AIRR Community Meeting II

NIH Fishers Lane Conference Center Rockville, MD, June 27-30, 2016 

Organizing Committee: Jamie Scott, Tom Kepler, Chaim Schramm, Danny Douek, Lindsay Cowell, Corey Watson, Steven Kleinstein, Eline Prak, Chaim Schramm, Erick Matsen and Felix Breden

Contact: breden@sfu.ca

Agenda

Tools and Resources Demos

Sponsors

Over the past few years, there has been a rapid accumulation of high-throughput sequence data characterizing adaptive immune-receptor repertoires (AIRRs).  A variety of issues have arisen that are specific to this type of data, and to address them, we have held one planning meeting and one larger meeting of the AIRR community (in Sept 2014 and May 2015, respectively). Based on the consensus from the May 2015 meeting (see Report from the AIIR Community Meeting) , we formed several Working Groups to develop recommendations for: (i) a common repository for AIRR sequence data, (ii) minimal standards for publishing or depositing such data, (iii) resources and guidelines to support the production of AIRR sequence data, and the development of statistically validated tools for analyzing such data.

We have planned a second Community Meeting (AIRR-II) to address these issues and further organize the burgeoning community that is producing and using AIRR sequence data.  As with our initial meetings, this meeting will bring together a diverse community: researchers sequencing antibody/B-cell receptor and T-cell receptor repertoires to profile the immune system in health and disease, industrial partners, statisticians, bioinformaticians, computer security experts, and scholars in the relevant aspects of ethics, law, and policy.

The AIRR-II Community Meeting will be held 27-30 June 2016 at the NIH’s Fishers Lane facility. As registration is now full, and to maximize participation of the AIRR Community, the meeting will be webcast with live chat (see below to register).  Holding the meeting at the NIH will facilitate participation by interested NIH staff members (e.g., those associated with DAIDS, BD2K, dbGaP, CHAVI-ID), and by Europeans and other international researchers. As high-throughput AIRR sequence data accumulate and continue to make inroads into both biomedical research and patient care, the research community will be looking to NIH, and other national and international agencies, for support of the infrastructure and guidelines to facilitate their effective use.

We have also obtained additional funding to subsidize attendance by new investigators interested in this field, and those in low- and middle-income countries. Through this meeting, we expect to build networking and mentoring to researchers who do not have ready access to this technology.

As described in the detailed agenda below, initial recommendations developed by the Working Groups will be presented on the first day, further revised by participants (including those attending virtually) during each session’s discussion period, and on the final day, voted upon by all participants. In follow-up to the meeting, the Organizing Committee (including Working Group co-leaders), and anyone who wishes to participate, will write a white paper(s) to convey to the larger community of scientists and other stakeholders the AIRR Community’s view of the issues advanced during the meeting, and its recommendations for resolving them.

As mentioned above, registration for this conference is full; however webinars will be available for all the daytime sessions, and each will include live chat, so that virtual attendees can communicate with the meeting (this includes the ability to vote during the final session). Please see the full agenda below and choose the sessions you want to attend, then go to webinar registration page to register.

NOTE: you must register separately for each session you wish to attend.  If you cannot attend the live webinars, don’t worry! They will be saved and posted after the meeting on this and other sites.

 

 

Agenda:

 

Day 1, Monday, June 27th

 

 Time

Location

Details

8:30 AM

Hilton Hotel Lobby

Working Group members will gather to walk to Fishers Lane Facility

9:00 AM – 12:00 PM

Fishers Lane Facility

Working Groups will meet concurrently and finalize recommendations

12:00 – 1:00 PM

Fishers Lane Cafeteria

Lunch

12:30 PM

Hilton Hotel Lobby

Conference Attendees will gather to walk to Fishers Lane Facility

1:00 – 1:15 PM

Fishers Lane Facility

Opening of meeting: Introduction of Conference Organizers, Working Group Leaders, and review of agenda

1:15 – 5:00 PM

 

All 3 Working Groups will convene with conference attendees to discuss recommendations from the Working Groups and Organizing Committee. (The recommendations will be returned to during the Sessions on Days 2 and 3)

 

 

End of Day at Fishers Lane. Attendees return to Hilton Hotel

6:00 – 8:00 PM

Hilton Hotel

Reception and Demos: Demos of software tools for analyzing high-throughput AIRR data with emphasis on access, validation and robustness. (Cash Bar. No Government funds will be used for food and drinks)

 

 

Attendees are on their own for dinner

 

Day 2, Tuesday, June 28th

 

 8:00 AM

Hilton Hotel Lobby

Attendees gather to walk to Fishers Lane Facility.

