
Additional demonstrated ability to detect FLT3 internal tandem duplications (ITDs) of various sizes and frequencies
in blood and bone marrow
Demonstrated ability to call relevant fusions (such as PML-RARA, RUNX1-RUNX1T1) in blood, bone marrow,
and control samples
Robust expression targets and controls correlate to qPCR expression measurements

18. 18 For Research Use Only. Not for use in diagnostic procedures.
Oncomine Myeloid Assay GX Produces Accurate Variant Calling
Variant calling in controls and FLT3–containing cell lines
Variant call All replicates
Seraseq™ Myeloid
Mutation Mix
SNV/indels
AOHC
SNV/indels
HD829
SNV/indels
FLT3-ITD
True positives 508 104 352 46 6
False negatives 11 1 8 2 0
False positives 1 1 0 0 0
Sensitivity (>95%) 97.8% 99.0% 97.8% 95.8% 100%
PPV (>95%) 99.8% 99.0% 100.0% 95.1% 100%
Reproducibility (>95%) 98.5%
N = 5 runs per sample, 8 samples/chip configuration
• Oncomine Myeloid Assay on Genexus System 6.2 met analytical specifications for detection of variants
• SNV/indel sensitivity >97%, PPV >99%, reproducibility >98%

19. 19 For Research Use Only. Not for use in diagnostic procedures.
FLT3-ITD Variants: 100% Sensitivity
Cell line ITD length
FLT3-ITD
detected
Run 1 Run 2 Run 3 Run 4 Run 5
Runs
detected (%)
MOLM-14 21 bp Detected Yes Yes Yes Yes Yes 100%
MOLM-13 21 bp Detected Yes Yes Yes Yes Yes 100%
MV4-11 30 bp Detected Yes Yes Yes Yes Yes 100%
PL-21 126 bp Detected Yes Yes Yes Yes Yes 100%
AOHC 21 bp Detected Yes Yes Yes Yes Yes 100%
Seraseq
Myeloid Mutation
DNA Mix
27 bp Detected Yes Yes Yes Yes Yes 100%
• All FLT3-ITD variants detected
• ITD lengths ranged between 21 bp and 126 bp
• Same top alleles called in all replicates

20. 20 For Research Use Only. Not for use in diagnostic procedures.
Fusion Detection—100% Sensitivity with Seraseq Myeloid Fusion RNA Control
Fusion detection All replicates
True positives 45
False negatives 0
False positives 0
Sensitivity (>95%) 100%
PPV (>95%) 100%
Fusions
Oncomine Myeloid Assay GX
avg fusion reads (n = 5 runs)
BCR(14)–ABL1(2)​ 7,700
ETV6(4)–ABL1(2)​ 341
ETV6(5)–ABL1(2)​ 7,596
FIP1L1(11)–PDGFRA(12)​ 30,363
KAT6A(17)–CREBBP(2)​ 6,083
PCM1(23)–JAK2(12)​ 5,091
PML(6)–RARA(3)​ 1,045
RUNX1(3)–RUNX1T1(3)​ 826
TCF3(16)–PBX1(3)​ 8,451
• Oncomine Myeloid Assay GX on Genexus
System 6.2 passed analytical specifications
for detection of fusion variants
• All 9 fusions successfully detected in all
replicates for 100% sensitivity

21. 21 For Research Use Only. Not for use in diagnostic procedures.
Oncomine™ Solutions for Hemato-Oncology Research
* Now available for the Genexus System.
Simplify your journey to answers
Childhood and young
adult assay
Ion Torrent™ Oncomine™ Childhood
Cancer Research Assay
Everything you need to expedite your path to hematology-oncology research insights in one place
Myeloid assays
Ion Torrent™ Oncomine™ Myeloid Assay GX*
Ion Torrent™ Oncomine™ Myeloid
Research Assay
Lymphoid assays
Ion Torrent™ Oncomine™ BCR IGH-LR Assay
Ion Torrent™ Oncomine™ BCR IGH-SR Assay
Ion Torrent™ Oncomine™ TCR Beta-SR Assay*
Ion Torrent™ Oncomine™ Lymphoma Panel
For Research Use Only. Not for use in diagnostic procedures.

