AIRR-Community Meeting IV: Bridging the Gaps

University of Genoa, Genoa, Italy

11-15 May 2019

Draft Agenda

 

Saturday, 11 May: WG Meetings, Workshops and WG Progress Reports

Start

End

 Activities

Location

9:00

9:30

 Registration open

Stradone Sant’Agostino

4th floor

9:30

10:00

 Coffee & snack

Stradone Sant’Agostino

Cloister

10:00

15:00

 WGs meet separately

  (Each WG will provide a separate agenda to its members)

Stradone Sant’Agostino

6 rooms

10:00

13:00

 Workshop I: Jamie Scott, Simon Fraser University (CA): “Fundamentals of the immune system”

Stradone Sant’Agostino

Room 4H

10:00

13:00

 Workshop II: Victor Greiff, University of Oslo (NO): “AIRR-seq data processing and analysis (including AIRR-C standards for data and storage)”

Stradone Sant’Agostino

Room 5H

13:00

14:00

 Registration open

13:00

14:00

 Lunch

Stradone Sant’Agostino

Cloister

15:00

15:30

 Break

15:00

15:30

 Registration open

Chiesa di San Salvatore

15:30

15:40

 Welcome and voting reminder by the Chair of the AIRR-C Executive Sub-committee: Felix Breden, Simon Fraser University (CA)

15:40

16:40

 Report from Executive Sub-committee

 Introduction to Working Groups, and reports on progress, future plans & leadership

  (20-min Reports + 10-min Discussion)

16:40

17:10

 Biological Reagents WG Report

17:10

17:40

 Germline DB WG Report

17:40

18:30

 Panel Discussion: Germline Databases (GLDB) WG

 “Beyond inferred alleles: Improving the quality, scope and openness  of GLDBs through software inference, open publication and population-level data”

 Chair: Christian Busse, German Cancer Research Center (DE)

 Panel Members:

 Martin Corcoran, Karolinska Institute (SE)

 Henk-Jan van den Ham, Enpicom BV (NL)

 William Lees, Birkbeck College, University of London (GB)

 Mike Stubbington, 10X Genomics (GB)

  Dinner on your own

Sunday, 12 May: WG and Communication Subcommittee Progress Reports

Start

End

 Activities

Location

9:00

9:30

 Registration open; Coffee & snack

Chiesa di San Salvatore

9:30

9:40

 Introduction to Day 2 of Progress Reports by the Chair of the AIRR-C Executive Sub-committee: Felix Breden, Simon Fraser University (CA)

 (20-min Report + 10-min Discussion)

9:40

10:10

 Software WG Report

10:10

10:40

 Data Representation WG Report

10:40

11:10

 Minimal Standards WG Report

11:10

11:40

 Common Repository WG Report

11:40

12:30

Light lunch

12:30

13:50

 Panel Discussion: Common Repositories, Data Representation and Minimal Standards WGs

“Towards Solutions: The Benefits and Challenges of Sharing AIRR-seq Data”

 Chairs: Christian Busse, German Cancer Research Center (DE) & Lindsay Cowell, University of Texas, Southwestern  Medical Center (US)

 Panel Members: 

 Bryan Briney, Scripps Research (US)

 Konrad Krawczyk, Natural Antibody (DE)

 Anton Langerak, Erasmus MC (NL)

 Xiao Liu, BGI Shenzhen (CN)

13:50

14:40

 Introduction to the Communications Subcommittee & Report

Chiesa di San Salvatore

15:00

18:00

 AIRR-C Meeting Welcome Reception & AIRR-seq Tool Demonstrations

Stradone Sant’Agostino

Cloister 4B-4C

16:00

18:00

 AIRR-seq Tool Demonstrations 

  (10-min/presenter)

 Chair: Lindsay Cowell, University of Texas, Southwestern Medical Center (US)

 Presenters:

 Nicola Bonzanni, Enpicom B.V. (NL): “Intuitively manage, store, analyze, and visualize repertoire sequencing data using the ImmunoGenomiX (‘IGX’) platform”

 Bryan Briney, Scripps Research (US): “Massively scalable genetic analysis of antibody repertoires”

 Brian Corrie, Simon Fraser University (CA): “iReceptor – A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories”

 Kenneth Hoehn, Yale University (US): “Phylogenetic analysis of B cell repertoires with IgPhyML”

 Steven Kleinstein, Yale School of Medicine (US): “The Immcantation Framework for analysis of AIRR-seq data” 

 William Lees, Birkbeck College, University of London (GB): “OGRDB – the Open Germline Receptor Database”

 Vadim Nazarov, National Research University (RU): “Bioinformatics software problems and how to make immune data analysis effortless with immunarch”

 Duncan Ralph, Fred Hutchinson Cancer Research Centre (US): “Partis: A tool for accurate and efficient annotation of germline and clonal family inference”

