Pricing Committee Meeting - Welcome to Centre for Genomic ...cgs.hku.hk/portal/files/GRC/Events/Seminars/2012/20120913/miseq... · RTA v1.16 Improved low diversity detection logic

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COMPANY CONFIDENTIAL – DO NOT DISTRIBUTE

MiSeq The Most Accurate and Easiest to Use

Benchtop Sequencer in the World

2 COMPANY CONFIDENTIAL – DO NOT DISTRIBUTE

Upgraded MiSeqs ship fully loaded

– Hardware

Compensator

Syringe

PC

– Software

MCS2.0

Upgraded MiSeqs Started Shipping August 7, 2012 Customers are talking!


The MiSeq Trade-In Program is in the News

Illumina’s trade-in program was a

‘win-win’ for my lab. Demand for 454

had decreased and the box was

more expensive to operate than

other platforms.

Shrikant Mane, Yale core

The labor that’s required to run the PGM

and GS Jr is immense and messy and

still too variable. With MiSeq we can with

high confidence set up a qPCR library

quant and set up a run in less than 30’

after library is generated.

Anonymous, Clinical Seq


What Our Customers are Saying About Their MiSeq

Upgrades

We achieved 8.9Gb output after our

MiSeq upgrade!

Pioner Hi-Bred

We achieved almost 10 Gb output on PhiX

after MiSeq upgrade and >80% Q30.

Shrikant, Yale

I believe that the 2x250 data gave us an assembly that was almost

exactly equivalent to a shotgun 454 FLX+ assembly in terms of

Contig number and N50 (though obviously cheaper and faster, and

The data are better for SNP calls with MiSeq)

Nick Bergman, NBACC/DHS


New Worldwide Grant Program!

What is it: MiSeq Grant Program

Who can apply: Anyone! Novice or experienced with NGS!

How to apply: Complete short abstract (500 or less words) on ILMN.com for

judging


Prize Package

Three grants, each including:

– One (1) MiSeq system

– Ten (10) Sequencing reagent kits

– Choice of sample prep:

Nextera XT DNA Sample Prep (384 Samples) or

TruSeq Custom Amplicon (384 Samples)

– BaseSpace cloud computing analysis and storage

– Avadis NGS, a biologist-friendly bioinformatics desktop tool


Judging Criteria, Timeline & Outbound Marketing

Scoring Criteria

– Scientific Merit

– Originality

– Fit with MiSeq

Timeline

– Campaign Launch: 8/22

– Submissions due: 10/15

– Internal Judging: 10/16 – 11/2

– ASHG Winner Announcement: 11/6


MiSeq v2 Chemistry Dramatically Improves Performance Longer Read Length, Same Great End-of-Read Quality

Quality scores at the 250th base with new chemistry similar to those at the

150th base with earlier chemistry (E. coli data)

Read 1 Read 2


MiSeq Reagent Portfolio Options at Every Read Length – Support for Multiple Applications

50-cycle 300-cycle 500-cycle

25bp

50bp

250bp 250bp

250bp 250bp

400bp 100bp

25bp 150bp 150bp

Single Read 50bp

–RNA-Seq,

–Chip-Seq

–Short Amplicon

Paired end 2x25bp

–Library QC

Paired end 2x150bp

–TSCA

–Small Genome de novo

–Standard Amplicon

Standard PE 2x250bp

Overlapping PE 2x250bp

(2x consensus in overlap)

Asymmetric PE generate

long (400+ bp) “fragment-

like” reads

150bp 150bp

Overlapping 2x150bp

– FFPE amplicon


Easy Forward & Backward Compatibility Mix and Match v1 and v2 kits with both instrument types

MiSeq v2 reagents are compatible with

legacy instruments

– Requires MCS 2.0 (available now!)

– Enables 2x250bp sequencing

– Single surface imaging only

MiSeq v1 reagents can be run on

upgraded MiSeq instruments

– Single surface imaging only

– v1 specifications

MiSeq

Instrument

Upgraded

MiSeq

MiSeq Kit v1

MiSeq Kit v2

Up to 1.5Gb

Up to 2x150

Up to 2.5Gb

Up to 2x250

Up to 7.5Gb

Up to 2x250

Up to 1.5Gb

Up to 2x150


MiSeq System - Upgraded


MiSeq Continuous Performance Improvements

Up to 4 M clusters/run

Up to 2 x 250 bp read length

ETA: late Q4 2012

100’s Mb

7 Gb

1-1.5 Gb

Gb

15-17 M clusters/run

2 x 250 bp read length

4.4-5.1 Gb at 2 x 150

7.5-8.5 Gb at 2 x 250

<5 min cycle time

5-7 M clusters/run

2 x 150 bp read length

5 min cycle time

• Read lengths get longer

- 66% increase

• Output grows

- 3 fold improvement

in number of clusters run


Setting New Standards in Benchtop Sequencing MiSeq is the most accurate and easiest to use benchtop sequencer in the world

Greater sequencing coverage for somatic mutation detection in gene panels

Higher multiplexing capability for sequencing of bacterial genomes

Improved de novo assembly of small genomes

Profile several gene expression samples per run

That’s almost 6Gb of Q30 data!


MiSeq System Performance Improving System Utility

Key Improvements

– Chemistry

Faster Clustering

Faster PE Chemistry

Faster SBS Cycle Time ~2 min

chemistry

– Yields Faster Run Times

– Hardware

More imageable area (dual surface)

Faster onboard PC

– Software

Illumina Experiment Manager

MiSeq Control Software

Real Time Analysis

MiSeq Reporter


MiSeq Software


Accelerated Flow Cell scanning (through partial scanning of FC)

Faster run times!