22. 22 For Research Use Only. Not for use in diagnostic procedures.
Genexus Assay Menu for Oncology Research
Oncomine Myeloid Assay GX
Oncomine
Pan-Clonality Assays
Oncomine Somatic
Hypermutation Assay
Oncomine Lymphoid
Assay GX
Oncomine Precision Assay
Oncomine Comprehensive
Assay v3
Oncomine Comprehensive
Assay Plus
Hemato-Oncology
Solid Tumor Profiling
• 40 DNA targets
• 29 fusion drivers
• ~700 fusion isotypes
Coming soon
• B cell receptors (BCRs)
• T cell receptors (TCRs)
• Clonality assessment and rare
clone detection
Coming soon
• Somatic hypermutation analysis of
the BCR IGHV gene with leader
priming
Coming soon
• Comprehensive gene panel
covering biomarkers for a range of
lymphoid disorders.
• 50 solid tumor genes
• Novel fusion detection
• Low sample input (10ng)
• FFPE + liquid biopsy
• 161 solid tumor genes
• Low sample input
• DNA + RNA targets
Coming soon
• 500 solid tumor genes
• TMB + MSI
• Low sample input
• DNA + RNA targets

23. The world leader in serving science
Thank You
For Research Use Only. Not for use in diagnostic procedures. © 2020 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of
Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Seraseq is a trademark of SeraCare Life Sciences, Inc. COL112773 0920

24. Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or
application of Thermo Fisher Scientific products presented by third parties during this seminar.
Information and materials presented or provided by third parties are provided as-is and without
warranty of any kind, including regarding intellectual property rights and reported results. Parties
presenting images, text and material represent they have the rights to do so.
24
Legal Disclaimer

25. Experience with the Oncomine Myeloid Assay GX and the
Genexus System
Kojo S. J. Elenitoba-Johnson, M.D.
Perelman School of Medicine
University of Pennsylvania
U.S.A.

26. • Introduction
• Myeloid malignancies
• Principles of Ion Torrent sequencing
• Introduction to Genexus workflow
• Results of preliminary studies
• Summary
• Q&A
26
Outline

27. Founding Director, Center for Diagnostics
Founding Director, Division of Precision and
Computational Diagnostics
27
Introduction

28. For Research Use Only. Not for use in diagnostic procedures.
28
Acute Myeloid Leukemia
Myelodysplastic Syndromes
Myeloproliferative Neoplasms
• Chronic Myelogenous Leukemia
• Essential Thrombocythemia
• Polycythemia Vera
• Primary Myelofibrosis
Hematopoiesis and Hematological Malignancies

