BGI@UCDavis:Transforming Data to Knowledge

Bart Weimer, Ph.D.Co-Director, BGI@UC DavisFaculty Coordinator, Office of Corporate RelationsProfessor, School of Veterinary Medicine

Sequencing Costs are Falling

Witt et al., 2011)

Sequencing Capacity Increasing

rdis et al., 2011)

HiSeq 2500• 2 modes

• 11 days• 1 day

• Data density options

Genome Projects Since 1995• Humans

Genotype Exome Small RNA Diagnostics

• Individual microbes Pathogens Environmental Diagnostics

• Microbiome Communities Functions Health & disease

• Expression RNAseq

• Multi-omics integration Metabolomics Proteomics Genomics Expression(Relman et al., 2011)

Costs Continue to Decline with Progress in Sequencing Technology Advances

James Hadfield (Cambridge Genomics Core); Jan 2012

Functional Genomics Bottlenecks

Witt et al., 2011)

UC Davis & Genomics

Campus Needs• Sequencing capacity• Reduced risk in

equipment investment in a very dynamic landscape

• Data analysis capacity

• Increased capacity to handle genomics enterprise at Davis

Campus Offers• World class science

and medicine• Very diverse

science Fundamental biology Agriculture Medicine Environment

• Genome Center• Genomics Shared

Resource

BGI’s Capability

• BGI is one of the world’s premier and largest genome sequencing centers

• Founded in 1999 as the Beijing Genome Institute, headquartered in Shenzhen, China

• BGI-Americas was established in 2010, Boston, MA

• BGI currently employs ~4,000 employees worldwide

• BGI has >135 Illumina HiSeq 2000 instruments world-wide

• Capacity to produce >5 TB/day (~2,000 human genomes/day)

BGI Goes Global

Copenhagen (Denmark)Canberra (Australia)CHOP (US)UC Davis (US)

(Science, Feb 3, 2012)

• Shenzhen - HQ • Hong Kong – sequencing• >100 sites in China

BGI@UC Davis Development

• Campus resources are pressed hard Numerous areas on campus

growing genomic, metagenomic, and microbiome projects

Current, large-scale projects need additional capacity

Instrumentation changing fast and expensive

• Numerous individual discussions with UC Davis faculty

• June 8, 2011 MOU signed to establish a partnership

• Chancellor appointed coordination group • Leadership team – Ralph Hexter,

Harris Lewin, Claire Pomeroy• Negotiation team - Steve Drown,

David McGee, Cindy Kiel, Bart Weimer• Numerous others for finance, facilities

& strategy• February 17, 2012

signature ceremony for facility

Faculty Workgroups

• Faculty consultation during process

• Provided a forum for faculty involvement

• 45-50 faculty members involved with workgroups

• Human/Animal health & wellness• Fred Meyers• Lars Burgland

• Biodiversity, food security, & ecological sustainability• Richard Michelmore

Facility Capacity• Located in Sacramento on med school campus• Temporary facility

Within IRC building• Long-term facility

Next to IRC in ~9,600 ft2 Expansion is part of building

plan

• BGI provides ~10x increase in sequencing

capacity Bioinformatics servers

• UC Davis provides Biological paradigms Large scale projects Applications that demand new

genomic and bioinformaticmethods or scale

Benefit to UC Davis

• Very competitive pricing structure Price is pre-negotiated

• Must meet or beat market pricing• ~50% reduction over open market price

Indexed 2x yearly Allows campus to leverage cost savings as sequencing costs decline

• Priority sample processing• Increase sequencing capacity to meet demands• Additional options for bioinformatics support

Price negotiated separately to sequencing

• New opportunities for proposal development with UC Davis faculty as the lead

• Additional services• Increases capacity of the UC Davis genomics

enterprise

Initial Progress and Interactions

• Temporary space Institute for Regenerative Cures (IRC) 3 HiSeq 2000 instruments 1 server rack

• Long-term space being built Anticipated move-in is spring/summer 2013 10-20 instruments

• HiSeq 2000 • HiSeq 2500

~16 server racks for sequence processing

• Incorporation into teaching David Segal – genome re-sequencing

Facility Governance

• Co-directors Hao Zhang – BGI Bart Weimer – UC Davis

• Steering committee UC Davis

• Richard Michelmore• Bart Weimer• Paul Dodd

BGI counterparts • Hao Zhang• Others pending

• Governance committee UC Davis

• Rick Grossberg• Dushyant Pathak

BGI counterparts pending

Co-Director Roles

• Weimer’s Role Represent Office of Research Facilitate interactions with facility Facilitate connections with BGI Facilitate support letters for grants Ensure UC Davis faculty are getting pricing and priority Ensure UC Davis is meeting obligation Advise about project scope for BGI collaboration requests

• Zhang’s Role Represent BGI in interactions with campus Ensure UC Davis projects are given priority Ensure UC Davis pricing provided Maintain facility and capacity for UCD Oversee daily operations at facility Link between BGI headquarters and UC Davis PIs Carry requests for collaboration to BGI leadership