Improved workaround for RFID read failures

Less customer complaints

Optional email notification for

RTA completion

MiSeq Reporter analysis completion

Fatal error during sequencing

Post-run wash now required to ensure extended life of MiSeq valves

MiSeq Control Software


Improved speed & performance (up to 35% improvement)

New user interface with better performance and improved graphics

Improved sample sheet validation before analysis

User can edit sample sheet on the fly through the user interface

New default aligner/variant caller:

MiSeq Reporter

Workflow Default Aligner Default Variant Caller

Resequencing BWA GATK

Custom Amplicon (TSCA) Banded Smith-

Waterman

GATK

PCR Amplicon (Nextera) BWA GATK

Library QC BWA N/A

*Can switch back to old Eland/Starling through config setting


RTA v1.16

Improved low diversity detection logic

If low diversity detected, switch to new matrix/phasing logic to improve detection

Address low diversity challenges especially for 16S metagenomics

BaseSpace Broker v2.0

Status of run (e. Paused, stopped) communicated to BaseSpace

Users can monitor run in real-time through BaseSpace via browser (no need for SeqMonitor)

Avadis NGS desktop software for Amplicon, RNA-Seq, ChIP-Seq, Small RNA analysis

ILMN customers get discount to Avadis software license http://bit.ly/IlluminaNGS

RTA, BaseSpace, and Avadis NGS

MiSeq instruments connected to BaseSpace will automatically receive Updater

Customers can manually update via Updater available at MyIllumina:

(http://icomadmin/Download/Edit/iHJn1IjhlUC9Wf63yynCrg)

http://bit.ly/IlluminaNGS

http://icomadmin/Download/Edit/iHJn1IjhlUC9Wf63yynCrg


MiSeq Upgrades and Logistics


MiSeq Hardware Upgrades

Upgrade Part Part Function Benefits

Single Board

Computer(SBC)

Controls image processing

and data analysis

Improved computational ability

to handle increased system

output

Compensator

Lens

Enables dual-surface

imaging of the flowcell

Higher output by running 14

tiles on top and bottom

surfaces.

Reagent valve

and syringe

Valve responsible for

reagent delivery to the

flowcell

Improved robustness when

used with new auto-wash

recipe in MCS.


Start MiSeq Upgrade

Pre-Upgrade Activities

Upgrade SBC Board/E-box

hardware

Replace the hard drive

Install and adjust the

compensator

Upgrade the syringe

Restore and configure files

Qualify the Upgrade

All done!

MiSeq Upgrade Workflow: ~ 1 day to complete

Valve Swap if needed


Applications


New Features for TruSeq Custom Amplicon (TSCA) Available August 31st

Increased plexity up to 1,536 amplicons per reaction – designs

covering up to ~600 kb of total content

More flexible amplicon sizes – smaller to enable custom panel support

for FFPE, and larger to take advantage of 2 × 250 bp read lengths

supported on the MiSeq system

Designs for non-human genomes – Early access to selectable

reference genomes for mouse, rat, and bovine


MiSeq improvements empower applications

What do 15M clusters and 2x250 bp reads give you?

Amplicon-based applications

– Larger TSCA up to 1,536

amplicons

– Higher sample throughput for

smaller amplicon panels

– Deeper coverage for rare somatic

mutations

– Larger amplicons

– Bidirectional sequencing of

smaller amplicons <250 bp for

ultimate confidence in results

Small Genomes

– Higher sample throughput per run

– Better de novo assemblies

– Larger insert Nextera XT protocol

coming soon!


Applications – RNA-Seq


RNA-Seq Applications

GEx Profiling Transcriptome Analysis

“Gene” level fold change

High Reproducibility

Simple Analysis

• 50 bp , SR or PE

• 5 – 10M reads

Discovery

Diff exp. of alt. transcripts

Detection of cSNPs, gene

fusions

• 50-75 bp, PE

• 50-100M reads


70

MiSeq 2 output will dramatically increase demand for RNA analysis

Increased output attractive to larger customer base

Fits broader range of study designs, including small mammalian studies

Competitive environment heavily pushing replacement for GEx arrays

5-10 M reads of 50 bp length from mRNA will give performance better than

any microarray

Paired end capabilities only available on MiSeq!

RNA-Seq application important for MiSeq

70 70


Introducing TruSeq ChIP Sample Prep

(Shipping Aug. 2012)

Directly MiSeq Compatible

Multiplexed ChIP-Seq analysis

– 24 unique indexes

Streamlined workflow

Low sample input requirement (5ng)

Only $54 per sample!!

– >75% reduction relative to

legacy

Offers multiple improvements over current ChIP-Seq Sample Prep kits!


Introducing Nano and Micro MiSeq Reagent Kits

Cost‐effective pricing for the amount of output that is

“just right”


Appendix


Compatibility Matrix

HW

upgraded? SW

version

Reagent

version Kit size

Clusters PF

(M) Paired

End Read Length

(bp) Output (Mb) Output (Gb)

no MCS

1.2 1

50-cycle 5 2 25 250 0.25

300-cycle 5 2 150 1500 1.5

no MCS

2.0 1

50-cycle 5 2 25 250 0.25

300-cycle 5 2 150 1500 1.5

no MCS

2.0 2

50-cycle 5 2 25 250 0.25

300-cycle 5 2 150 1500 1.5

500-cycle 5 2 250 2500 2.5

yes MCS

2.0 2

50-cycle 15 2 25 750 0.75

300-cycle 15 2 150 4500 4.5

500-cycle 15 2 250 7500 7.5

Documents

Pricing Committee Meeting - Welcome to Centre for Genomic ...cgs.hku.hk/portal/files/GRC/Events/Seminars/2012/20120913/miseq... · RTA v1.16 Improved low diversity detection logic