29. 29
2017 WHO Classification of Myeloid Malignancies
Acute Myeloid leukaemia (AML) and related
precursor neoplasms.
AML with recurrent genetic abnormalities
AML with t(8;21)(q22;q22.1); RUNX1-RUNX1T1
AML with inv (16)(p13.1 q22) or t(16;16)(p13.1;q22);
CBFB-MYH11
Acute promyelocytic leukaemia with PML-RARA
AML with t(9;11)(p21.3;q23.3); KMT2A-MLLT3
AML with t(6;9)(q23;q34.1);DEK-NUP214
AML with inv(3)(q21.3q26.2) or t(3;3)(q21.3q26.2);
GATA2 MECOM
AML (megakaryoblastic) with t(1;22)(q13.3;q13.1);
RBM15-MKL1
AML with BCR-ABL1
AML with mutated NPM-1
AML with biallelic mutation of CEBPA
AML with mutated RUNX1
AML with myelodysplasia-related changes
Therapy-related myeloid neoplasms
Acute myeloid leukaemia, NOS
AML with minimal differentiation
AML without maturation
AML with maturation
Acute myelomonocytic leukaemia
Acute monoblastic and monocytic leukaemia
Pure erythroid leukaemia
Acute megakaryoblastic leukaemia
Acute basophilic leukaemia
Acute panmyelosis with myelofibrosis
Myelodysplastic syndromes
Myelodysplastic syndrome with single lineage dysplasia
Myelodysplastic syndrome with ring sideroblasts and single
lineage dysplasia
Myelodysplastic syndrome with ring sideroblasts and
multilineage dysplasia
Myelodysplastic syndrome with multilineage dysplasia
Myelodysplastic syndrome with excess blasts
Myelodysplastic syndrome with isolated del(5q)
Myelodysplastic syndrome, unclassifiable
Refractory cytopenia of childhood
Blast plasmacytoid dendritic cell neoplasm
Acute leukaemias of ambiguous lineage
Acute undifferentiated leukaemias
Mixed-phenotype acute leukaemia with
t(9,22)(q34.1;q11.2); BCR-ABL1
Mixed-phenotype acute leukaemia with t(v;11q23.3); KMT2A-
rearranged
Mixed-phenotype acute leukaemia, B/myeloid, NOS
Mixed-phenotype acute leukaemia, T/myeloid, NOS
Mixed-phenotype acute leukaemia, NOS, rare types
Acute leukaemias of ambiguous lineage, NOS
Myeloproliferative neoplasms
Chronic myeloid leukaemia, BCR-ABL1-positive
Chronic neutrophilic leukaemia
Polycythemia vera
Primary myelofibrosis
Essential thrombocythemia
Chronic eosinophilic leukaemia, NOS
Myeloproliferative neoplasm, unclassifiable
Myeloid/lymphoid neoplasms with eosinophilia and
gene rearrangement
Myeloid/lymphoid neoplasms with PDGFRA rearrangement
Myeloid/lymphoid neoplasms with PDGFRB rearrangement
Myeloid/lymphoid neoplasms with FGFR1 rearrangement
Myeloid/lymphoid neoplasms with PCM1-JAK2
Mastocytosis
Cutaneous mastocytosis
Indolent systemic mastocytosis
Systemic mastocytosis with an associated haem. neoplasm
Aggressive systemic mastocytosis
Mast cell leukemia
Mast cell sarcoma
Myeloid neoplasms with germline predispositions
Acute myeloid leukaemia with germline CEBPA mutation
Myeloid neoplasms with germline DDX41 mutation
Myeloid neoplasms with germline RUNX1 mutation
Myeloid neoplasms with germline ANKRD26 mutation
Myeloid neoplasms with germline ETV6 mutation
Myeloid neoplasms with germline GATA2 mutation
Myeloid sarcoma
Myeloid proliferations associated with Down syndrome
Transient abnormal myelopoiesis associated with
Down syndrome
Myeloid leukaemia associated with Down syndrome

30. 30
Current Testing for Myeloid Malignancies: A Multi-Modal Process
FISH
Classical Cytogenetics
Morphology
Next Generation
Sequencing
qPCR
Flow Cytometry
Fragment Analysis Sanger Sequencing

31. 31
Key Disease-Associated Variants
Need to assess several genes for a
range of variant types:
• Point mutations
• Insertions
• Deletions
• Translocations (fusions)
• Copy number variants
• Gene expression profiles
• Low frequency alleles
• Known and novel variants
NCCN™ Guidelines (Acute Myeloid Leukemia 3.2017,
Myelodysplastic Syndromes 1.2018, Myeloproliferative Neoplasms 2.2018)
MDS MPN
AML
BCOR
ETV6
PRPF8
STAG2
NF1
PTPN11
CALR
IDH1
IDH2
JAK2
MPL
SH2B3
CSF3R
BCR-ABL1
CBFB-MYH11
DEK-NUP214
KMT2A (MLL)
MLLT3
PAX5-JAK2
PML-RARA
RUNX1-RUNX1T1
CEBPA
FLT3 TKD/ITD
IDH1
IDH2
KIT
NPM1
WT1
ASXL1
CBL
DNMT3A
EZH2
KRAS
NRAS
RUNX1
SETBP1
SF3B1
SRSF2
TET2
TP53
U2AF1
ZRSR2
JMML CMML

32. 32
Myeloid malignancies are characterized by diverse clinically actionable structural alterations
In recent years, we have made
tremendous progress in
understanding the genetic
abnormalities underlying
myeloid malignancies.
This knowledge of how biology and
genetics are the drivers of disease
is helping rapidly advance
precision oncology research for
these disorders.

