MassARRAY ® System – a proven technology for translational genomics and precision medicine Darryl Irwin PhD Lianxing Yang PhD Senior Scientist – Applications and Technology September 2012 The MassARRAY® System is for Research Use Only. Not for Use in Diagnostic Procedures.
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MassARRAY® System – a proven
technology for translational genomics
and precision medicine
Darryl Irwin PhD
Lianxing Yang PhD
Senior Scientist – Applications and Technology
September 2012
The MassARRAY® System is for Research Use Only. Not for Use in Diagnostic Procedures.
Presentation Outline
.
The MassARRAY® System, iPLEX Pro Sample ID, and LungCarta™ Panels are for Research Use Only.
Not for Use in Diagnostic Procedures.
� Sequenom MassARRAY applications overview
� Application of key types of genomic biomarkers in Cancer� LungCarta – Broad somatic mutation screening panel in lung
cancer
� SampleID – Sample Tracking and QC
� From comprehensive to Focused Panels – OncoFocus: EGFR/KRAS/BRAF/NRAS + Custom content
� Ultra-sensitive techniques for detecting rare somatic mutations
� Translocations – EML4-ALK: a key biomarker class for precision medicine
� ADME panel
� Quantitative DNA methylation analysis in cancer
� Conclusions and Q&A
2 | Improving healthcare through revolutionary genetic analysis solutions
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Quality of Science
A Company driven by technology and innovation
Over 1,800 citations
used the MassARRAY
System in peer-
reviewed publications
http://www.sequenom.com/literature
3 | Improving healthcare through revolutionary genetic analysis solutions
MassARRAY® Applications
.
One Platform, Multiple ApplicationsMiniaturized SpectroChip
Data Analysis Packages
Mass Spectrometry
Biochemistry Processes
GenotypingMethylation
Analysis
Quantitative Gene Analysis
Comparative Sequence Analysis
Molecular Diagnostics:
CF, RHD, AMD
……
4 | Improving healthcare through revolutionary genetic analysis solutions
Matrix Assisted Laser Desorption Ionization Time Of
Flight Mass Spectrometry (MALDI-TOF MS)
.
De
tecto
r+
+
Matrix/AnalyteLaser Desorption and IonizationAcceleration and Detection
+
+
Mass Spectrum m/z
Combines sensitivity of PCR with the accuracy of MS
5 | Improving healthcare through revolutionary genetic analysis solutions
Why accurate?
.
DNA consists of a four-letter alphabet:A, C, G, T
Each letter (and building block within a DNA strand)has defined molecular mass:
• RET - 8 missense mutations in 6 residues + 6 INDELs
• ACK1 - S985N
FFPE Clinical Research Study
29 | Improving healthcare through revolutionary genetic analysis solutions .
55 FFPE samples + 13 Cell Lines with known
mutation signatures
58/64 known mutations identified• 31 Unique mutations in sample set
• 3/6 unidentified mutations <10% frequency
• 6/6 unidentified mutations in highly
fragmented samples (<100 intact template)
25 novel mutations identified• 24/25 novel mutations identified in highly
fragmented samples (<100 intact template)
Mutational Spectrum
30 | Improving healthcare through revolutionary genetic analysis solutions .
0
1
2
3
4
5
6
7
8
BRAF G469EBRAF L597Q
BRAF V600E
BRAF V600K
BRAF K601E
BRAF K601N
EGFR G719S
EGFR E746_A750del
EGFR E746_S752>I
EGFR E746_S752>V
EGFR E746del
EGFR E746K
EGFR L747_P753>Q
EGFR L747_P753>S
EGFR T751_I759>S
EGFR D761N
EGFR S768_V769>IL
EGFR S768IEGFR V769_D770insASV
EGFR D770_N771insSVDEGFR T790M
EGFR L858R
KIT W557G
KIT L576P
KIT K642E
KIT D816Y
KRAS G12C
KRAS G12D
KRAS G12V
KRAS G13D/N
KRAS G13S
KRAS Q61R
NRAS G12C/Y
NRAS G13C/Y
NRAS Q61H
NRAS Q61K
NRAS Q61LNRAS Q61R
Series1
Series2
Confirmed
Mutations
All Detected
Mutations
Resistance – A Sensitivity Challenge
• High-sensitivity detection may aid in personalizing therapy based on a patient’s mutational status
• Detection of low-level mutations does not always correlate with later clonal expansion in patients treated with Tyrosine Kinase Inhibitors (TKIs)1:
• Mutant forms of BCR-ABL (T315I), KIT (T670I), and EGFR (T790M) confer resistance TKIs imatinib, gefitinib, and erlotinib
• Need to balance sensitivity vs. clinically relevant load in source tissue
1. Willis SG, Lange T, et al. High-sensitivity detection of BCR-ABL kinase domain mutations in imatinib-naive patients: correlation with clonal cytogenetic evolution but not response to therapy. Blood. 2005;106 (6): 2128-2137.