Operational Structure

BGI@UC Davis

yUC Davis Faculty Non-UC Davis

• BGI can take outside samples

• They don’t get UC Davis price or priority

Funding Agency

UC Davis collaborator

• UC Davis cannot be a broker for cheap sequencing

• Documented account for sequencing

Interaction Options

• Transaction methods Fee-for-service Joint projects Large scale

collaboration• Service model

Quote will be provided PI retains IP and data Existing mechanism

with BGI Coordinate with co-

directors for scheduling

• Proposal development Sub-contract as service Letters of support Co-PI model

• Requires BGI approval from headquarters

• Collaborations More than free

sequencing “Joint” development

options• Requires IP consideration

on individual basis• Requires governance

body approval for financial considerations

Methods to Interact with BGI@UC Davis

• Directly Hao Zhang (co-director) Bart Weimer (co-director) Fiona Gao (sales)

• Via Genome Center Richard Michelmore Sequencing core Bioinformatics core

• Via Genomics Shared Resource Jeff Gregg Cliff Tepper

UCD Genome Center Service Cores

• DNA Technologies

• Sequencing

• Library construction• Expression Analysis• Proteomics• Metabolomics• Bioinformatics

• Richard Michelmore• Ryan Kim

www.genomecenter.ucdavis.edu

Technical Director: Cliff Tepper, Ph.D.

2805 50th StreetRoom 2460Sacramento, CA 95817

(T) 916-703-0366(F) 916-703-0367(E) mpsr@ucdavis.edu

Director: Jeff Gregg, M.D.

BGI@UC DavisLocation

17 miles from Davis campusSample delivery options Hand deliver Pick up Will evolve as

projects begin

Sequencing Facility - IRC

BGI@UC Davis

Facility Floor PlanStockton Blvd

Sequencing Post PCR

Office

Sample RecSample Prep

Servers

Parking Lot

Mechanism for Sample Submission

• Contact co-directors Sample timing, coordinate runs, or project size Consult with other groups on campus if needed Coordinate scheduling Determine best location for project Define scope Define level of bioinformatics needed

• Visit web site for sample submission form Get quote from BGI PI signs the quote for scope

• Send sample Initially – PI makes or gets library made Robotics underway for Deliver sample

• Sequence • Return data• Payment

Sample Submission Form

• Obtain sample form Available on website Initiates a quote Moving to online

submission form

• Departmental PO established for business office use

Initial Sample Submission

• PI provides library until permanent space completed

• Possible to run samples at other BGI locations Project scale in part determines physical location PI can ask for BGI@UC Davis only Changes library construction for PI

• Export control considerations Possible that samples can only be done in US

• Davis• CHOP

Defined sample form for PI consideration

Data Return

• Reads possible• Trimmed and tag removal is usual• Additional bioinformatics to be defined at

beginning of project via the quote• Files on hard drive • Download possible• Data will be stored for 3 months

Plan early for storage and back ups BGI@UC Davis will not be long term data storage

option

Bioinformatics Support

• Your own lab• Use existing resources on campus• Negotiate additional services from BGI• Collaborations with other groups

IP Ownership

• Contract defines ownership for individual projects based on how PI interacts with facility

• PI controls the mechanism Fee-for-service

• PI controls • data • IP• publication

Joint proposal submission• Clearly define role of BGI@UC Davis and BGI• Result of discussions before submission to define IP• Letter of support always available

Collaborative projects• Shared IP• Short descriptions for strategic collaborations

Publication

• PI controls authorship• Accepted contribution standards• Co-directors role is consultation and

facilitation

Joint Projects

• Option for jointly funded projects• Proposal submission needs to clearly

define interaction• Joint IP ownership• Speak with co-directors to begin process• BGI (Shenzhen) approves• Local leadership approves

• Think big….unique….solve bottlenecks• Think Science/Nature cover projects…..

Grant Submissions

• Letter of support always available• Sub-contract = fee-for-service• Collaborator

Define role Appropriate scale and scope

• Contact co-directors initiate collaboration Tough sequencing samples New methods Large, multi-national projects

• SPO integration for F/A• Example collaborations

Cancer Center Vegetables & crops Microbes Heart disease

Co-host International Genomics Meeting• Yearly international meeting on campus• Initial planning stages now• Anticipate late winter 2013• 2 day meeting• Organizational committees forming

Campus Communication

• Web site Being expanded Central information location Forms and contacts http://bgi.ucdavis.edu

• Listserv Sign up for updates

• Routine updates Progress updates New methods Sample submission and handling

Questions?

• General questions bgi-ucdavis@ucdavis.edu

• Qiaoning Guan Started May 1 qiaoning.guan@bgiamericas.com

• Fiona Gao gaoshuang@genomics.cn

• Jamie Shattuck jkshattuck@ucdavis.edu

• Hao Zhang Hao.Zhang@bgiamericas.com

• Bart Weimer bcweimer@ucdavis.edu 530-752-5819

http://bgi.ucdavis.edu