Introducing HiSeqTM 2000HiSeq 2000

Abizar Lakdawalla

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Abizar Lakdawallaalakdawalla@illumina.com

Simple Illumina Sequencing Workflow

SIMPLIFIED SAMPLE PREP

cBot CLUSTER GENERATION

HiSeq 2000 SEQUENCING

DATA PROCESSING & ANALYSIS

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Parallel sample processing

Automated clustergeneration

Automated sequencing

Simple, efficient data analysis

HiSeq 2000 Comparison with the Genome Analyzer

HiSeq 2000(at launch)

GAIIx

(at 50G)

Gb per run 150-200 50

GAIIx

(at 95G)

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Gb per runGb per dayCluster density in KClusters/mm²**Read lengthAvailable surface area (mm²)*

150-20020-25

260-3502 x1002880

505

4902 x100

510

*GAIIx with single surface, single FC, HiSeq 2000 with dual surface, dual FC**Clusters passing filter

957

6202 x150

510

HiSeq 2000 - two surface scanning

1. Line scanner2. Epi-illumination3. Top surface (all 4 colors) scanned in one pass4. Bottom surface (all 4 colors) scanned in 2nd pass4. Bottom surface (all 4 colors) scanned in 2nd pass5. 2 scanning swaths in each lane of a flow cell

Clusters

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Bottom surface

Top surface

HiSeq 2000New flow cell design

LARGER, DUAL-SURFACE ENABLED

>5x increase in imaging area>5x increase in imaging area

Retains 8 lane format

Compatible with cBot

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HiSeq 2000 Dual Flow Cell DesignExperimental flexibility

SIMPLE FLOW CELL LOADING

Flow cells held by vacuum

No oil needed

LED switch ensures correct connection

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HiSeq 2000 Plug-and-play reagents

PRE-CONFIGURED SEQUENCING REAGENTSPRE-CONFIGURED SEQUENCING REAGENTS

Only two minutes hands-on time

Up to 200 cycles per flow cell

Bar-coded for tracking

Temperature-controlled compartment

Integrated paired-end fluidics

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HiSeq 2000A leap forward in sequencing innovation

MOST WIDELY ADOPTED AND PROVEN CHEMISTRY

Leverages Illumina’s reversible terminator based SBS chemistry Leverages Illumina’s reversible terminator based SBS chemistry

INNOVATIVE ENGINEERING

Dual flow cell, dual surface imaging

Four camera system with cutting edge scanning technology

HUMAN INTERACTION DESIGN ELEMENTS

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HUMAN INTERACTION DESIGN ELEMENTS

Simplest user experience

HiSeq Control SoftwareTouch screen user interface

SIMPLE OPERATION

Step-by-step run set up

Real time run monitoring

Reagents usage tracking

Remote monitoring from web browser

Enter read length, single, paired-read, indexing

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Remote monitoring from web browser

Multimedia help menu

HiSeq Control SoftwareTouch screen user interface

SIMPLE OPERATION

Step-by-step run set up

Real time run monitoring

Reagents usage tracking

Enter read length, single, paired-read, indexing

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HiSeq Control SoftwareTouch screen user interface

SIMPLE OPERATION

Step-by-step run set up

Real time run monitoring

Reagents usage tracking

Remote monitoring from web browser

Enter read length, single, paired-read, indexing

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Remote monitoring from web browser

Multimedia help menu

HiSeq 2000 Data AnalysisA simple, familiar workflow

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HiSeq CONTROL SOFTWARE

Read Generation

CASAVA

Alignments, variations, builds

VISUALIZATION

GenomeStudio, or favorite browser

HiSeq 2000Sequencing redefined

HIGHEST OUTPUT

200 Gb per run at launch200 Gb per run at launch

FASTEST DATA RATE

~25 Gb/day

7-8 days for 2 x 100 bp

HIGHEST NUMBER OF READS

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HIGHEST NUMBER OF READS

One billion single-end reads

Two billion paired-end reads

Whole Transcriptome Studies: Two Runs

INDIVIDUAL HUMAN TISSUES

16 tissues, 1 lane per tissue, 2x50 bp

Standard poly A+ mRNA-Seq Library Preps

Body Map 2.0 ProjectAdrenal, Adipose, Brain, Breast, Colon, Heart, Kidney, Liver, Lung, Lymph Node, Ovary, Prostate, Skeletal Muscle, Testis, Thyroid, White Blood Cells

TOTAL HUMAN TRANSCRIPTOME

Equal Mixture of 16 Human Tissues

3 libraries–polyA+ mRNA, normalized polyA+, normalized ribominus RNA method

Strand-specific mRNA-Seq, 1x100 bp

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Format PF readsAverage error rates

(phiX spike-ins) Yield

Individual human tissues 2x50 2.24 B 0.27%, 0.18% >100 Gb in <5 days

Total human transcriptome 1X100 1.19 B 0.67%, 0.81% >100 Gb in <5 days

Thyroid, White Blood Cells

SUMMARY OF RUN METRICS

HiSeq 2000Unmatched cost-effectiveness

HiSeq 2000$690K

cBot$55K

$690K

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Total run cost US List

Price per run (2 flow cells, 2 x 100 bp, 200 Gb)

Price per human genome (1 flow cell, 100 Gb)

$19,800

$9,900

*available shortly after launch

Consumables cost estimates

Bacterial genomes (5Mb at 30x depth)

– 1000 – 2000 samples per run

– $10-20 + sample prep cost / sample

Whole human exomes (30Mb at 50x depth)

– 100-200 samples per run

– $100-200 + sample prep cost / sample

Human transcriptomes (20M templates/sample)

– 50 samples per run (50bp)

– $200 + sample prep cost/sample

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– $200 + sample prep cost/sample

Whole human genome (3Gb at 30x depth)

– 2 samples per run

– $10000 per sample

Thank you

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