.31 | Improving healthcare through revolutionary genetic analysis solutions
Single Allele Base Extension Reaction
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T C A T C A T C AG CG T C A T G C C C T T C G G
TT790M EXT
G Control EXT
G
T C A T C A C C AG CG T C A T G C C C T T C G G
T C A T C A C AG CG T C A T G C C C T T C G GT
T C A T C A C C AG CG T C A T G C C C T T C G G
Control EXT
No Extension
WT DNA
T790M DNA
X
WT DNA
T790M DNA
SABER
Mass spectrometry
GUEP
Inte
nsity
Control
No peak
UEP
Inte
nsity
WT
TUEP
Inte
nsity
T790M
0
10
20
30
40
50
60
70
80
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
100%
0
5
10
15
20
25
30
35
40
45
50
55
60
65
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
9.1%
0
10
20
30
40
50
60
70
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
1.2%
0
10
20
30
40
50
60
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
0.6%
0
5
10
15
20
25
30
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
0.3%
0
10
20
30
40
50
60
70
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
DW
0
10
20
30
40
50
60
70
80
90
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
gDNA
0
5
10
15
20
25
30
35
40
45
50
55
5100 5150 5200 5250 5300 5350 5400 5450
C T
...0M_Control#1
EGFR_T790M_Control#1
Intensity
Mass
H1975
Sensitivity Required for Plasma Analysis
• Noninvasive prenatal diagnostics
– On average 1,400 molecules of any DNA sequence present per ml
– 4% fetal DNA is about 60 molecules: hence 4% ± 1.35% detection
sensitivity suffices but quantification is impossible without
haplotyping
• Noninvasive cancer diagnostics
– Early stage cancer assume a comparable number of molecules of
any DNA sequence per ml: 1,400
– Hence 0.21% detection sensitivity will detect almost anything
with 95% confidence but quantification will require haplotyping
.33 | Improving healthcare through revolutionary genetic analysis solutions
Importance of Sensitivity:
Detection of EML4-ALK – Clinical Research
.
A Novel Mass Spectrometry-Based Assay for
Diagnosis of EML4-ALK-Positive Non-Small
Cell Lung Cancer
Kazuko Sakai, Isamu Okamoto, Ken Takezawa, Tomonori Hirashima,
All Samples ALK FISH positive*Kwak EL et al. Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung
Cancer. N Engl J Med. 2010 October 28; 363(18): 1693–1703
Assays by Sequenom (AbS)*–
Customer Collaborative Panels
*Assays by Sequenom is for Research Use
Only. Not for Use in Diagnostic Procedures.
.
Pancreatic AbSPancreatic Cancer
140+ mutations in
42 genes
Colon AbSColon Cancer
32+ mutations in 7
genes
OncoCarta v3105+ Mutations in
22 genes
41 | Improving healthcare through revolutionary genetic analysis solutions
MelaCarta AbSMelanoma
70+ Mutations in
17 genes
Gynecology AbSOvarian + Uterine
92+ Mutations in
12 genes
OncoCarta v2152+ Mutations in
18 genes
RW9
Slide 41
RW9 Please only list the Assay by Sequenom that have been custom developed. If Gyencology Abs, Pancreatic AbS and Colon AbS and OncoCarta v3are 'pipeline' products, you must delete from this slide.Robin Weiner, 3/25/2013
Adverse drug reactions a leading cause of
death globally2
Identifying a sub-group of patients likely to
respond can dramatically increase the cost-
effectiveness of a drug1
>$750B annual global drug sales in 20091
$350B annually spent on ineffective
medicines globally1
90% of drugs work in 30-50% of individuals1
Building the Case for Personalized
Medicine
Need for ChangeStrong case for personalized medicine
Many major Pharma have biomarker programs for drug development!1. McKinsey Quarterly: The microeconomics of personalized medicine, February 2010
2. Lazarou J, Pomeranz BH, Corey PN. “Incidence of adverse drug reactions in hospitalized patients: a meta analysis of prospective studies.” JAMA. 1998; 279:1200-1205; Gretchen E. Parker, PhD, RAC,
Usha Srinivasan, MS, RAC and Gretchen M. Bowker, MS, RAC, Overcoming Challenges through Innovation and Regulation
42 | Improving healthcare through revolutionary genetic analysis solutions .
Defining the Gene & Variants in the
iPLEX® ADME Pharmacogenetics (PGx) panel
Absorption
Distribution
Metabolism Excretion
43 | Improving healthcare through revolutionary genetic analysis solutions .
