GoldenGate GenotypingA New Evolution in High-Throughput Screening

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Sequencing Enabled iScan

Addressing Breadth of Customer Needs

110102103104105106107108>109

Discovery Focused Research/Validation Screening

Whole Genome Single Marker

GenomeAnalyzer

• WG Resequencing• WG Gene Expr.• miRNA Discovery

& Profiling• WG ChIP-Seq

• Candidate Resequencing

• Chromosome sequencing

BeadXpress

• Low/mid density GT/GEX

• Protein applications• Biomarker screening• Biomarker panels

• Gene Expr.• WG GT• WG CNV• Biomarker

Discovery

• HT Biomarker Validation

• Custom GT• Focused Expr.• FFPEiScan

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Comprehensive Solution: Discovery to Validation to Screening

Discovery - Any variant. Any species. The Genome Analyzer and iScan Reader combine high throughput, accuracy, and application flexibility. Taking you beyond simple discovery.

Validation - Informative markers. Validated discoveries. Research with confidence using the Genome Analyzer, iScan Reader and BeadXpress platforms.

Screening - Accelerate the transition from lab-to-field using the iScan and BeadXpress Readers. Quickly and easily screen your markers of interest in large populations.

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Agrigenomics ApplicationsPane

l Plex

Year

2005          2009     2010     2011     2012     2013     2014  2015

>1M

>500K

100K

10K 

3K

<500

<100

Genome‐wide Selection

MAB

Q4 2008Fingerprinting

Genome‐wide Selection

Q4 2008Genetic Merit

Q4 2008Parentage ID

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Agrigenomics Applications – Low Plex ScreeningPane

l Plex

Year

2005          2009     2010     2011     2012     2013     2014  2015

>1M

>500K

100K

10K 

3K

<500

<100 MAB

Q4 2008Fingerprinting Q4 2008Genetic Merit

Q4 2008Parentage ID

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GoldenGate Assay

Pre-optimized and robust assay, tolerant of poor template quality

Accurate SNP genotyping through allele specific extension

Uses Universal Assay Chemistry – up to 1536 Assays in a single reaction

G‘illumiCode’ Address

Allele Specific Extension &Ligation

Universal PCR Sequence 1

Universal PCR Sequence 2

Universal PCR Sequence 3’

Genomic DNA [T/C] [T/A]

Allele-specific Extension & Ligation

A

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GoldenGate BeadArray

GoldenGate® Custom Genotyping

96 to 1536-plex

DNA input ~ 250ng

iScan system

LIMS/Automation

BeadChips

~288 samples/day

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Universal-32 BeadChip for the GoldenGate Assay

Designed for the flexible, pre-optimized GoldenGate Assay

– Available for 96 to 1536 SNPs– Custom designs for any species

Compatible with the iScan and BeadArray– Up to 128 samples per iScan run– 96 samples scan in less than 30 min.

Designed for 8 channel pipette loading

Autoloader capability

Ideal for streaming with Infinium processes

Automation and LIMS supported

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Powerful and economical platform

Fully automated operation

Compact bench top system

Highest Resolution (0.54)

Forward Compatible

Fastest Scan Times

Modular– Automatization– Microarray– Next-Gen-Sequencing

iScan

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Illumina LIMS Solution

Prevent sample mix-up

Increase confidence and efficiency:

Complete system integration

Maximize quality, save resources:

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GoldenGate VeracodeGoldenGate BeadArray

GoldenGate® Custom Genotyping

48 to 384-plex

DNA input ~ 250ng

BeadXpress system

Automation

VeraCode

~288 samples/day

96 to 1536-plex

DNA input ~ 250ng

iScan system

LIMS/Automation

BeadChips

~288 samples/day

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VeraCode TechnologyDesigned for the flexible, pre-optimized GoldenGate Assay

– Available for 48 to 384 SNPs

Cylindrical glass microbeads

240 μm length x 28 μm diameter

Compatible with the BeadXpress Reader

CODE IMAGE

1 0 1 1 0 1 0 1 0 0 0 0 1 0 1

BINARY CODE DECIMAL CODE= 41133

CODE GENERATED BY CREATING EMBEDDED HOLOGRAPHIC DIFFRACTIVE ELEMENTS

CONVENTIONALCCD CAMERA

BEAD

“READING”BEAM

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BeadXpress – Built for flexibility

100000

10000

1000

100

10

10.1 1 10 100 1000 10000

Conc (pM)

Cou

nts

AnalyteFit3-sigma LOD

GENE REGULATION PROTEIN EXPRESSION

GENOTYPING

0 1 2 3 4 5

Log10(Conc pg/ml)

IL-6 (6152)

2

3

4

5

Lo

g1

0(N

et R

FU

)

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STOP STOP

STOP

Make SUD(Single Use DNA)

Add MEL(Make Extension and Ligation)

Make ASE plate(Allele Specific Extension)

Inoculate and Cycle PCR Bind PCR HYB WASH and SCAN

GoldenGate Workflow for BeadArray and VeraCode

STOP

STOP Potential or recommended stopping point

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GoldenGate VeracodeGoldenGate BeadArray

GoldenGate® Custom Genotyping

48 to 384-plex

DNA input ~ 250ng

BeadXpress system

Automation

VeraCode

~288 samples/day

96 to 1536-plex

DNA input ~ 250ng

iScan system

LIMS/Automation

BeadChips

~288 samples/day

GoldenGate Indexing

96 to 384-plex

DNA input ~ 250ng

iScan system

LIMS/Automation

BeadChips

>2000 samples/day

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Introducing GoldenGate IndexingThe next evolution of GoldenGate

+ +

GoldenGate Indexing Technology Offers Optimal Combination of Throughput and Cost for Low Complexity

Sample Screening

Highest Throughput: Greater than 2,000 samples per day

Highly Flexible: Advanced multiplexing enables analysis of 96 to 384 loci per sample

Fully Integrated: Automated platform incorporating LIMS

Proven Technology: Robust assay used in genotyping centers worldwide with averagecall rates > 99%

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GoldenGate Indexing Assay

Sample 1A Sample 1B Sample 1C Sample 1D

Row1/ColumnA

OPA ACodes: 1-384

OPA BCodes: 385-768

OPA CCodes: 769-1152

OPA DCodes: 1153-1536

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STOP STOP

STOP

Make SUD(Single Use DNA)

Add MEL(Make Extension and Ligation)

Make ASE plate(Allele Specific Extension)

Inoculate and Cycle PCR Bind PCR HYB WASH and SCAN

GoldenGate Indexing Workflow

STOP

Pool ASE

STOP Potential or recommended stopping point

Utilizing Pre-PCR with 96 tip head and current Post-PCR automation

Pooling to save time and cost in Post PCR

2 Technicians on a split shift

Applicable to all plexity

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Rat Citrus

Wheat HoneyBee

Armadillo

Cacao

Rhesus

Cat

Canola

Rice

Atlantic Cod

LettuceFalse

Brome

SheepSwine

HorseCattle

Human

PeachPoplar

Rye grass

Turkey

Soy Bean BarleyCitrus

Cotton

Rapeseed Spruce

MouseCornPine

Chicken

Dog

Tomato

Atlantic Salmon

Grape Vine

Sweet Sorghum

P. falciparum

Zebra Finch

Zebra Fish

Custom Genotyping on the GoldenGate Assay

Applications

Targeted panels

SNP validation

Agriculture fingerprinting panels

Commercial Agriculture screening panels

The Right Content Lets you Capture More Biology

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Discover. Validate. Screen

A new evolution in agriculture genetic analysis.