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November 20, 2012

DNA Services Overview. November 20, 2012. Sequencing & Analysis Services at a glance. WHAT WE CAN DO . . . . Illumina or Agilent library preparation Clustered flowcell generation Paired end and single end sequencing 2x100 Whole genome Adapted libraries Prepared flowcells

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November 20, 2012

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  1. DNA Services Overview November 20, 2012

  2. Sequencing & Analysis Services at a glance WHAT WE CAN DO . . . • 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 SureSelectexomes • Agilent SureSelect custom targeted • Illumina TruSeqAmplicon-Cancer panel* • Data Analysis • *available January 2013

  3. Sequencing & Analysis Services at a glance WHAT WE DO NOT CURRENTLY OFFER . . . • 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

  4. 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. Employing Proven Technologies & World-Class Automation… Current Platforms Automation Targeted Capture Sequencing Analysis Sample & Process Tracking • PerkinElmer Informatics LIMS: providing sample tracking and status updates • PKI JANUS Automated Workstations • PKI EnSpire Plate Reader • Caliper Labchip GXII • Agilent SureSelect • Illumina HiSeq 2000 system • Illumina MiSeq • PerkinElmer Informatics Analysis Edition: private cloud implementation 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

  6. Workflow flexibility to accommodate customer needs • Prepared by us • Libraries • Captures • Flowcells • Prepared by customer • Libraries • Captures • Flowcells

  7. Illumina HiSeq 2000-Overview • Variable read lengths (50-100bp) • Sequence in one or two directions • Up 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

  8. 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 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. Library Preparation Guidelines 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 • Picogreenfluorometry -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

  10. Targeted Capture Guidelines We currently use Agilent SureSelect products • Whole exome • Custom • Kinome • Others Can/will sequence captured materials sent to us • TruSeqExome Enrichment • Nimblegen

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

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