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11 © 2009 PerkinElmer © 2010 PerkinElmer November 20, 2012 DNA Services Overview.

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Presentation on theme: "11 © 2009 PerkinElmer © 2010 PerkinElmer November 20, 2012 DNA Services Overview."— Presentation transcript:

1 11 © 2009 PerkinElmer © 2010 PerkinElmer November 20, 2012 DNA Services Overview

2 22 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...

3 33 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...

4 44 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

5 55 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

6 66 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

7 77 Variable read lengths ( 50-100bp ) Sequence in one or two directions Up to 2.8 x10 9 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

8 88 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 @ along with electronic copy of shipping manifest and tracking number Samples should be shipped overnight via express shipping Follow 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

9 99 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

10 10 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

11 11 Thank You! For additional information, please contact: Phone: +1-877-737-5468

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