High-Throughput Sample ID
and QC for Biobanking and other
new applications
Welcome! – Agenda for today’s talk:
• Brief Overview – Sequenom MassARRAY Analyzer 4 platform
• Biobanking and use of IPLEX Pro Sample ID panel, for combined
sample ID confirmation and DNA copy number quantitation plus
analysis algorithm for data reporting
• New Exome ID panel
• New OncoFocus panel – Contains key “actionable” mutations for
EGFR (incl EGFR Exons 19/20), BRAF, Kras, Nras, c-Kit
• New UltraSeek panel – Assay enables >1% tumor level detection
(down to 0.2%) via new “ultrasensitive” assay
• Other new panels available via Assays By Sequenom include: EML4-ALK, Ret, Ros fusions, BCR-ABL, EGFR T790M, AML, Colon,
Pancreas, Breast, Ovarian/Uterine,
* Growth rate of 30% from 2011-2015 according to www.laboratoryfocus.ca/the-future-of-biobanking
2 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Sequenom CSPs World-wide
v
Certified CSP
In certification
In pipeline
3
January 15, 2014
Confidential
.
The MassARRAY® System
One System – Many Applications
• Genotyping
• Mutation Detection
• DNA Methylation
• Gene Expression
• Copy Number Variance
• Haploid Sequence
Variance
4 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
MassARRAY® Analyzer 4:
A powerful MALDI-TOF Mass Spectrometer
5 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
MassARRAY ® Assay Workflow Overview
6 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Genotyping Assay (iPLEX®) Chemistry
iPLEX® reagents are for Research Use Only. Not for use in diagnostic procedures.
7 | Improving healthcare through revolutionary genetic analysis solutions
.
Typical SNP Panel (31-plex)
The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
8 | Improving healthcare through revolutionary genetic analysis solutions
The Role of Biobanks in Research
• World-wide, biobanking is on the rise*:
– Various types of biobanks that serve diverse research needs
– Biobanks at government, academic, and private institutions
– Ongoing efforts to standardize sample collection, quality, and sharing
practices; provide broader access to samples
• Today’s biomedical research requires access to large sample
numbers:
–
–
–
–
Biomarker discovery and validation projects
Epidemiology and population-based studies
Pharmaceutical preclinical research and clinical trials
Especially important in translational cancer research
* Growth rate of 30% from 2011-2015 according to www.laboratoryfocus.ca/the-future-of-biobanking
9 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
The Importance of Sample Quality in
Research Studies
• Building sample collections can take years
– Criteria for sample inclusion can change
– Sample utility and research needs can change
– Resulting collections can be diverse in quality
• Sample quality standards ensure broad sample utility and
longevity
• Collection maintenance costs are reduced by eliminating
poor quality samples
• Uniform sample quality and identity standards enable
sharing and collaborations
10 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
The Importance of Accurate Sample
Identification in Research Studies
 Laboratory procedures can
lead to mistaken identity
 Samples can be mislabeled or
contaminated
 Incorrect samples can lead to
erroneous data resulting in
repeat experiments, time
delays, and/or retraction of
publications
 The challenge of the research
community is to ensure correct
samples are used and reported
in research studies
“Lab Mistakes Hobble Cancer Studies But
Scientists Slow to Take Remedies”
Health Industry Blog - Marcus, WSJ 2012
11 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Available Methods for Sample ID
Method
Advantage
Disadvantage
External label barcode
Simple, fast, low cost
Can be lost or damaged;
identifies the tube or well, not
the sample
STR genotyping
Fewer markers required than
SNP panels; low-cost
STRs can be unstable; low
multiplexing and throughput;
weak tumor-normal matching
InDel genotyping
More stable than STRs; lowcost
Low multiplexing and
throughput; weak tumornormal matching
Genotyping by Sequencing
May discover novel
polymorphisms
High cost and low throughput
SNP genotyping with standard
PCR
Simple
Low multiplexing; low
throughput
SNP genotyping with MALDI-TOF Automated; multiplexed; highMS (MassARRAY® System)
throughput; low cost; effective
tumor-normal matching
Cannot assay STRs
13 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
SNP Genotyping as a Choice Method for
Sample Identification
14 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Pharmacogenomics (2013)
15 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Sample Identification using the
MassARRAY® System
• Used by top institutions and major research initiatives,
including:
–
–
–
–
–
The Broad Institute
The Marshfield Clinic
Nationwide Children’s Hospital; TCGA Consortium
International Genomics Consortium
William Beaumont Hospital Research Institute
• Researchers can design a custom ID panel or use the
Sequenom-designed panel: iPLEX® Pro Sample ID Panel
• Takes advantage of the MassARRAY System, a versatile, highthroughput genetic analysis platform for research use only
16 The MassARRAY® System and the iPLEX® Pro Sample ID Panel are for Research Use Only. Not
for use in diagnostic procedures.
