Upload
others
View
0
Download
0
Embed Size (px)
Citation preview
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential ©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
Automated Genomic Solutions
21 June, 2018
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential ©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
Your next discovery just got the green light. Introducing the Biomek i-Series Automated Workstations for Genomics workflows
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential ©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
• Genomics Workflow Overview
• Example Extraction: FFPE
• Example NGS: Truseq Standed mRNA
(Illumina)
• Summary
Agenda
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
3
Biomek Automated Solutions for Genomic Applications Low to High-Throughput – Efficiency – Reliability - Productivity
Efficiency so you can
do more with less
• Increased throughput to
maximize sequencing runs
• Minimize hands-on time and
cost
• Support and Versatility to
adjust to your changing needs
Reliabilitiy so you can
trust your data
• Improved library quality with
Standardized sample prep
• Solutions that deliver results
from challenging samples
• Advanced sample ID tracking
Productivity so you can
get to results faster
• Quick method implementation
• Vast portfolio of proven
methods
• Software supports easy
operation
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
4
LT, Entry-level
Biomek NXP
MT
Biomek 4000
HT, Hybrid
Biomek i7
Increasing throughput , flexibility, and walk-away time
MT
Biomek i5
Inve
stm
en
t
Biomek Automated Solutions for Genomic Applications Low to High-Throughput – Efficiency – Reliability - Productivity
Extraction & Purification
• Nucleic Acid extraction from
many sample types, including
FFPE
• Cleanup from enzymatic
reactions
• Size selection
Array Technology
• Affymetrix
• Illumina
Next Generation Sequencing
library construction
• Whole genome sequencing
• Transcriptome sequencing
• Targeted sequencing (exome
or panels)
• HLA sequencing
• Single-Cell sequencing
• Epigenetic sequencing/ATC-
Seq
Amplification & QC
• PCR and qPCR setup
• Quantification
• Normalization
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
DNA Isolation
DNAdvance
Genfind v2
Formapure DNA
CosMC Prep
RNA isolation (also micro
RNA)
RNAdvance Cell
RNAdvance Blood
RNAdvance Tissue (miRNA)
FormaPure RNA
(miRNA)
PCR Purification & Cleanup
AMPure XP
CleanSEQ
RNAClean XP
NGS Sample Prep
SPRIselect (size selection)
Demonstrated Library
Construction for popular kits
Biomek Automated Solutions for Genomic Applications Example: Extraction from FFPE samples
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE for Biomarker discovery in cancer research
Biomarker
Discovery
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
7
Challenges with FFPE and nucleic acid extractions
• Formalin creates crosslinking of
intracellular molecules.
• Formalin can cause nucleic acid
damage
o Fragmentation
o Deamination
o Pyrimidine dimers
• Improper storage and fixing
conditions can affect quality of
nucleic acids.
• Uneven distribution of the tissue
in blocks can cause variable
yield.
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE Extraction – Customers talk, we listen!
• Product Performance / Quality
o Purity
o Yield
o Integrity
• Compatibility with downstream applications
o Next Generation Sequencing
o qPCR
• Simplified workflow
o Minimize total hands-on and purification time
• Safety
o Avoid using xylene
• Compatibility with automation
o High throughput
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
- 9 steps
- 1 centrifuge steps (manual)
- 0 for Automation
- No Xylene required.
- 3 temperatures
- No Risk of clogging
Simple Workflow
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FormaPure DNA: DNA/RNA isolations
Split protocol allows you to isolate total nucleic acids from one sample.
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
11
RNA isolation using FormaPure DNA
Advantages to isolating DNA and RNA from a single sample from an NGS
Perspective
Next Generation DNA Sequencing Next Generation RNA Sequencing
• Low expression level genes are easier to
detect.
Single nucleotide variants and indels can be
detected.
• Focuses on gene expression profile.
Probes the dynamics of gene expression, ie
changes in regulation.
• Able to see copy number variants. • Detects alternative splicing events.
• Can detect chromosomal rearrangement
events where RNA is not expressed.
• Can detect fusion transcripts
Known to occur in cancerous cells across a
range of cancers, ie, gastric, prostate,
colorectal, breast cancers, and leukemia.
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
12
Unique and Challenging sample types • Customer samples: brain cancer tissues mounted on microscope slides high in myxoid (a type of
glycosaminoglycan).
