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The Laboratory Robotics Interest Group

April 2009 Meeting

Seventh Annual Sample Management Meeting

Automated Biorepositories: Enabling Technologies

Joint meeting presented by LRIG Mid
Atlantic
, LRIG New England, and the
Automated Repositories Working Group
of ISBER – the International Society for
Biological and Environmental Repositories

Date: Tuesday, April 7, 2009

Place:
Groton Inn & Suites

99 Gold Star Hwy (State Hwy 184)

Groton, CT 06340
Directions:
http://www.grotoninn.com/directions.html
, and see
our detailed directions page
Agenda: Tours of Pfizer facility 11:00 am – 1:00 pm

Buses will leave from the conference center for the short trip to Pfizer
at regular intervals between 11:00 am and 1:00 pm. You must be on
a bus to enter Pfizer.
Exhibition & Social Period 11:00 am – 3:30 pm
Food & Beverages 2:00 pm – 3:30 pm
Presentations 3:30 pm – 7:00 pm

Registration:

 
/member/meetings.asp?rid=1

Please Note:
For security reasons, you MUST
register to go on the tour at Pfizer.

Agenda:  Following last year’s
extremely successful meeting

Automated Biorepositories: Successful Models
, LRIG is pleased to
present a third event focused on this emerging area.

This meeting will be held in the Groton CT area. We will feature tours of the
Pfizer Kings Heights Technology
Center
including their sample management operations, Compound Liquid
Store, and DNA & BioFluids Store. The

Pfizer DNA & BioFluids Store
is one of two large-scale automated
biorepositories in the world, the other being the

UK Biobank
which was presented in this meeting last year. The technology exhibition,
social networking time with buffet, and presentations will be held in the
Groton Inn and Suites
conference center just a short distance away. Transportation between the
conference center and Pfizer will be provided.

We are pleased to open up this meeting for exhibits. Providers of automated
systems and enabling technologies will display their newest products and be on hand to discuss their solutions.



A buffet and refreshments will be available FREE OF CHARGE
during the Exhibition & Social Period. As well, during the presentations
there will be sandwiches, finger food and beverages available to eat at your
seats.

There is always a Job posting board at the social. Please encourage your recruiters to
give you material to post and distribute. Openings may also be posted at:


/forums/forumdisplay.php?f=3

There is no fee to attend the meeting.

For information on participating at this event or future meetings on
compound, biological and environmental repositories, please contact Andy Zaayenga,

Tours:  A highlight of the April 2009 LRIG meeting will be
a behind the scenes tour of Pfizer’s Kings Heights Technology Center. You’ll
have the opportunity to tour the processing labs for Pfizer’s Liquid Compound
Center of Emphasis and the BioBank. Other areas covered during your visit are
the -80˚C cascade freezer farm, the BioBank mechanical room and both the BioBank
and Liquid Compound large scale REMP stores.

There will be buses leaving regularly from the conference center to the Pfizer facility
for tours of the Pfizer Compound Liquid Store, and DNA & BioFluids Store.

Our tour hosts:

Diane Johnson, Associate Director, DNA & BioFluids Center of
Emphasis, Pfizer Inc.

Diane’s research has centered in the field of Drug Metabolism, Laboratory
Automation, High Throughput Technologies and Material Management during her 30+
years at Pfizer Global Research & Development. Currently she is the Head of
Pfizer’s DNA & BioFluids Center of Emphasis at Kings Heights Technology Center
in Groton, CT. Diane is currently a member of The International Society for
Biological and Environmental Repositories, The Society of Biomolecular
Screening, The Laboratory Robotics Interest Group and The Association of
Laboratory Automation. Additionally, Diane serves as a role model for Women in
Technology, a program at the Community College of Rhode Island committed to
helping women and minorities to understand more fully the opportunities that are
available in technology related programs of study.

Craig Hines, Manager, Liquid Store Center of Emphasis, Pfizer Inc.