.
iPLEX® Pro Sample ID Panel
 Single-well assay with 44 SNPs, 3 gender markers, and copy
number controls
 Enables sample identification and estimation of amplifiable
genomic copies
 Ideal for sample tracking and identification important for
banked clinical trial and research samples
 Sample DNA qualification prior to PCR-based methods
including MassARRAY® panels* and next generation
sequencing
 Runs on the MassARRAY System – MALDI-TOF Mass Spec
technology for robust, high-throughput, and low cost analysis
18 The MassARRAY® System and iPLEX® Pro Sample ID Panel are for Research Use Only. Not for
use in diagnostic procedures.
.
Uses for the iPLEX Pro Sample ID Panel
• Sample identification with unique “barcode”
– Extremely high discrimination; chances for sample mix-up are
extremely low
• High-confidence sample matching
• High-confidence Tumor-Normal pair matching
• Sample quality assessment
– Is the DNA amplifiable?
• Sample quantity assessment
– Is there sufficient DNA?
• Help determine what assays to use with samples
19 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
iPLEX Pro Sample ID Panel
 Paired comparison of all valid
samples across a set of 44 SNPs
 Option for local comparison or
historical comparison against a
sample database
 Option for tumor to normal
comparisons
 3 outcomes include unexpected
mismatch, unexpected match, and
expected match
20 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
SNPs, Gender Markers, and Copy Number
Controls in the Sample ID Panel
Copy number
controls
Gender
markers
21 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
Quality Control Check for Every Sample
 Samples with < 30 successful SNP calls will fail
 Not enough SNPs to make an accurate match or mismatch
for identification
 Samples with < 500 amplifiable copies will fail
 500 copies represent ~1 ng DNA
 Key for identifying samples of unknown copy number such
as formalin-fixed paraffin embedded tissue
 Sample may not be suitable for an OncoCarta™ Panel or
next generation sequencing run that require ~10 ng DNA
23 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
Proposed Workflow & Outcomes
using the iPLEX® Pro Sample ID Panel
Incoming
sample
10 ng
DNA
iPLEX Pro Sample ID Panel
- Genotype with 44 SNPs
- Genotype Gender
- Assess Copy Number
Expected
Match
Proceed to MA4
or NGS run
> 500
copies
Incoming
sample
10 ng
DNA
iPLEX Pro Sample ID Panel
- Genotype with 44 SNPs
- Genotype Gender
- Assess Copy Number
Unexpected
Match or
Mismatch
Acquire new
sample (biological
issue)
Rerun sample
(technical issue)
< 500
copies
24 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
Information Provided by the iPLEX Pro
Sample ID Panel
Report Type
Description
Report Summary





Local or historical options
Number of samples and comparisons
Plates used to generate report
Number of failed samples
Unexpected results
Plate Report






Results for every well in the plate
Number of SNP calls
Number of amplifiable copies
Gender
Pass/Fail quality control
Number of matches & mismatches found
Match Report



Samples with unexpected match or mismatch
Comparison of SNP calls
Number of matches and mismatches
Sample Report




SNP calls for sample
Number of amplifiable copies for 5 assays
Gender identification for 3 assays
Why sample failed quality control if relevant
26 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
iPLEX Pro Sample ID Panel - Unexpected
Mismatch Report
Two samples
unexpectedly
mismatch with
the same
identifier
32 The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures.
.