 Mikael Salson, Universite de Lille - VidjlNet (FR): “Vidjil: an open-source platform for interactive repertoire analysis”

Stradone Sant’Agostino

Room 4B-4C

  Dinner on your own

Monday, 13 May: Scientific Progress & Challenges (Basic Science)

Start

End

 Activities

Location

8:00

8:30

 Registration open

Chiesa di San Salvatore

8:00

8:30

 Coffee available at the meeting site

8:30

8:40

 Introduction to the Meeting and the Keynote by the AIRR-C Executive Sub-committee Chair, Felix Breden, Simon Fraser University (CA)

8:40

9:30

 Keynote: Sai Reddy, ETH Zurich (CH): “Integration of systems immunology and immune repertoires”

  (40-min talk + 10-min Q&A)  

9:30

9:40

 Advances in Understanding Biological Processes of the AIRR

  (25-min talks + 10-min Q&A)

 Chair: Andrew Collins, University of New South Wales (AU): Session introduction

9:40

10:15

 Talk 1: Nicholas Schwab, University of Muenster (DE): “Sex bias in MHC I-associated shaping of the adaptive immune system”

10:15

10:50

 Talk 2: Lindsay Cowell, University of Texas, Southwestern Medical Center (US): “Statistical classifiers for detecting phenotype-associated biophysicochemical motifs in AIRR”

10:50

11:20

Coffee

11:20

11:55

 Talk 3: David Klatzmann, Sorbonne Universite (FR): “How specific is specific (in the T-cell response)?”

11:55

12:30

 Talk 4: Tom Parks, University of Oxford (UK): “Germline immunoglobulin heavy-chain locus variation and susceptibility to group A streptococcal disease”

12:30

13:00

 Short Oral Presentations selected from Poster Abstracts (3x10 minutes, no discussion)

 Chair: Ramit Mehr, Bar-Ilan University (IL)

 Presenters:

 Kenneth Hoehn, Yale University (US): Repertoire-wide phylogenetic models of B-cell molecular evolution reveal evolutionary signatures of aging and vaccination” 

 Ivana Mikocziova, University of Oslo (NO): “AIRR-seq reveals a large number of germline polymorphisms in the variable immunoglobulin genes”

 Pieter Meysman, University of Antwerp (BE): “On the viability of unsupervised T-cell receptor sequence clustering for epitope preference”

13:00

15:00

 Lunch Break + Poster Session

Stradone Sant’Agostino

Cloister + Hallway

15:00

15:10

 Challenges in Processing and Storing Massive AIRR-seq Data (>1bn sequences)

  (20-min talk + 15-min discussion)

 Chair: Uri Laserson, Icahn School of Medicine at Mount Sinai (US): Session introduction

Chiesa di San Salvatore

15:10

15:45

 Talk 1 + Discussion - Processing & Annotation: Mikhail Shugay, Skolkovo Institute of Science and Technology (CZ): Challenges in motif discovery and comparative analysis of large T-cell receptor repertoire datasets 

15:45

16:20

 Talk 2 + Discussion - Analysis: Bryan Briney, Scripps Research (US): “Commonality despite exceptional diversity in the baseline human antibody repertoire

16:20

16:55

 Talk 3 + Discussion - Data Storage & Access: Xiao Liu, BGI Shenzhen (CN): “Pan Immunome Initiative and applications in health and disease”

17:00

19:00

 Pipeline + Data Repository Tutorials + light reception

  (pre-registration required through registration site, attendees may register for up to two 45-min sessions)  

 Presenters:

 Nicola Bonzanni, Enpicom B.V.: “IGX”

 Cecilie Boysen, Biomatters Ltd.: ”Geneious Biologics”

 Bryan Briney, Scripps Research: “AbCloud”

 Scott Christley, UT Southwestern Medical Center: “VDJServer”

 Brian Corrie, Simon Fraser University: “iReceptor”

 Khalil EL Mazouari, AbnomX: “Antibody-Extractor”

 Jacob Glanville, Distributed Bio: “AbGenesis”

 Kenneth Hoehn, Yale University: “Immcantation and IgPhyML”

 William Lees, Birkbeck College, University of London: “OGRDB”

 Vadim Nazarov, National Research University: “PyTorch”

 Mikhail Shugay, Skolkovo Institute of Science and Technology: “VDJtools”

Stradone Sant’Agostino

Cloister 4B-4C

  Dinner on your own

Tuesday, 14 May: Scientific Progress & Challenges (Clinical and Translational Science)

Start

End

 Activities

Location

8:00

8:30

 Registration open

Chiesa di San Salvatore

8:00

8:30

 Coffee available at the meeting site

8:30

8:40

 Introduction to the Keynote by AIRR-C Chair-Elect Nina Luning Prak, University of Pennsylvania (US)