Craig received his BS in Chemical Engineering from Michigan State University
in 1980 where he was also licensed by the Nuclear Regulatory Commission as a
Reactor Operator for the university’s research nuclear reactor. Upon graduation
he was an R&D engineer for DuPont at the Savannah River Laboratory, specializing
in the solvent extraction of Uranium and Plutonium from irradiated fuel. Later,
he was a shift supervisor for several of the nuclear reactors at the Savannah
River Plant. He joined Northeast Utilities in 1987 to teach Nuclear Reactor
Theory and Thermodynamics to the operators at the four nuclear power plants in
Connecticut and was licensed as a Senior Reactor Operator. During his tenure
with Northeast Utilities, he also spent eight years as an engineering supervisor
for instrument and controls engineers at the Millstone Nuclear Power Station.
Craig joined Pfizer in 2001 and was the business lead for several large
automation initiatives at the Kings Heights Technology Center. In 2003 he
transitioned to the role of operational manager responsible for supporting the
daily production activities for Material Management at Kings Heights. As part of
that role, he was responsible for representing the business during the design,
construction, and testing of the automation to support the DNA & BioFluids
Center of Emphasis. In April of 2007, he was appointed to his current position
as the lead for the Liquid Store Center of Emphasis at Kings Heights but
continues in an advisory role on the operation of the REMP -20/-80 store for the
storage and retrieval of DNA & BioFluids.

3:30 pm Presentation: 
The cancer Biomedical Informatics Grid®
(caBIG®): Resources to support
translational research

Donna Messersmith, PhD; Integrative Cancer Research Product
Representative

National Cancer Institute – Center for Bioinformatics and Information Technology

caBIG® is an NCI Initiative to establish
a virtual network of organizations developing and adopting interoperable
databases and analytical tools to facilitate translational cancer research. It
is an open-source, open-access program, and all the tools and resources are
freely available for the research community. Mature tools have been bundled into
the Life Sciences Distribution and Clinical Trials Management Suite.

The Life Sciences Distribution includes tools that allow management
and annotation of microarray data (caArray), biospecimens (caTissue), clinical
information (CTODS), in vivo images (NCIA), genome-wide association studies (caGWAS),
as well as integrated analysis and annotation of sequence and expression data (geWorkbench).
All the LSD tools are connected to caGrid, which makes it possible for the
databases at multiple institutions to be interconnected to support data sharing
and integration.

The Clinical Trials Management Suite is a comprehensive set of modular
and interoperable tools to support the management of study participant
information through the clinical trial lifecycle. The Suite enables management
of tasks such as: screening and registering patients for accrual to clinical
trials; scheduling and tracking of patient encounters during the course of a
study; integrating laboratory results with the patient record; tracking and
managing adverse events; capturing, storing, analyzing and routing clinical data
in a meaningful manner.

More information on caBIG® is available
at https://cabig.nci.nih.gov/.

4:00 pm Presentation: 
Tracking Biological Samples and Associated Experiments in a
Biology-Aware Search Environment

G. Scott Lett, Ph.D., CEO

The BioAnalytics Group



 A recently deployed system tracks a global research group’s tissue
samples and all data associated with them. Thousands of tissues are housed in
the repository, and many thousands of data files from experiments that have been
run on these samples are available. The repository contains tissue samples from
mouse xenografts and human patient biopsies. Blood, cell lines and other
archived samples can also be tracked in the same system. All experimental data
types, images, and documents are addressed, e.g. microarray, PCR,
immunohistochemistry images, pathologist reports, in-situ hybridization (FISH,
SISH) and western blot; new technologies are easily added on the fly. The
lightweight, web-based system facilitates collaborative data sharing. With
appropriate permissions, researchers are able to find tissues with particular
properties in seconds, and locate where the sample is stored, greatly
accelerating the process of setting up for a new research project. Researchers
are able to find all data recorded from each sample, avoiding wasted new
experimentation. Researchers quickly adopted the system and reported immediate
productivity gains.

Dr. Lett’s experience includes modeling and simulation, quantitative data
analysis, and automated image processing. After years in the spacecraft and
natural resource industries, he became involved with biological simulation in
the 1990s. Among other industry roles, he has served on the NIH Study Section
focused on Modeling and Analysis of Biological Systems and on the faculty of the
Biomedical Engineering Department of The College of New Jersey . Founded in 2003
as a spinout from Physiome Sciences, The BioAnalytics Group offers advanced data
analysis services, intellectual property and technology assessments, and the
BioPathwise® software suite for pathway-centric collaboration and biomedical
research data management. BioPathwise® products were developed, in part, through
the NIAID PRIME Immune Modeling for Biodefense Center under contract NIAID
HHSN266200500021C.