8:30 – 8:45 AM

Fishers Lane Facility

Introduction to Day 2 Agenda

8:45 – 9:30 AM

 

Keynote Presentation; Steve Rosenberg, National Cancer Institute

Session 1: Organized by the Common Repository Working Group

9:30 – 11:00 AM

 

Presentations

9:30 – 9:55 AM

 

Erica Saphire, The Scripps Research Institute

10:00 – 10:25 AM

 

John Tsang, NIAID & Trans-NIH Center for Human Immunology

10:30 – 10:55 AM

 

Bjoern Peters, La Jolla Institute for Allergy and Immunology

11:00 – 11:30 AM

Fishers Lane Cafeteria

Refreshment Break

11:30 AM – 12:30 PM

 

Community Discussion: Recommendations of the Common Repository Working Group

12:30 – 2:00 PM

Fishers Lane Facility

Boxed lunches and Poster Session I

Session 2: Organized by the Minimal Standards Working Group

2:00 – 3:30 PM

 

Presentations

2:00 – 2:25 PM

 

Andrew Collins, University of New South Wales

2:30 – 2:55 PM

 

Christian Busse, German Cancer Research Center

3:00 – 3:25 PM

 

Sai Reddy, Swiss Federal Institute of Technology, Zürich

3:30 – 4:00 PM

Fishers Lane Cafeteria

Refreshment Break

4:00 – 5:00 PM

 

Community Discussion:  Recommendations of the Minimal Standards Working Group

 

 

End of Day at Fishers Lane. Attendees return to Hilton Hotel

6:00 – 8:00 PM

Hilton Hotel

Reception and Demos: Pipelines and platforms for analyzing high-throughput AIRR data with emphasis on access and sharing. (Cash Bar. No Government funds will be used for food and drinks)

 

 

Attendees are on their own for dinner

 

 Day 3, Wednesday, June 29th

 

 Time

Location

Details

8:00 AM

Hilton Hotel Lobby

Attendees will gather to walk to Fishers Lane Facility

8:30 – 8:45 AM

Fishers Lane Facility

Introduction to Day 3 Agenda

Session 3:  Organized by the AIRR Tools and Resources Working Group

8:45 – 10:15 AM

 

Presentations

8:45 – 9:10 AM

 

Deborah Dunn-Walters, University of Surrey

9:15 – 9:40 AM

 

Mikhail Shugay, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry

9:45 – 10:10 AM

 

Chris Vollmers, University of California, Santa Cruz

10:15 – 10:45 AM

Fishers Lane Cafeteria

Refreshment Break

10:45 – 12:15 PM

 

Community Discussion:  Recommendations of the AIRR Tools and Resources Working Group

12:15 – 1:30 PM

Fishers Lane Cafeteria

Boxed lunches and Poster Session II

Session 4: The Future of AIRR Research. Organized by the AIRR Community Meeting Organizing Committee

1:30 – 3:00 PM

 

Presentations

1:30 – 1:55 PM

Fishers Lane Facility

Tom Kepler, Boston University School of Medicine

2:00 – 2:25 PM

 

Nick Haining, Dana-Farber Cancer Institute

2:30– 2:55 PM

 

Jim Crowe, Vanderbilt University Medical Center

3:00 – 3:30 PM

Fishers Lane Cafeteria

Refreshment Break

3:30 – 4:25 PM

 

Presentations

3:30 – 3:55 PM

Fishers Lane Facility

John Wilbanks, Sage Bionetworks

4:00 – 4:25 PM

 

Jan Reichert, The Antibody Society

4:30 – 5:00 PM

 

Discussion of whether to form a formal AIRR Society

6:30 – 10:00 PM

 

Attendees convene at Carluccio’s Restaurant for dinner

 

Day 4, Monday, June 27th

 