050
100150200250300350400450500
1 2 3
Yie
ld (
ng)
Replicate
Brain Cancer Tissue Type 1
FormaPure DNA Supplier P
0
2
4
6
8
10
1 2 3
Yie
ld (
ng)
Replicate
Brain Cancer Tissue Type 2
FormaPure DNA Supplier P
A Competitive Look: High Performance
A260/A280
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
13
RNA isolation using FormaPure DNA
Superior RNA quality
Stomach
Breast
Lung
Liver
FormaPure DNA
Supplier Q
nt sizes
Flu
ore
scent
units
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
14
RNA isolation using FormaPure DNA
NGS Compatible
Illumina TruSeq® RNA Access Library Preparation kit
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
15
Biomek i-Series Automated Workstations
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
16
Features and Benefits of Biomek i-Series Automated
FFPE-Based Biomarker Workflow
FormaPure DNA FFPE Extraction
Place FFPE curls directly on-deck using BEC Matrix Tube Rack for
deparaffinization.
Scalable from 1 to 96 FFPE curl samples.
Incubations done on-deck using standard Inheco Static Peltier.
Complete walk-away solution.
Illumina TruSeq Exome
Supports TruSeq Exome kit configurations for 1-96 samples / 1 to 8
pools.
Biomek Method Launcher and Method Interface allow for ease of use
and reduction of setup errors.
Optional on-deck thermocycler option for increased walk-away time.
Modular method design supports all Illumina approved stop points and
provides maximum scheduling flexibility.
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
17
Biomek i7 Dual Hybrid NGS Workstation
BEC Orbital
Shaker
Inheco Static
Peltier
Thermo ATC Biometra TRobot
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
18
• What it is:
– Simple point-and-click interface to
launch and monitor methods
• What it does for you:
– Focus on system operation, no
need to open method authoring
interface
– Can reduce error by providing
step-by-step guidance
– Protects validated methods from
being altered inadvertently by
operators
Biomek Method Launcher is an add-on for system operators
Efficient step-by-step instructions to help operator accurately set up the deck,
avoiding runtime errors
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
i-Series Demonstrated Method Interface
1. Biomek Method
Launcher 2. Method Option
Selector
3. Guided
Labware Setup
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
20
New – Coming in June – Camera Deck
Verification
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
Biomek i7 Automated FormaPure DNA
Hands-
On
Time
(HOT)
Dewax,
Lysis, and
Decross
Time
Nucleic Acid
Isolation
Time
Samples
Processed
15 min 4 hr, 45 min 1hr, 33 min 96 DNA
15 min 3 hr, 23 min 2hr, 57 min 96 RNA
15 min 3 hr, 29 min 3hr, 31 min 96 DNA and
96 RNA
Automated Automation Protocol
Manual Dewax Decross Lysis Nuclease
Treatment Wash 1 Bind Wash 2 Elute
One technician
One Biomek
~1.5hr of HOT
500 samples/week
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE DNA Extraction using FormaPure DNA
on the Biomek i7 Dual Hybrid
Sample Supplier Type Age Technical
Replicates
Curl
Sizes
HD200 Horizon Horizon
Reference
N/A 8 N/A
FFPE 76 Asterand Breast 4 years 4 10 micron
FFPE 96 Asterand Breast 3 years 4 10 micron
FFPE 110 Asterand Lung 4 years 4 10 micron
FFPE 121 Asterand Lung 5 years 4 10 micron
FFPE 107 Asterand Liver 3 years 4 10 micron
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE DNA Extraction using FormaPure DNA
on the Biomek i7 Dual Hybrid
0.0
200.0
400.0
600.0
800.0
1000.0
1200.0
1400.0
Hori
zo
n 1
Hori
zo
n 2
Hori
zo
n 3
Hori
zo
n 4
Hori
zo
n 5
Hori
zo
n 6
Hori
zo
n 7
Hori
zo
n 8
76-1
76-2
76-3
76-4
96-1
96-2
96-3
96-4
110
-1
110
-2
110
-3
110
-4
121
-1
121
-2
121
-3
121
-4
107
-1
107
-2
107
-3
107
-4
Yie
ld (
ng)
Sample
FFPE DNA Yield
Molecular
Devices
SpectraMax i3
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE DNA Extraction using FormaPure DNA
on the Biomek i7 Dual Hybrid
96-1 (Breast)
DIN 3.6
107-1 (Liver)
DIN 3.3
110-1 (Lung)
DIN 2.1 121-1 (Lung)
DIN 2.2
76-1 (Breast)
DIN 2.2
Horizon 1
DIN 9.6
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
FFPE DNA/RNA Split Extraction using
FormaPure DNA on the Biomek i7 Dual Hybrid
0
0.5
1
1.5
2
2.5
3
Stomach Breast Liver Lung
Yiel
d (
ug)
RNA Yield
0
0.5
1
1.5
2
2.5
3
Stomach Breast Liver Lung
Yie
ld (
µg)
DNA Yield
Lung FFPE
RNA (RIN 2.4)
Lung FFPE
DNA (DIN 2.1)
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
DNA Isolation
DNAdvance
Genfind v2
Formapure DNA
CosMC Prep
RNA isolation (also micro
RNA)
RNAdvance Cell
RNAdvance Blood
RNAdvance Tissue (miRNA)
FormaPure RNA
(miRNA)
PCR Purification & Cleanup
AMPure XP
CleanSEQ
RNAClean XP
NGS Sample Prep
SPRIselect (size selection)
Demonstrated Library
Construction for popular kits
Biomek Automated Solutions for Genomic Applications Example: Sample Prep Truseq Standed mRNA (Illumina)
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
27
Biomek Automated Solutions for Genomic Applications Example: Sample Prep Truseq Stranded mRNA (Illumina)
Illumina TruSeq® Stranded mRNA Sample Preparation Kit protocol converts mRNA from total RNA into a template
sample of known origin. The protocol first uses poly-T oligo attached magnetic beads to isolate mRNA. Strand
specificity is attained by replacing dTTP with dUTP in the second strand cDNA synthesis step. Knowing the strand
origin improves transcript annotation accuracy and alignment efficiency, reducing sequencing costs per sample.