33. 33
Generic NGS Workflow
0
5
10
15
20
25
30
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 >30
Days
Heme TAT Distribution
Extraction:
Batched
• 1-3 days until extracted, but takes 2
days to perform.
Perform
Library Prep:
Batched
•1 day
Sequence:
Batched •30 hrs
Bioinformatics
Processing:
Batched
• 20-24 hrs
Variant
Review •3-5 days
Director
Signoff
•1-3 days
Verification • 1-2days
CPD

34. 34
Considerations for NGS Testing of Myeloid Samples
Testing results sometimes
need to be available in
rapid time (1-2 days)
An NGS platform that can
provide results in this
timeframe would be
advantageous
A test should ideally be
able to accurately detect
multiple types of genetic
alterations, including SNVs,
insertions, deletions,
translocations (fusions)
from DNA and RNA
Traditionally, NGS has
required specialized
expertise and complex
bioinformatics.
Need simplified, automated
workflows to improve the
accessibility of the
technology at a broad
spectrum of laboratories
The panel should feature a
broad spectrum of gene
targets associated with all
relevant myeloid
categories.
DNA
RNA

35. 35
Why we are interested in the Oncomine Myeloid Assay GX for our research
• Efficient utilization of precious clinical research
samples
• Rapid TAT
• Workflow enhancements can pave the way to a
future where NGS can be considered for first-line
interrogation of suspected myeloid leukemias
• Report results within a relevant timeframe (1-2 days)
For Research Use Only. Not for use in diagnostic procedures.

36. 36
Oncomine Myeloid Assay GX Gene Content
Hotspot Full gene Fusion Expression
Control
ABL1
BRAF
CBL
CSF3R
DNMT3A
FLT3
GATA2
HRAS
IDH1
IDH2
JAK2
KIT
KRAS
WT1
MPL
MYD88
NPM1
NRAS
PTPN11
SETBP1
SF3B1
SRSF2
U2AF1
ASXL1
BCOR
CALR
CEBPA
ETV6
EZH2
IKZF1
NF1
PHF6
PRPF8
RB1
RUNX1
SH2B3
STAG2
TET2
TP53
ZRSR2
ABL1
ALK
BCL2
BRAF
CCND1
CREBBP
EGFR
ETV6
FGFR1
FGFR2
FUS
HMGA2
JAK2
KMT2A
(MLL)
MECOM
MET
MLLT10
MLLT3
MYBL1
MYH11
NTRK3
NUP214
PDGFRA
PDGFRB
RARA
RBM15
RUNX1
TCF3
TFE3
BAALC
MECOM
MYC
SMC1A
WT1
EIF2B1
FBXW2
PSMB2
PUM1
TRIM27
For Research Use Only. Not for use in diagnostic procedures.

37. 37
Genexus system
• Sequencing reagents and consumables
are stable on instrument for two weeks
• Conical tubes remain on instrument and only
replaced by the service engineer annually
For Research Use Only. Not for use in diagnostic procedures.

38. 38
Intuitive user interface facilitates reagent loading in designated slots

39. 39
Instrument Deck

40. 40
Genexus Software Overview
For Research Use Only. Not for use in diagnostic procedures.