Increasing sample value through additional
biomarker profiling
• Biobanked samples have higher value when associated with
additional disease- or pharmacogenetics- relevant data
– Can be included/excluded in research studies using specific criteria
relevant to study
• A broad variety of genomic biomarker panels can be profiled
with the MassARRAY® System
– Standard “off the shelf” panels
– Custom Assays by Sequenom panels
– Independent (user-designed) panels
• Examples: cancer mutations, ADME/PGx polymorphisms,
disease-associated SNPs, DNA methylation markers
33 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Ritchie et al. Am.J.Med.Gen. 2010
BioVu at Venderbilt U.
EMR – linked DNA Bank
Xu et al. J.Med.Inf.Assoc. 2011
Ramirez et al. Pharmacogenomics 2012
34
.
BioVu: an EMR-Linked “DNA Data Bank”
• Large DNA repository linked to Electronic Medical/Health Records
(EMR/HER)*
– Actively recruits samples from individuals treated at Vanderbilt Medical
Center
– ~75,000 samples in bank; will grow to ~250,000
– Patient identity is hidden for privacy
• Genotyping for disease and pharmacogenetic markers is carried out
with the MassARRAY® System:
– Utilizing focused custom genotyping panels
– Linked genotypes to phenotypes and EMRs/EHRs
– Created an invaluable resource for pharmacogenetics and disease genetics
research
• Successfully demonstrated the use of a genotyping approach for
pharmacogenetics research (warfarin case study)
– Xu et al. 2011; Ramirez et al. 2012
*Source: http://www.vanderbilthealth.com/main/25443
35 The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures.
.
Sequenom’s Pre-designed Research Panels
Panel
Content
Intended Use
Advantage
OncoCarta™
238 somatic mutations
in 19 cancer-related
genes
Solid tumor somatic
mutation profiling
Broad coverage; highthroughput, highsensitivity, and low cost
LungCarta™
214 somatic mutations
in 26 cancer-related
genes
Lung cancer somatic Comprehensive, highmutation profiling
throughput, highsensitivity, and low cost
iPLEX® ADME
PGx Panel
192 ADME-relevant
SNPs and InDels
Pharmacogenetics
preclinical and
clinical research
32 OncoCarta, LungCarta, and iPLEX ADME panels are for Research Use Only. Not for use in
diagnostics procedures.
Comprehensive, highthroughput, high call
rates, and low cost
.
Mutation Analysis with the MassARRAY® System
Gold standard for somatic mutation screening
37 The MassARRAY® System and panels are for Research Use Only. Not for use in diagnostic
procedures.
Lung Adenocarcinoma Testing Paradigm
Test for other
Mutations ?*
+
Image based on Horn L and
Pao W: EML4-ALK: Honing in
on a new target in non-smallcell lung cancer. J Clin Oncol
27:4232-4235, 2009
+
Test for KRAS
Mutations
Cytotoxic
Chemotherapy
(15-30%)
38 | Improving healthcare through revolutionary genetic analysis solutions
+
Test for EGFR
Mutations
-
Test for
EML4-ALK
translocation
(*) “Other” includes
BRAF, MEK1, AKT1, PIK3CA,
DDR2……and/or intensive
research to identify
new driver mutations
ALK Kinase
Inhibitor
(5-10%)
EGFR Tyrosine
Kinase
Inhibitor (10%)
Test for acquired
resistance (e.g.
EGFR_T790M)
.