CYP2C9 Celecoxib treatment of osteoarthritis, rheumatoid arthritis, acute pain, painful
menstruation and menstrual symptoms
Warfarin anticoagulant
CYP2D6 Atomoxetine treatment of attention-deficit hyperactivity disorder (ADHD)
Fluoxetine HCL antidepressant
Codeine sulfate Cough Diarrhea Mild to moderate pain usw.
NAT Rifampin bactericidal antibiotic
TPMT Azathioprine suppresses the immune system(organ transplantation)
UGT1A1 Irinotecan treatment of cancer
Nilotinib chronic myelogenous leukemia (CML)
VKORC1 Warfarin anticoagulant
44 | Improving healthcare through revolutionary genetic analysis solutions .
Haplotypes Detected with iPLEX ADME Pharmacogenetics panel
.
Genes GenesHaplotypes Haplotypes
iPLEX® ADME PGx panel is for Research Use Only. Not for use in diagnostic procedures.
45 | Improving healthcare through revolutionary genetic analysis solutions
Screening Approach: iPLEX ADME PGx panel
• Quickly and easily screen known, high-value mutations
• 192 mutations in 36 pharmacogenetically relevant genes
• Biologically relevant data with ADME PGx panel covering
>99% of Pharma Core list*
• Identify SNPs, insertions /deletions and copy number
variants (CNVs)
• Rapid genotyping assay
• Cost effective – 8 wells for 200 assays
• Proven technology1,2,3
*list available at http://www.pharmaadme.org/joomla/
1. Elke Schaeffeler et al., Highly Multiplexed Genotyping of Thiopurine S-Methyltransferase Variants Using MALDI-TOF Mass Spectrometry: Reliable Genotyping in Different Ethnic Groups
2. Fabiana BK, et.al., Molecular diversity oat the CYP2D6 locus in healthy and schizophrenic southern Brazilians.
3. .Yan Shi, et.al., Analysis of50SNPsin CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOFmass spectrometry in Chinese Han population.
.46 | Improving healthcare through revolutionary genetic analysis solutions
47 | Improving healthcare through revolutionary genetic analysis solutions
Sequenom EpiTYPER applications
Quantitative DNA methylation
analysis in cancer
.48 | Improving healthcare through revolutionary genetic analysis solutions
Overview of Sequenom’s
EpiTYPER® Technology
• Flexible & scalable for investigating a few or several hundred regions over multiple samples
• Long reads up to 600 bp in one reaction enable discovery of differential methylation within large promoter regions
• Robust analysis from a range of sample types including Formalin Fixed Paraffin Embedded (FFPE) samples
.49 | Improving healthcare through revolutionary genetic analysis solutions
EpiTYPER for Quantitative DNA Methylation
Analysis Using the MassARRAY System
.
Sequenom Application Note
Introduction to EpiTYPER for
Quantitative DNA Methylation
Analysis Using the MassARRAY
System
Mathias Ehrich, Devan Correll, and
Dirk van den Boom
Doc. No. 8876-007 R02
CO 060109
50 | Improving healthcare through revolutionary genetic analysis solutions
Potential Large Scale Application of EpiTYPER for
Characterizing DNA Methylation in NSCLC
Overall Goal: Present a previously uncharacterized
method for high-throughput DNA methylation
analysis that utilizes MALDI-TOF mass spectrometry
Methodology:
Use the IGF2/H19 region to show that a single
base-specific cleavage reaction is sufficient to
discover methylation sites and to determine
methylation ratios within a selected target region
Results:
• Successfully applied this method under high-
throughput conditions to quantitatively assess
methylation differences between normal and
neoplastic lung cancer tissues from 48
patients in 47 genes
• Demonstrate that quantitative methylation
results allow accurate classification of samples
according to their histopathology
.51 | Improving healthcare through revolutionary genetic analysis solutions
Colorectal Cancer Cases can be Classified
into Distinct Epigenotypes
Overall Goal: Gain insight into epigenotype
development in colorectal carcinogenesis,
especially intermediate-methylation and its
correlation to KRAS-mutation (+) in adenoma
Methodology:
• Use EpiTYPER to analyze the methylation
status of a new cohort of adenoma, crypt
foci, and normal mucosa samples
• Use iPLEX to analyze BRAF 1799 and KRAS
34, 35, and 38 mutation status
Results:
• Significant correlation with intermediate-
methylation epigenotype and positive KRAS
mutation status
• Epigenotype development occurs at an
earlier stage than carcinoma formation and
is already completed at adenoma stage
.52 | Improving healthcare through revolutionary genetic analysis solutions
Use of EpiTYPER Technology to Assess
Methylation Status of KLF5 in AML
Overall Goal: To show that expression of KLF5 is a requirement for
granulocyte differentiation of 32D cells
Methodology:
