11 © 2009 PerkinElmer© 2009 PerkinElmer© 2009 PerkinElmer© 2010 PerkinElmer

November 20, 2012

DNA Services Overview

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Sequencing & Analysis Services at a glance

Illumina or Agilent library preparation Clustered flowcell generation Paired end and single end sequencing 2x100

Whole genome Adapted libraries Prepared flowcells

Target capture by hybridization Agilent SureSelect exomes Agilent SureSelect custom targeted

Illumina TruSeq Amplicon-Cancer panel* Data Analysis

*available January 2013

WHAT WE CAN DO . . .

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Sequencing & Analysis Services at a glance

In house DNA or RNA extraction - Rutgers In house RNA to cDNA conversion Specialized/custom sample prep – chip / methyl Long-read sequencing De novo assembly – will allign to provided reference

WHAT WE DO NOT CURRENTLY OFFER . . .

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Sequencing & Analysis Services at PKI

Product Offering

High Throughput Sample Prep• Automated library prep for sequencing• Automated target capture by hybridization•Strict SOP-driven processes •Extensive quality checking•CT licensed clinical lab (No. CL-0685)•CLIA registered ( ID# 07D2034530)• Project consulting services

Sequencing Apps• Exome re-sequencing• Targeted re-sequencing• Microbial re-sequencing• Prepared library re-sequencing• Whole genome re-sequencing (on demand)• RNA• Clinical sequencing

Operational Infrastructure• 4—6 week turnaround•LIMS for sample tracking• 3 HiSeqs + 1 MiSeq

• > 6000 samples successfully processed to date• Secure private cloud in sequencing center; semi-public cloud hosted by PerkinElmer Informatics

• Current analysis capacity of 50-60 exomes per day—highly scaleable computing infrastructure

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PerkinElmer is focused on bringing best in class technologies – we continually evaluate new technologies to ensure we are providing

the best available systems & processes to our customers

…ensures faster turn-around-times and high quality control

Employing Proven Technologies & World-Class Automation…

SAMPLE & PROCESS TRACKING

PerkinElmer Informatics LIMS: providing sample tracking and status updates

CURRENT PLATFORMS

PKI JANUS Automated Workstations

PKI EnSpire Plate Reader

Caliper Labchip GXII

AUTOMATION

Agilent SureSelect

TARGETED CAPTURE

Illumina HiSeq 2000 system

Illumina MiSeq

SEQUENCING

PerkinElmer Informatics Analysis Edition: private cloud implementation

ANALYSIS

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DNA Library preparation

Target Enrichment [Optional]

Automated Amplification (Clustering)

Automated Sequencing

Automated Data

Analysis

Workflow flexibility to accommodate customer needs

Prepared by us•Libraries•Captures•Flowcells

Prepared by customer•Libraries•Captures•Flowcells

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Variable read lengths (50-100bp)Sequence in one or two directionsUp to 2.8 x109 reads per flow cell (280 Gb)Run time is variable 1 x 50bp =~ 2.5 days 1 x 100bp = ~6 days 2 x 100bp = ~12 days

Output deliverables can vary depending on project requirements

Illumina HiSeq 2000-Overview

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Sample Submission

Each sample submission needs to be accompanied by sample manifest Required DNA concentration is ≥25 ng/µL Required concentration for ready-to-sequence libraries is ≥ 10nM Required amount of SureSelect XT library for capture ≥ 700ng

When submitting, send shipping notification to Seqproject @ perkinelmer.com along with electronic copy of shipping manifest and tracking numberSamples should be shipped overnight via express shippingFollow instructions contained in “Sample Prep and Shipping Guidelines_v3.2” for sample purity, concentration, etc.

Not following instructions will delay the project

Include hardcopy of sample manifest with samples

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We use either Illumina TruSeq or Agilent SureSelect for library prep Currently evaluating Nextera, but not yet in production We do not use NuGen kits

Required for everything but sequencing of PCR products Whole genome resequencing Targeted resequencing RNA-Seq

Minimal sample requirements (as per kit providers protocols) 1 µg purified DNA for TruSeq libraries 3 µg for purified DNA for SureSelect libraries

Lower input amounts are at sample owners risk All incoming DNA samples subjected to QC

Gel electrophoresis-qualitative assessment for degradation Picogreen fluorometry -quantitation

Samples failing QC will not be processed without consent of owner Any unused sample can be returned to owner or destroyed

Return requires charges for packaging and shipping Any unused library can be returned to owner or destroyed

Return requires charges for packaging and shipping

Library Preparation Guidelines

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We currently use Agilent SureSelect products Whole exome Custom Kinome Others

Can/will sequence captured materials sent to us TruSeq Exome Enrichment Nimblegen

Targeted Capture Guidelines

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Thank You!

For additional information, please contact:dawn.casey@perkinelmer.comSeqSales@perkinelmer.comPhone: +1-877-737-5468