8:40

9:30

 Keynote: Antonio Lanzavecchia, Institute for Research in Biomedicine (CH): “Lessons from the analysis of the immune response to P. falciparum: The power of clonal selection”

  (40-min talk + 10-min Q&A) 

9:30

9:40

 Advances in AIRR-seq Data Addressing Human Health and Disease

  (25-min talks + 10-min Q&A)

 Chair: Steven Kleinstein, Yale School of Medicine (US): Session introduction

9:40

10:15

 Talk 1: Rachael Bashford-Rogers, University of Oxford (UK): “Mapping B-cell receptor repertoires in immune-mediated diseases”

10:15

10:50

 Talk 2: Rob Holt, BC Cancer Research Centre, UBC/SFU (CA): "Mining the tumor-associated T cell repertoire for TCR therapeutics"

10:50

11:20

 Coffee Break

11:20

11:55

 Talk 3: TBA

11:55

12:30

 Talk 4: Ziv Shulman, The Weizmann Institute of Science (IL): “Dynamics of B cell immune responses in intestinal tissues”

12:30

13:00

 Short Oral Presentations selected from Poster Abstracts (3x10 minutes, no discussion)

 Chair: Ramit Mehr, Bar-Ilan University( IL)

 Presenters:

 Felix Breden, Simon Fraser University (CA): “iReceptor Plus facilitates sharing and analysis of AIRR-seq data”

 Xihao Hu, Dana Farber Cancer Institute (US): “Landscape of B-cell immunity and related immune evasion in human cancers”

 Keshav Motwani, University of Florida (US): “T-cell receptor repertoires in peripheral blood encode type-1 diabetes status”

13:00

14:30

 Lunch Break + Poster Session

Stradone Sant’Agostino

Cloister + Hallway

14:30

14:40

 Patient & Community Engagement  (15-min talk + 5-min Q&A)

 Chair: Tania Bubela, Simon Fraser University (CA): Session introduction

Chiesa di San Salvatore

14:40

15:00

 Short Talk 1: Tania Bubela: TBA

15:00

15:20

 Short Talk 2:  Harriet Teare, University of Oxford (UK): “Dynamic consent: Individual oversight and control of data and samples”

15:20

15:40

 Short Talk 3: Namaste Marsden, BC First Nations Health Authority (CA): “We are relational: The challenge of Indigenous collective rights in bio-ethics”

15:40

16:10

 Panel Discussion: Patient & Community Engagement

16:10

16:30

 Coffee

16:30

16:40

 Engaging Industry

  (15-min talk + 5-min Q&A)

 Chair: Jean-Philippe Bürckert, BISC Global Inc. (US): Session introduction

16:40

17:00

 Short Talk 1: Jacob Glanville: Distributed Bio (US): “Applied repertoire analysis - Computational immunoengineering of therapeutic antibodies and TCRs”

17:00

17:20

 Short Talk 2: Jonathan Carlson: Microsoft Research (US): “The Adaptive-Microsoft TCR-Antigen Map Project”

17:20

17:40

 Short Talk 3: Nicola Bonzanni: Enpicom (NE): “Bridging the gap: Manage, analyze, visualize and interpret repertoire sequencing data using the IGX platform” 

17:40

19:00

  Industry Reception

  Meet with and learn more about the innovations of our meeting sponsors: 10x Genomics, AbnomX, BISC Global, CZ Biohub, Distributed Bio, Geneious Biologics, Grifols, Hamilton, Roche, Takara Bio

Stradone Sant’Agostino

Glass Room 4th floor

19:30

22:00

 Group Dinner at Osteria di Vico Palla (pre-registration required)

Osteria di vico Palla

Wednesday, 15 May: AIRR-C Organisational Session

Start

End

 Activities

Location

8:30

9:00

 Coffee available at Meeting Site

Chiesa di San Salvatore

9:00

9:10

 Introduction to the AGM of the AIRR-Community Members by Chair and Chair-Elect: Felix Breden, Simon Fraser University (CA) & Nina Luning Prak, University of Pennsylvania (US)

9:10

11:10

 AIRR-C Working Groups work plans and leadership

  Each of the 6 WGs

  •  Recap proposed work plan as a motion (vote)  
  •  Leadership as a motion (vote)

  (20 min each including voting!)

11:10

11:30

 Coffee

11:30

12:30

 AIRR-C Sub-committee(s) plans and voting

  •  Recap proposed work plans as a motion (vote)  
  •  Leadership as a motion (vote)

11:30

12:00

 Executive Sub-committee  (ratify governance revisions)

12:00

12:15

 Meeting Sub-committee (ratify where & when will the next meeting be held)

12:15

12:30

 Communications Sub-committee (ratify as a new standing sub-committee)

12:30

14:30

 Meeting adjourned & lunch on your own

14:30

17:30

 Sub-committees and Working Groups - wrap-up meetings

Stradone Sant’Agostino

6 rooms

2019-04-14 Draft Agenda