Time

Location

Details

  8:00 AM Hilton Hotel Lobby Attendees will gather to walk to Fishers Lane Facility
Session 5: Finalizing Recommendations and Planning the Future of the AIRR Community
8:30 – 9:30 AM Fishers Lane Facility Report from the AIRR-Repository Working Group. Presentation of recommendations for a Common Repository site, terms of access, policies on human subjects approvals and IP sharing, recommendations for the future of this Working Group (including future projects), and ratification of recommendations.
9:30 – 10:30 AM   Report from the Minimal Standards for AIRR Data Working Group.  Presentation of recommendations for minimal standards for AIRR data and metadata, recommendations for the future of this Working Group (including future projects), and ratification of recommendations.
10:30 – 11:00 AM Fishers Lane Cafeteria Refreshment Break
11:00 AM – 12:00 PM   Report from the AIRR Resources and Tools Working Group. Presentation of recommendations for biologic standards, for validation tools for AIRR-data analysis software, recommendations for the future of this Working Group (including future projects), and ratification of recommendations.
12:00 – 1:00 PM Fishers Lane Facility New Business: Discuss and vote on forming a formal consortium or professional society, and future issues to work on (e.g., virtual seminar series, further “problem areas” in obtaining and/or analyzing AIRR data, suggesting research initiatives to funding agencies).
1:00 – 1:30 PM   Review of an outline for the AIRR Community White Paper and request for participants to work on it. Once completed, a draft copy will be made available for review, feedback, and ratification by the Community
CONCLUSION OF MEETING
2:30 – 5:30 PM   Working Group members and interested participants will meet to summarize the recommendations for each Working Group, and begin work on the White Paper.
   

Notes:

Meeting sessions will be recorded (audio & video) and broadcast live & with chat for those who cannot attend the meeting in person by means of Go-To Webinar. Virtual attendees must register for each Session that they wish to attend. Registration instructions have been emailed to the Community, and are available on the registration site. https://palladianpartners.cvent.com/AIRR2016

 

Tools and Resources Evening Demos Expanded Agenda

 

Day 1, Monday, June 27th

 

Time

Location

Details

6:00 – 8:00 PM Hilton Hotel Reception and Demos: Demos of software tools for analyzing high-throughput AIRR data with emphasis on access, validation and robustness. (Cash Bar. No Government funds will be used for food and drinks)
6:30 – 6:42 PM   Eric Matsen B cell receptor sequence analysis via comprehensive probabilistic modeling
6:45 – 6:57 PM   Avidan Neuman On the importance of multiple barcodes, multiple time-points-of view, singletons and single-timers in the kinetic analysis of tcr repertoires
7:00 – 7:12 PM   Aaron M. Rosenfeld AIRRDB: a system for the analysis and exploration of high­throughput adaptive immune receptor sequencing data
7:15 – 7:27 PM   Wei Zhang An analytical methodology for predicting tcr and bcr germline genes and alleles from rearranged repertoire data
7:30 – 7:42 PM   Martin Corcoran IgDiscover, a novel analysis tool for the identification of germline ig genes and alleles from next generation sequencing data
7:45 – 7:57 PM   Simon Frost IgSCUEAL: assigning germline genes in antibody repertoires using phylogenetic placement

 

Day 2, Tuesday, June 28th

 

Time

Location

Details

6:00 – 8:00 PM Hilton Hotel Reception and Demos: Pipelines and platforms for analyzing high-throughput AIRR data with emphasis on access and sharing. (No Government funds will be used for food and drinks)
6:30 – 6:42 PM   Jason A. Vander Heiden The immcantation framework for analysis of high-throughput immunoglobulin sequencing data and its application to myasthenia gravis
6:45 – 6:57 PM   Yariv Wine A computational pipeline for the integration of data from high throughput sequencing of b cells and shotgun proteomics of serum antibodies
7:00 – 7:12 PM   Felix Breden Ireceptor: bioinformatic platform for storing and sharing next generation sequencing (NGS) data from immune repertories
7:15 – 7:27 PM   Scott Christley VDJServer query
7:30 – 7:42 PM   Sanchita Bhattacharya ImmPort

 

Sponsors:

 

amgen logo                                  

     Antibody Society

 

Genentech logo       

Grifols logo

Illumina logo

TTP Labtech logo