4:30 pm Presentation: 
Mixed phase 21st century, world class biobanking story

Steve Arsenault, directeur de l’exploitation

Biobanque Génome Québec

Challenges of implementing a world class Biobank

Building a public resource: The Genome Quebec – Centre hospitalier affilié
universitaire régional de Chicoutimi Biobank

Evaluating and choosing a cost-effective and sustainable infrastructure

Implementation Process and Timeline

Current Biobank Operations

5:00 pm Presentation: 
DNA Extraction Technology Overview – Increasing Capacity 10X

Robert J.Corr

Pfizer Global
Research & Development, DNA & BioFluids Center of Emphasis, Pfizer Inc., Kings
Heights, Groton, CT

New protocols, extensive multiplexing, increased sensitivity of detection,
and advances in miniaturization and automation have substantially reduced the
amount of DNA required for downstream assays prompted the question: are we
banking an appropriate amount of DNA?

The current DNA extraction platform at the DNA & BioFluids CoE was designed to
extract large quantities of DNA from large volumes of human whole blood. After
discussions with our colleagues in Exploratory Research, it was determined that
decreasing banked DNA amounts while increasing throughput was preferable to the
current model. This presentation describes the process of reviewing the current
technology landscape with the intent of increasing daily DNA extraction capacity
by ten fold while maintaining quality and reducing operating cost. The
exploration of the technology landscape included the review of chemistry
(solid-phase, precipitation, silica, and magnetic bead technologies) and various
automation options. Additionally, in-house and outsourcing processing costs were
compared.

5:30 pm Presentation: 
Development of a Robotic Frozen Sample Aliquotting System

Dale Larson, Draper Laboratory (and Harvard Medical School), Cambridge,
MA

John Slusarz, Harvard Medical School, Cambridge, MA

Steve Bellio, Draper Laboratory, Cambridge, MA

Vincent Chun, CryoXtract Instruments LLC, Quincy, MA

Helena Judge Ellis, Brown University, Providence, RI

Nader Rifai and Gary Bradwin, Children’s Hospital, Boston, MA 

Freezing samples is a ubiquitous method of preserving the fidelity of
biological specimens during long term storage. Some proteins and RNA are known
to degrade if not frozen, small molecule compounds in DMSO absorb water vapor
compromising the solubility of some of the compounds, and cell life is prolonged
by freezing. All current methods of processing these frozen samples require
thawing before aliquots can be prepared — exposing them to freeze-thaw cycling
that is detrimental to the quality of the specimens. Moreover, the thawing and
mixing are time consuming. Freeze-thaw cycling is particularly problematic for
biomarker research, both discovery and validation, where the troubling question
is “Was a biomarker present but no longer there?” A robotic system is being
developed that eliminates the need to thaw the samples before extracting
aliquots; thus, maintaining biological stability and integrity of the remaining
quantities, extending the usable life of biological specimens, decreasing
operating costs, increasing throughput, and reducing lead times. Conceptually,
the technology is a specialized core drilling system that uses a hollow Titanium
tube with a cutting profile at its distal tip to cut a core from the frozen
specimen under cryogenic conditions that will remain in the tube when the needle
is withdrawn. The robotic system then positions the needle over an empty
cryovial and deposits the core. The prototype will be deployed in the Rhode
Island BioBank at Brown University in the spring of 2009. Commercialization is
envisioned for both benchtop systems as well as integration with automated
frozen storage systems. This talk will present the initial proof of principle
data and describe the prototype design.

6:00 pm Presentation: 
Development of QC methods to monitor cross-contamination from
fixed-tip automation used to extract DNA from clinical blood samples

Stephanie K. Hall1, Jason Harraden2
and Diane L. Johnson2

Pfizer Global Research & Development, 1Groton
Laboratories, Pfizer Inc., Groton, CT 06340 2DNA/Biofluids
BioBank, Pfizer Inc., Kings Heights, Groton, CT 06340

Clinical studies and gene-based target discovery require high quality DNA for
genotyping, genetic association studies and resequencing efforts. Rigorous
quality control (QC) procedures are required to assess the DNA extracted from
our automated DNA extraction process to ensure high standards and sample
integrity for the material used in our studies. Our DNA extraction process uses
fixed-tip automation which could increase the potential of sample contamination.
The QC procedures that have been developed to monitor cross-contamination will
be discussed in our presentation.