Uniform high coverage provided by the Stranded mRNA Sample Preparation Kit protocol ensures its suitability for
multiple applications such as discovering alternative transcripts, gene fusions, and allele-specific expression (Illumina
TruSeq® Stranded mRNA Library Prep Guide15031047-e).
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
28
Biomek i7 Dual Hybrid NGS Workstation
BEC Orbital
Shaker
Inheco Static
Peltier
Thermo ATC Biometra TRobot
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
29
Biomek Automated Solutions for Genomic Applications Example: Sample Prep Truseq Stranded mRNA (Illumina)
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
30
Consistent and reproducible results
• Yield correlates to amount of input RNA, replica very close to each other
Biomek Automated Solutions for Genomic Applications Example: Sample Prep Truseq Stranded mRNA (Illumina)
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
31
Biomek Automated Solutions for Genomic Applications Example: Sample Prep Truseq Stranded mRNA (Illumina)
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
32
Application Biomek FXP
Hybrid
Biomek i7
Hybrid
Difference
Number of plates/time
TruSeq DNA PCR-
Free 1/ 5hr 11min
1/ 4hr 9 min 1 hr, 2 min
TruSeq Nano DNA 1/ 8 hr, 36 min
1/ 5hr,12 min
3 hr, 24 min
FormaPure DNA 1/ 5hr, 56 min
1/ 5hr, 5 min 51 min
AmpureXP Batch Cleanup
5/ 50 min
7/ 1hr, 5 min
~1 min per plate
Application Biomek FXP
Hybrid
Biomek i7
Hybrid
Difference
() negative
Number of Intervention Points
TruSeq Nano DNA 2 0 (2)
Biomek Automated Solutions for Genomic Applications Throughput and timings
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
33
Biomek i7 Dual Hybrid NGS Workstation
BEC Orbital
Shaker
Inheco Static
Peltier
Thermo ATC Biometra TRobot
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
34
Biomek i5 Span-8 NGS Workstation
BEC Orbital
Shaker Inheco Static
Peltier
Thermo ATC Biometra TRobot
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
35
Biomek 4000 NGS Workstation
BEC Orbital
Shaker Inheco Static
Peltier
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
36
Extensive Portfolio of Demonstrated Biomek Methods Growing Portfolio of Methods for the i-Series
*All Trademarks are the property of their respective owners
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
37
Extensive Portfolio of Demonstrated Biomek Methods Growing Portfolio of Methods for the i-Series
*All Trademarks are the property of their respective owners
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
38
Extensive Portfolio of Demonstrated Biomek Methods Growing Portfolio of Methods for the i-Series
*All Trademarks are the property of their respective owners
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
39
Extensive Portfolio of Demonstrated Biomek Methods Growing Portfolio of Methods for the i-Series
*All Trademarks are the property of their respective owners
©2016 Beckman Coulter, Inc. All rights reserved. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks used herein are the trademarks or registered trademarks of Beckman Coulter, Inc. in the United States & other countries. Internal | Company Confidential
40
Summary
Beckman offers low to high throughput Biomek automated solutions for
genomic sample prep workflows.
The Biomek i- Series platforms include features that improve efficiency and
throughput/productivity and can decrease hands-on and processing time.
Beckman offers a large portfolio of demonstrated ready- to- implement NGS
sample prep methods for all platforms. The list is growing quickly for the i-
Series.
Demonstrated methods interface makes implementation, training and daily
running of method EASY!