Building Technology Infrastructure and Sustaining It into the Future

Judith Van Houten

Director, Vermont Genetics Network (Vermont INBRE) and Vermont EPSCoR

October 23, 2008

NERLSCD Meeting

IDeA Institutional Networking for Biomedical Research Excellence (INBRE) Awards are intended to build biomedical research infrastructure.

Infrastructure can be many things: undergraduate or K-12 programs for workforce development, career development of faculty and graduate students, hardware acquisition, renovations, among other things.

I will focus today on the facilities infrastructure in the Vermont Genetics Network (VGN).

Highlight How We Built Two New VGN Facilities:

Microarray and Proteomics

In the beginning:

•Determine Need

• Find Talented Staff

•Make a Plan for Service

Build a user base

Evaluate Impact on

•Funding Competitiveness

•Outreach Programs

Plan for the future

First Step for VGN Microarray Facility:

•Ascertain the need for a Microarray Facility.

•Demand is not always the same as need for research competitiveness.

•Outside consultants helped us to determine the need in Vermont and then helped us to decide on the platform and services to start our Microarray Facility.

Step Two: Find the best staff

The most important thing you can do to make a new facility succeed is to recruit the best, talented staff who are

•service-oriented and like to work with researchers as collaborators

•willing to work in a collaborative team

•creative and want to learn as the field and its technology expand

•networking with peers and industry reps

Tim Hunter and Scott Tighe

Next Steps:

Plan for the service from sample preparation to data analysis

Work flow

Quality control

Quality publishable data

To insure good outcomes:

Control over sample preparation

Assist in Experimental Design

Provide data analysis support -Crucial for high quality data that are publishable!

Web based as much as possible

Database for Assessment and Reporting

UVM Microarray Facility at the University of Vermont:The UVM Microarray Facility staff provides comprehensive support to all projects submitted including RNA extraction techniques, RNA concentration, and other issues that can present regarding upfront preparation of samples. Microarray Brochure (Mission, Access Guidelines and Prices)

Guidelines for Facility Access and Sample SubmissionStep 1: Initial Consultation: All investigators who wish to pursue a project through the facility are strongly encouraged to meet with the Microarray and Bioinformatics Facility staff together to ensure proper experimental design and a clear understanding of sample requirements for processing through the facility including turnaround times. Please contact Tim Hunter at 656-2557 or Jeff Bond at 656-4068 to arrange a consultation meeting.

From the VGN Microarray Website

Step 2: Submit Total RNA samples for quality assessment .……………The facility staff will meet to discuss results and a report including traces will be given back to the investigator and consulted how to proceed. Once you have submitted your samples for Bioanalyzer chip analysis, you are considered to be in the queue for target preparation.

Step 3: Submit RNA samples for Target prep. …….

Step 4: Test Chip Hybridization and Scanning. We recommend a representative test chip be run for each batch of target preparations. …..An experiment report will be provided to the investigator.

Step 5: Hybridization and scanning of target chip. A CD will be provided to the investigator…………

Step 6: Data Analysis: Detailed analysis is the responsibility of the investigator in collaboration with the Bioinformatics Core

Next Step:

Developing the User Base and Loyal Clientele

•Early Success

•Early Low or No Fees

•Seminars and Education Outreach to the Research Community

•Celebrating our successes

•Continuing Education of the Staff

•Finding New Ways to Save on Client Fees

•Surveys and assessment

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50

100

150

200

250

300

350

400

450

2003 2004 2005 2006 2007 2008

PicoChips

NanoChips

GeneChips

Impact Grant Year 3 2007-08

Experimental design consultations with 16 investigators

Completion of 27 microarray projects (292 GeneChips)

Performed 93 RNA assessments: 59 PicoChips, 118 NanoChips, 3 small RNA’s chip (new service, implemented, August, 2008)

Impact 2007-08Publications (8)

Grant Applications

Trained graduate students, postdocs, techs

Seminars & presentations (11)

Support of Outreach Programs

AssessmentQuantitative Data

Survey results

2007-2008

Microarray Research is so user-friendly at UVM that we take it into college lab classes all across the state in our Outreach Program!

MICROARRAY OUTREACH

2007-2008 Green Mt. College

Marlboro College

Norwich University

Middlebury College

Johnson State

Castleton State

Saint Michael’s College

Janet Murray and Pat Reed

Tim Hunter and Scott Tighe

Bioinformatics Core is essential to the success of the Microarray Facility

Front end consulting for experimental design

Data Analysis

Jim Vincent

Bryan Fleming

Jeff Bond

Rama Kocherlakota

Bioinformatics Core is essential to the success of

the Proteomics Facility

Front end consulting for experimental design

Data Analysis

Jim Vincent

Bryan Fleming

Jeff Bond

Proteomics Facility

In the beginning:

•Determine Need

• Find Talented Staff

•Make a Plan for Service

Build a user base

Evaluate Impact on

•Funding Competitiveness

•Outreach Programs

Plan for the future

Proteomics FacilityEstablish Level of Need

•Need for MS for protein analysis was clear from meetings with faculty members from around the State.