• qPCR showed reduced KLF5 expression significantly lower in
AML samples compared to controls
• EpiTYPER used to analyze methylation of 150 CpGs in a 4.4 kb
region spanning the proximal promoter to exon2 of KLF5
Results:
• In selected AML cases, reduced expression is associated with
hypermethylation of the KLF5 locus in the proximal promoter
and/or intron 1, suggesting that this may represent a Class II
genetic lesion in the development of AML
• DMR1 in the proximal promoter was hypermethylated in 31%
of AML patients
• DMR2 in the first intron was hypermethylated in 41% of de
novo AML samples
• Inverse correlation between methylation and expression could
be confirmed with demethylating agents
.53 | Improving healthcare through revolutionary genetic analysis solutions
Use of EpiTYPER Technology to Confirm a
Breast Cancer Methylation Biomarker
Overall Goal: Map MicroRNAs (miRNAs) within the previously described promoter (P1) and
a novel promoter Has-mir-200b cluster (P2) and their role in breast cancer
Methodology:
• Use HRM to assess methylation in 15 promoters in breast cancer cell lines
• Use EpiTYPER to analyze methylation in miR-200b promoter in Grade 3 FFPE samples
Results:
• P1 and P2 were differentially methylated and inversely correlated to expression
• Data suggests an association between miR-200b regulation and breast cancer subtypes
• Potential use of DNA methylation in miRNA promoters as a breast cancer biomarker
.54 | Improving healthcare through revolutionary genetic analysis solutions
Use of EpiTYPER Technology to Validate
Methylation Differences in Ovarian Cancer
.
Overall Goal: Identify epigenetic-based biomarkers for diagnosis of ovarian cancer
Methodology:
• Use genome-wide methylation (MeDIP) to discover epigenetic-based biomarkers in A2780 and CaOV3
ovarian cancer cell lines
• Use EpiTYPER to validate methylation differences within 21 gene promoters identified by the MeDIP-Chip
Results:
• A panel of 6 genes (ARMCX1, ICAM4, LOC134466, PEG3, PYCARD & SGNE1) were shown as a potent
discriminator of cancer vs. normal
• A putative pseudogene of ZNF300 was identified as an individual discriminator
• The potential biomarker panel can hold great promise as a diagnostic test for high-grade (Type II) serous
ovarian cancer
55 | Improving healthcare through revolutionary genetic analysis solutions
miRNA Expression and Methylation Changes
Common in Oral Squamous Cell Carcinoma
.
Overall Goal: Analyze epigenetic regulation and expression of miRNAs in oral squamous cell
carcinoma (OSCC)
Methodology:
• Use TaqMan miRNA low density arrays to perform initial screen of non-metastatic and
metastatic tumors and matched control tissue
• Use EpiTYPER to further evaluate 10 miRNAs in a larger sample set
Results:
• miRNA expression patterns were consistent in healthy oral epithelium and stroma, but
broadly altered in both tumor and adjacent tissue from OSCC patients
• “A broad spectrum of CpG methylation patterns were observed, ranging from
completely methylated to unmethylated, demonstrating the dynamic range of the
MassARRAY® System”
• Five miRNAs were identified as promising candidates for further investigation
56 | Improving healthcare through revolutionary genetic analysis solutions
Verification of Genes Frequently Silenced by
Methylation in Melanoma
.
Overall Goal: To identify and confirm novel candidate genes frequently methylated in
melanoma
Methodology:
• Integrate gene expression and methylation array analysis to identify candidate
genes
• Use EpiTYPER to validate the methylation status of the most promising tumor
suppressor genes as a follow up to methylation arrays
Results:
• UCHL1, COL1A2, THBS1, and TNFRSF 10D inversely correlated with promoter
methylation
• Identification of candidate TSGs and future research will increase understanding
of etiology of melanoma and provide tools for its early diagnosis
57 | Improving healthcare through revolutionary genetic analysis solutions
EpiTYPER Summary
• EpiTYPER method provides a research tool for discovering methylation status in targeted regions
• EpiTYPER method provides a highly useful research tool for verifying key regions for their methylation status across larger sample sets
• EpiTYPER method can be used as a cross-platform tool for array validation and/or correlation to expression
• Recent publications suggest the value of methylation status as a potential biomarker or for future diagnostic use
.58 | Improving healthcare through revolutionary genetic analysis solutions
MassARRAY® System* – Proven Research Tool
for Biomarker Validation and Translation
• Very high quality data: quantitation, sensitivity, precision