Evaluating samples for cross contamination using water control samples is a
critical step in our QC methodology. TaqMan genotyping assays were used
initially to evaluate water samples from our DNA extraction process.
Cross-contamination rates approaching 20% were detected in early development of
the DNA extraction process. Enhanced tip washing procedures were implemented in
addition to a tip bleaching step. These modifications significantly reduced
observed cross-contamination levels to <2%. One limitation of the TaqMan assay
is its inability to precisely quantitate the contamination that was detected.
Copy number and plus/minus real-time PCR assays were developed and used with
serially diluted DNA of known concentration to provide absolute quantitation of
contamination levels. Using these assays, we have been able to detect
contamination at levels of 1 pg/ul. A mixing experiment was performed to assess
whether low level system contamination could alter the performance of extracted
DNA samples in genotyping assays. A contaminated water sample from an individual
homozygous for one SNP allele was combined in equal proportion with DNA from an
individual homozygous for the other SNP allele. TaqMan genotyping assays were
performed and no alteration in the genotype of the DNA sample was observed. The
genotypes were always reflective of the DNA allele and were not affected by the
presence of contamination from the combined water sample. Future enhancements
are being developed to provide QC methods to evaluate clinical DNA samples
extracted on our automated system.

Note: These presentations will be archived on our Presentations page:


/meeting_presentations.htm

Exclusive Sponsor:


Exhibitors:


bullet Agilent Technologies / Velocity11



bullet ArcticWhite



bullet Artel



bullet Autogen



bullet Axygen Scientific



bullet Beckman Coulter – Agencourt



bullet Biomatrica



bullet Brady



bullet CyBio



bullet Dataworks – Freezerworks



bullet Electronic Imaging Materials



bullet Flow Sciences



bullet GenVault



bullet Hamilton Storage Technologies



bullet HighRes Biosolutions



bullet Lab Storage Monitoring



bullet Labcyte



bullet LabVantage Solutions



bullet MatriCal Bioscience



bullet Micronic



bullet Millipore



bullet Nexus Biosystems



bullet Parallabs



bullet PerkinElmer



bullet Qiagen



bullet REMP



bullet RTS Life Science



bullet Seahorse Bioscience



bullet Tecan



bullet The Automation Partnership (TAP)



bullet Thermo Fisher Scientific



bullet Titian



bullet Tomtec



bullet TWD TradeWinds / Kimble-Chase



bullet VWR



bullet Wheaton Science Products / Computype


If you are interested in exhibiting at this meeting, please review our
Exhibitors Information page.

Door Prizes:


bullet Association for Laboratory
Automation (ALA)
Travel Mugs



bullet Association for Laboratory
Automation (ALA)
Pens



bullet Association for Laboratory
Automation (ALA)
Hats



bullet International Society for Biological
and Environmental Repositories (ISBER)
Ceramic Mugs (36 of them!)



bullet LRIG Photon Keyring Lights



bullet LRIG Laser Pointers



bullet REMP 4Gb Swiss Army USB memory
sticks



bullet REMP Leatherman multi-tools



bullet REMP dynamo flashlight cell phone
charger



bullet REMP -80C coffee mugs (several
dozen)



bullet and more… many exhibitors bring their door prizes to the meeting


Menu

Served at 1:30 – 3:30 in the exhibition hall

bullet Steamship Round of Beef –Carving Station
bullet Chicken Picatta
bullet Vegetable Lasagna
bullet Red Bliss Potatoes w/Parsley & Butter
bullet Grilled Seasonal Vegetables
bullet Tossed Salad
bullet Three Bean Salads
bullet Rolls & Butter
bullet Ice Cream Nut Roll
bullet Chocolate Mousse
bullet Hot Apple Crisp
bullet Coffee, Tea, Decaf, Water, Soda
bullet Chef selection of hors d’oeuvres
bullet Cheese & Cracker, Chip & Dip

Served at 5:00 PM in the presentation hall, and will be available
throughout the presenations

bullet Assorted Sandwiches
bullet Coffee, Tea, Decaf, Water, Soda
bullet Cookies & Chips

Food and refreshments are free of charge to attendees – they are paid for by
the exhibitors, so please be sure to visit all their tables!

Hotel:

We have negotiated with the Groton
Inn & Suites
for a discount rate of $94.00 per night including breakfast. To
qualify please make your reservation by March 23 and mention the LRIG meeting.

DON’T FORGET TO REGISTER TO INSURE THAT THERE IS ENOUGH FOOD AND SEATS. 


/member/meetings.asp?rid=1

Visit The Laboratory Robotics
Interest Group homepage at


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