•Meetings helped us to make the decision to purchase a mass spectrometer (LC-LTQ) and fold an existing Maldi-TOF into the nascent facility.

Our First LC-LTQBin Deng, Manager

Bryan Ballif Co-Director Dwight Matthews Co-Director

Bin Deng Manager

Find Talented Staff

Second LC-LTQ

LC-LTQ Orbitrap for High Mass Accuracy

Maldi-TOF

Equip the Facility

Plan for ServiceFrom the Proteomics Wed Site: Guidelines for Facility Access, Sample Submission, and Data Management

Step 1: Initial consultation: Investigators should sign up for a consultation prior to sample submission to ensure a clear understanding of sample requirements for processing through the facility. Sign up for a consulation by booking a time here: Consultation SignupsIf you need help please contact Dr. Bin Deng at 656-9722 or email to proteomics@uvm.edu.

Proteomics and Bioinformatics staff participate!

Step 2: Fill out the on-line sample submission form and answer the questions listed. Each sample must be accompanied by a completed form. The information you provide helps to ensure proper handling of your sample.

Step 3: Only trained persons directly operate mass spectrometers in the facility. However, the users are welcome to come, learn and participate in their sample analysis.

Proteomics Facility Staff and Bioinformatics Core will provide data analysis.

It is best to send samples via FedEx if you are a non-UVM user.

Next Steps 2006-2008:

Developing the User Base and Loyal Clientele

•Early Successes

• No Fees

•Seminars and Education Outreach to the Research Community

•Advertising and celebrating our successes

•Continuing Education of the Staff

•Surveys Under Construction

•Attract more outside clients

Impact over 2 years94 projects completed, 85 for Vermont researchers and 9 for researchers outside Vermont

32 projects were with COBRE faculty, 1 with the CCTS, 52 with INBRE faculty

9 papers have been published in peer-reviewed journals (5 with COBRE faculty)

Grant proposals using MS data?? Yes! One recent R01 funded and also a paper in Science for a COBRE investigator

Satisfied Clients with new Publications

Two-D gels and mass spec analysis are being beta tested at UVM before being taken to baccalaureate institutions throughout the state.

PROTEOMICS OUTREACH

Janet Murray and Pat Reed

Bin Deng and Bryan Ballif

Future Steps

Business Plans to be Updated

Personnel

Equipment depreciation

Next generation of equipment/services

Consumables

Overhead

•Plan for Sustaining this Facility

Sustaining Facilities into the Future

Getting Started

Facilitate with your VPR an institution-wide over-view of existing facilities

Assess the impact of the existing facilities on research competitiveness

Have clear measures of impact of the facility on the institution’s and region’s research endeavor

Draw up business plans for each facility

Review what is available within the institution and encourage the use of existing facilities rather than recapitulating instrumentation through faculty set up for an individual’s lab.

Review what is available in the region for sharing of facilities and agreements on services and pricing.

Why start with regional? In-person training; ease of shipping samples; shared seminars and hands-on tutorials

Find Synergies

Thank you NERLSCD!!

Regional Facilities Database at www.uvm.edu/vgn

Partner with other institutions so that a university or state does not feel compelled to build every possible facility.

Decision about which facilities to sustain on campus and long term plan drawn up for sustaining and reviewing this decision.

The JVH sustainablity plan would include: •Someone with an over-view of the facilities at the university and authority to coordinate the facilities into a working whole. Autonomous but collaborative….•A policy to look toward outside sources first if the need for a technology arises; decisions should be driven by data: user base and impacts•Brokered agreements so that faculty at the institution are given good prices and priority service if they must go outside for services•For facilities at the institution, there should be yearly updated business plans that address the consumables, maintenance fees, staffing and depreciation of equipment•Impacts should be reported yearly and an evaluation of the suite of cores and facilities on campus revisited periodically

•The institution should commit to supporting the staff salaries on base budget of the facilities to be sustained and recoup the other costs through fees for service.

Most Important

Why support personnel?•Talented personnel are key to the success of a facility.•If the best technology cannot be made to work well and produce high quality outcomes it will not improve research competitiveness. •It might even produce artifacts that will embarrass the researcher and institution.

Leverage: partner with other grant-funded infrastructure building programs and private sector.

(NSF EPSCoR, DOE EPSCoR, and NASA EPSCoR are just three.)

Thank you for your attention!