41. 41
Results
Run quality results and display
Successful run

42. 42
Results
Unsuccessful run

43. 43
Study design
• Oncomine Myeloid Panel (common gene targets compared with in-house capture-based assay)
• Sample description
• Seraseq® NGS reference controls (100 variants)
• Acute leukemias
• N = 24 samples (12 DNA, 12 RNA)
• Somatic aberrations – SNVs [37], Indels [n = 32], Gene fusions [n =12])
• VAF range (SNVs/Indels [3.5 – 93%])
• Turn-around-time

44. 44
Depth of coverage across multiple variants
GX Myeloid
In house capture

45. 45
Depth of coverage across multiple genes

46. 46
Variant allele frequencies across multiple genes

47. 47
TP53 SNV

48. 48
FLT3 ITD

49. 49
Selected genes and variants: Comparison of GX with capture-based platform
PDCXXXXXX DNMT3A p.L889P c.2666T>C 45.13/44.9
DNA 2 PDCXXXXXX IDH2 p.R140Q BCOR p.D420E*20 (99.5%VAF) c.419G>A 41.62/44
PDCXXXXXXX NPM1 p.W288Cfs*12 c.863_864insCATG 43.22/47.5
PDCXXXXXXX DNMT3A p.G707R c.2119G>C 48/41
PDCXXXXXX FLT3 p.Y589N c.1765T>A 45.37/44.8
DNA 3 PDCXXXXXXX NRAS p.G12D p.G13D c.G35A 18.98/18.6
PDCXXXXXX DNMT3A p.R882H c.G2645A 45.92/45.6
PDCXXXXXXX KRAS p.Q61H c.A183C 15.77/18.9
PDCXXXXXX U2AF1 p.Q157R c.A470G 47.47/45.1
PDCXXXXX BCOR p.N1387Kfs*3 c.4161_4170del 7.69/6.8
PDCXXXXXX STAG2 p.D445Gfs*4 c.1332_1333dupGG 36.86/38.4
DNA 4 PDCXXXXXX ABL1 p.T334I/p.T315I c.C1001T 5.0/4.0
ID Gene p.change GX only c.change VAF

50. 50
Selected gene-fusions : Comparison of GX with qRT-PCR/FISH
RNA2 PML-RARA PML(6)-RARA(3)
RNA3 PML-RARA PML(3)-RARA(3)
RNA4 RUNX1-RUNX1T1 RUNX1(3)-RUNX1T1(3)
RNA5 PML-RARA PML(6)-RARA(3)
RNA6 PML-RARA PML(6)-RARA(3)
RNA8 CBFB-MYH11 CBFB(5)-MYH11(28)
RNA12 CBFB-MYH11 CBFB(4)-MYH11(28)
RNA18 CBFB-MYH11 CBFB(5)-MYH11(33)
RNA20 RUNX1-RUNXT1 RUNX1(3)-RUNXT1(3)
RNA13 PML-RARA (low positive) Not called
RNA15 PML-RARA (low positive) Not called
RNAX NUP214-ABL1 (FISH) NUP214(29)-ABL1(2)
ID
qRT-
PCR/FISH
GX

51. 51
Results
Quantitative comparison between Genexus and In-house assay (SNVs and Indels)
Capture
VAF
(%)
Genexus VAFs (%)

52. 52
Results
• N = 24 samples (12 DNA, 12 RNA)
• Somatic aberrations
• SNVs [n = 37]
• Indels [n = 32]
• Gene fusions [n =12]
Type of aberration
Concordance of Genexus Myeloid Panel with
In-House Capture NGS and RT-PCR Based Assays
(Qualitative)
SNV 91%
Indel 77%
FLT3-ITD (<160bp) 100%
Gene fusion 83%

53. 53
Summary
• Single touch point – 10 minutes total hands-on time
• On-instrument analysis on-board
• Under 21 hours from nucleic acid to result
• Multiplex capability – DNA and RNA fusions
• 2 weeks on-instrument chip and reagent stability
• Concordant results (91% in real-world samples) with
orthogonal capture-based platform
For Research Use Only. Not for use in diagnostic procedures.

54. 54
Conclusions
• Easy to use
• Rapid turn-around-time
• Robust detection of variants from contrived and real-
world samples
• Simplifies workflow
• Can eventually lead to a future opportunity for first-
line implementation of NGS for triaging suspected
myeloid malignancies
For Research Use Only. Not for use in diagnostic procedures.
Today
Future

55. Thank you
55
For Research Use Only. Not for use in diagnostic procedures. © 2020 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of
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