DNA Services Overview

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5 Νοε 2013 (πριν από 4 χρόνια και 2 μέρες)

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© 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 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

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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 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


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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.com

SeqSales@perkinelmer.com

Phone: +1
-
877
-
737
-
5468