EGFR – Complex Efficiency
2236F
2256R
EGFR Exon 19
Deletions
------------c.2236_2256del21--------------2253R
----------c.2236_2253del18--------c.2230
-----c.2236_2250del15-----
c.2280
2250R
ATC
AAG
GAA
TTA
AGA
GAA
GCA
ACA
TCT
CCG
AAA
GCC
AAC
AAG
GAA
ATC
CTC
I
K
E
L
R
E
A
T
S
P
K
A
N
K
E
I
L
----------c.2239_2256del18---------
p.760
p.744
---------_c.2239_2256>CAA-------2239F
------------c.2236_2256>ATC--------------2236F
39 | Improving healthcare through revolutionary genetic analysis solutions
2256R
.
EGFR – Complex Efficiency
2248F
2237F
2233F
2235F
2245R
2239F
2250R
2256R
2252F
2254F
2254R 2258F
2277R
EGFR Exon 19
Deletions
2249R
c.2230
c.2280
ATC
AAG
GAA
TTA
AGA
GAA
GCA
ACA
TCT
CCG
AAA
GCC
AAC
AAG
GAA
ATC
CTC
I
K
E
L
R
E
A
T
S
P
K
A
N
K
E
I
L
2247R
p.744
2236F
2251R
2240F
2253R 2257R
2244R
2303F
c.2293
2276R
2248R
2253F
2258R
2252R
2316R
2309F 2310R
2312F
2317R 2322F
2238F
2296R
2255R
2326F
c.2331
GTG
ATG
GCC
AGC
GTG
GAC
AAC
CCC
CAC
GTG
TGC
CGC
CTG
V
M
A
S
V
D
N
P
H
V
C
R
L
EGFR Exon 20
Insertions
2308R
p.765
2298R 2300R
2307R
2303R
2312R
2311R
2308F 2311F
2315R
40 | Improving healthcare through revolutionary genetic analysis solutions
2320F
p.760
2327R p.777
.
OncoFOCUS – EGFR, BRAF, KRas, NRas
4 Genes / 200+ Mutations (SNP&INDEL) / 12 Reactions / only 20ng
Gene Mutations Detected with the EGFR/KRAS/BRAF/NRAS Panel
EGFR
(Missense) R108K, T263P, A289V, A289D, G598V, E709K, E709Q/H, E709A, E709G, E709V, E709fs*1, G719S, G719C, G719A, G719D, E746K, E746V, L747P, L747S,
T751I, S752P, S752Y, P753Q, P753S, I759N, D761N, D761Y, S768I, S768N, D770N, R776C, R776H, T790M, T854A, L858M/K/R, L858R, L861Q, L861R
EGFR
Exon 19
K745_E749del, E746_E749del, E746_A750del, E746_T751del, E746_T751>I, E746_A750>IP, E746_T751>IP, E746_S752>I, E746_T751>A,
E746del/I744_K745insKIPVAI1, E746_S752del, E746_T751>I, E746_P753>IS, E746_T751>Q, E746_A750>QP, E746_T751>L, E746_P753>LS,
E746_T751>S, E746_T752>A, E746_T751>V, E746_T751>VAorVP, E746_P753>VS, E746_S752>V, E746_A750>VP, E746_T751>VA, E746_T751>VP,
E746_P753>VQ, E746V/K745_E746insVPVAIK1, E746_S752>D, L747_A750>P, L747_T751>Q, E746_A750>DP, L747_T751>P, L747_S752>Q,
L747_S752>QH, L747_E749del, L747_S752del/L747_S752>Q, L747_P753>Q, L747_T751>A, L747_K754del/L747_K754>N1,
L747_T751>S,L747_T751del,L747_P753>S, L747S/L747_K754>ST1, T751_I759>N, T751_I759>REA, T751_I759>S1, T751_I759del1, S752_I759del,
P753_I759del, T751_I759>S1
EGFR
Exon 20
M766_A767insAI, A767_S768insTLA1, S768_V769>IL1, V769_D770insMASVD, D770_P772>ASVDNR, V769_D770insCV1, V769_D770insASV,
D770_N771>AGG, V769_D770insASV1, V769_D770insGSV/V769_D770insGVV/D770>GY1, D770_N771insG, D770_N771insAPW, D770_N771insGL,
N771>GF, N771>GY, D770_N771insG/D770_N771insGD1, D770_N771insSVD, N771_P772>SVQNR, N771>TH, N771>SH, D770_N771insMATP1,
H773_V774insNPH, H773_V774insH, H773_V774insPH, H773_V774insQ1, V774_C775insHV, N771_P772insN1, D770fs*611,
N771_P772insRH/P772_H773insTHP1, P772_H773insV1, P772_H773insHV1, H773>NPY1, V774_C775insHV1
