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©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


Your next discovery just got the green light. Introducing the Biomek i-Series Automated Workstations for Genomics workflows


• 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

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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


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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


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


FFPE for Biomarker discovery in cancer research

Biomarker

Discovery


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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.


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


- 9 steps

- 1 centrifuge steps (manual)

- 0 for Automation

- No Xylene required.

- 3 temperatures

- No Risk of clogging

Simple Workflow


FormaPure DNA: DNA/RNA isolations

Split protocol allows you to isolate total nucleic acids from one sample.


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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.


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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


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Superior RNA quality

Stomach

Breast

Lung

Liver

FormaPure DNA

Supplier Q

nt sizes

Flu

ore

scent

units


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NGS Compatible

Illumina TruSeq® RNA Access Library Preparation kit


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Biomek i-Series Automated Workstations


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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.


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Biomek i7 Dual Hybrid NGS Workstation

BEC Orbital

Shaker

Inheco Static

Peltier

Thermo ATC Biometra TRobot


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• 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


i-Series Demonstrated Method Interface

1. Biomek Method

Launcher 2. Method Option

Selector

3. Guided

Labware Setup


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New – Coming in June – Camera Deck

Verification


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


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




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




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


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)


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)


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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).


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BEC Orbital

Shaker

Inheco Static

Peltier



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Consistent and reproducible results

• Yield correlates to amount of input RNA, replica very close to each other



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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


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BEC Orbital

Shaker

Inheco Static

Peltier



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Biomek i5 Span-8 NGS Workstation

BEC Orbital

Shaker Inheco Static

Peltier



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Biomek 4000 NGS Workstation

BEC Orbital

Shaker Inheco Static

Peltier


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Extensive Portfolio of Demonstrated Biomek Methods Growing Portfolio of Methods for the i-Series

*All Trademarks are the property of their respective owners


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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!

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