BRAF
D594G, D594V, G469S, G469E, G469A, G469V, G469R, G469R/S, L597Q, L597V, L597R, L597S, V600E, V600K, V600M, V600L
KRAS
G12S, G12R, G12T, G12V, G12F, G12P, G12A, G12C, G12W, G12D, G12N, G12I, G12L, G12Y, G12E, G12D/V, G13C, G13S, G13A, G13V/I, G13D/N, G13R,
A59T, Q61K, Q61E, Q61L, Q61R, Q61P, Q61H
NRAS
G12S/N, G12R/P, G12C/Y, G12D/E, G12A, G12V, G13S/N, G13R, G13C/Y, G13D, G13A, G13V, Q61H, Q61L, Q61R, Q61P, Q61K, Q61E, Q61Q/K
1INDELs
detected in 1 direction only
41 | Improving healthcare through revolutionary genetic analysis solutions
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Applications for Ultra-Sensitive Detection
 High-sensitivity detection may aide in personalizing
therapy based on a patient’s mutational status
 Heterogeneous tumor samples typically harbor low
abundant mutations
 Mutations may be informative for monitoring minimal
residual disease
 Other sources could potentially serve as a surrogate to
tumor samples for mutation profiling
42
January 15, 2014
.
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
 Assume a comparable number of molecules of any DNA sequence
per ml: 1,400 for early stage cancer
 Hence 0.21% detection sensitivity will detect almost anything
with 95% confidence but quantification will require haplotyping
43
.
Circulating plasma DNA (cpDNA) concentration
elevated in patients with solid tumors
44
January 15, 2014
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Circulating plasma DNA (cpDNA) concentration
elevated in patients with solid tumors
 DNA concentrations classified by tumor types from
patient cohort in Phase I clinical trial
 cpDNA median conc. ~17 ng/ml
 3-fold higher cpDNA conc. in advanced cancers vs.
normal individuals
45
January 15, 2014
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cpDNA a Promising Source for Biomarker
Studies
 Paired tumor and plasmas evaluated for concordance
using the OncoCarta™ Panel v1.0
 Considerably less DNA used for cpDNA compared with
FFPE (~1-2 ng. vs. 20 ng.)
 Low cpDNA concentrations can limit detection, but could
be resolved with higher starting plasma volumes
 Biochemistry could be improved as existing method
detects ~5-10% mutation frequency
 Additional research and development of analytically
validated assays for cpDNA of high value
46
January 15, 2014
.
Concordance between paired FFPE tumors
and cpDNA with the OncoCarta™ Panel v1.0
The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures
47
January 15, 2014
.
Mutation Status May Confer Resistance
During Subsequent Therapy
… mutations could be present
below the detection limit of
conventional direct sequencing…
The detection has a sensitivity of
~0.5% BCR-ABL mutation
frequency compared with 10%
for direct sequencing…
… In 64 patients, 132 additional
mutations were detected by
mass spec alone (50 of 132
mutations were resistant …
48
The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures
.
Clinical Research: Mass Spec MALDI-TOF Identifies more
EGFR T790M Mutations than Direct Sequencing
In non-treated patients:
25.2% vs. 2.8%; P < .001;
In treated patients, before TKI:
31.5% vs. 2.7%; P < .001;
After TKI:
83.3% vs. 33.3%; P = .0143
Kang-Yi Su, Hsuan-Yu Chen et al. Pretreatment Epidermal Growth Factor Receptor (EGFR)
T790M Mutation Predicts Shorter EGFR Tyrosine Kinase Inhibitor Response Duration in
Patients With Non–Small-Cell Lung Cancer . J Clin Oncol 2012 Feb 1; 30(4) :433-40
49 | Improving healthcare through revolutionary genetic analysis solutions
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Single Allele Base Extension Reaction
T C A T C AT G C AG C T C A T G CC C TT C G G
EGFR_T790M_Control#1
H1975
40
35
50
Intensi ty
Intensi ty
40
25
20
30
15
20
10
10
5
0
0
5150
5100
5200
5250
Mass
5300
5400
5350
5100
5450
40
Intensi ty
Intensi ty
30
30
25
20
10
T C A T C
10
5
0
0
5100
5150
5200
5250
C AG C T C A T G CC C TT CG G
Control EXT
Mass
5300
5350
5400
5450
5100
Intensi ty
Intensi ty
5150
5200
5250
Mass
5300
5350
5150
5250
Mass
5300
5350
5400
5450
T
70
C
. . . 0M _ Co nt r ol#1
90
5200
EGFR_T790M_Control#1
T
60
80
gDNA
70
60
DW
50
Intensi ty
40
Intensi ty
Intensity
5100
5450
EGFR_T790M_Control#1
G
C
Intensity
5400
50
30
40
30
20
20
10
10
0
0
5100
50 | Improving healthcare through revolutionary genetic analysis solutions
T
0
5100
T790M DNA
No peak
5450
5
0
. . . 0M _ Co nt r ol#1
UEP
5400
10
10
UEP
5350
15
20
Control
5300
20
30
WT
Mass
0.3%
25
40
Mass spectrometry
5250
C
T
C
. . . 0M _ C on t r ol#1
30
0.6%
50
5200
EGFR_T790M_Control#1
EGFR_T790M_Control#1
60
T790M
5150
. . . 0M _ C on t r ol#1
G
T
5450
40
15
X
ACG
5400
5350
1.2%
50
35
20
No Extension
5300
T
45
Control EXT
60
9.1%
50
Mass
C
70
55
5250
. . . 0M _ C on t r ol#1
60
T
65
C AG C T C A T G CC C TT CG G
C
T
TG
G
Intensity
5200
EGFR_T790M_Control#1
. . . 0M _ C on t r ol#1
T790M EXT
T C A T C A
UEP
5150
EGFR_T790M_Control#1
T790M DNA
WT DNA
100%
60
30
T
70
45
SABER
80
C
50
. . . 0M _ C on t r ol#1
T
55
C
. . . 0M _ Co nt r ol#1
T C A T C ACG C AG C T C A T G CC C TT CG G
WT DNA
EGFR_T790M_Control#1
5150
5200
5250
Mass
5300
5350
5400
5450
5100
.
5150
5200
5250
Mass
5300
5350
5400
5450
Biochemistry Overview—iPLEX® Pro with
modified biotinylated termination and capture
steps
1. PCR
2. SBE using ddUTP specific for
the mutant allele
ddUTP-
3. Capture and wash
ddUTPA
C
ddUTPC
C
ddUTPC
ddUTP-
SBE= Single Base Extension
The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures
1%
0.25%
0.5%
0.125%
0.25%
0%
The MassARRAY® System is for Research Use Only. Not for use in diagnostic procedures
Capture Ctrl. 4
Capture Ctrl. 3
EPHA3
DDR2
Albumin Ctrl
Capture Ctrl. 2
G-Mix
All Spectra
Capture Ctrl. 1
Capture Ctrl. 4
Capture Ctrl. 3
EPHA3
DDR2
Albumin Ctrl
Capture Ctrl. 1
Capture Ctrl. 2
New Capture Controls to Assess Workflow in
Absence of Wild-type Extension
Highlights from poster presented at ESHG
2013
A Novel Approach for Multiplex Ultrasensitive Detection of Somatic Mutations in Tumor Samples, June 2013
Anders Nygren, Michael Mosko, Eunice Flores, Aleksey Nakorchevsky, Mathias Ehrich, Christiane Honisch, and Dirk van den Boom
53 | All Sequenom products and assays are for Research Use Only. Not for use in diagnostic procedures.
.
UltraSEEK Oncogene Panel v1.0
Gene
ABL1
AKT1
ALK
BRAF
EGFR
AA
T315I
E17K
F1174L
V600E
V600K
V600R
G719S
T790M
L861Q
E746-A750del
4 multiplexes (3C, 1T)
56 |
Gene
FLT
IDH1
IDH2
JAK2
KRAS
AA
I836del
R132H
R140Q
R172K
V617F
G12A
G12D
G12V
G12C
G12S
G13D
Gene
NRAS
PIK3CA
EGFR
AA
Q61K
Q61R
E545K
E542K
H1047R
L858R
EGFR in separate well (1G)
CONFIDENTIAL
.
UltraSEEK Oncogene Panel v1.0 Software
Summary View
Assay View
Mutation View
Simplified views
Chip View
57 |
CONFIDENTIAL
.
UltraSEEK Road Map
Research Use Only
UltraSEEK
Assays by
Sequenom
UltraSEEK
Oncogene
Panel
UltraSEEK Assay
Design Suite &
Reagent Set
Mid 2014
Early 2014
Late 2013
.
Assays by Sequenom (AbS)
Customer Collaborative Panels
AbS Tumor Specific Panels
AbS Oncogene Panels
MelaCarta/Melanoma Tumor
70+ Mutations in 17 genes
Ovarian & Uterine Tumor
92+ Mutations in 12 genes
Pancreatic Tumor
140+ mutations in 42 genes
Colorectal Tumor
32+ mutations in 7 genes
Lung Cancer
9 variants in EML4-ALK
OncoCarta v2
152+ Mutations in 18
genes
OncoCarta v3
105+ Mutations in 22
genes
OncoFocus
(BRAF/EGFR/KRAS/NRAS)
200+ Mutations in 4 genes
59 | All Sequenom products and assays are for Research Use Only. Not for use in diagnostic procedures.
.
Summary: iPLEX® Pro Sample ID Panel
 A high-throughput, low cost SNP genotyping panel for sample
identification and tracking
 Comprehensive coverage with 44 SNPs and 3 Gender ID
markers
 Enables copy number quantification prior to MassARRAY or
next gen sequencing runs
 Enables tumor-normal sample matching
 Automated summary reports for convenient, rapid samples
comparisons within a single plate or against a historical
database
 Designed for the MassARRAY® System, a flexible genetic
analysis platform enabling many additional types of assays
62 The MassARRAY® System and iPLEX® Pro Sample ID Panel are for Research Use Only. Not for
use in diagnostic procedures.
.
Conclusions – Biobanks and
Sample Quality, Identity, Value
• Successful biobanks implement standardized sample quality
control and identity tracking systems
• Sample value is tied to its quality/quantity, correct identity,
and additional data such as EMRs and biomarker profiles
• The MassARRAY® System provides an open and flexible
solution for sample tracking, quality control, and genetic
biomarker profiling:
– Sample ID Panel for sample identification; DNA quality and quantity
assessment
– Pre-designed cancer marker and pharmacogenetic panels
– Easy to design custom panels for a variety of genomic markers
64 The MassARRAY® System and iPLEX® Pro Sample ID Panel are for Research Use Only. Not for
use in diagnostic procedures.
.