The AIRR Community Diagnostics Working Group is excited to announce season 2 of the On AIRR podcast series!
The series aims to disseminate the goals and values of the Community, with a focus on their application to diagnostics and other clinical applications. We are committed to presenting conversations with a diverse group of experts, and gathering the attention of a broad audience, including students, and researchers from both industry and academia.
Every podcast episode is co-hosted by Ulrik and Zhaoqing:
- Dr. Ulrik Stervbo holds a PhD in immunology and is team leader at Ruhr-Universität Bochum and Charité – Universitätsmedizin Berlin. His work focuses on the immune response in immunocompromised patients, in particular transplant patients. Ulrik has a long-standing fascination of the adaptive immune receptor repertoires with an emphasis on T cell receptors. He is also the current co-lead of the AIRR Community Diagnostics Working Group.
- Dr. Zhaoqing (Ching) Ding obtained her M.S. and Ph.D. in immunology from UCSD and Stanford University, respectively, and is currently a Director of Translational Medicine at Gossamer Bio working on biomarker strategies in clinical staged programs in immune-related diseases. Prior to Gossamer Bio, Dr. Ding has led multiple early discovery and development programs in the infectious disease, oncology, and autoimmune space at Johnson and Johnson and Takeda Pharmaceuticals. Throughout Dr. Ding’s career, she has been fascinated with leveraging the information from the adaptive immune receptor repertoires for deconvoluting antigenic drivers. biomarker discovery and translating the repertoires themselves into therapeutic products.
If you have questions for our next guest, suggestions for guests that you would like us to invite, or interesting topics to discuss, send us an email at onairr@airr-community.org. If you share podcast-related content in social media, please use the hashtag #onairr.
Podcast Episodes
| Podcast | Date | Description |
|---|---|---|
| S02 E05 | Oct 2023 | On AIRR 15: Germline databases or adventures into the allelic underworld Guests: Dr. Corey Watson and Dr. William Lees. Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding We talk about the recent work by the Germline Database Working Group of the AIRR-Community. We discuss the challenges in creating a database to hold all relevant and potentially relevant germline information, and reflect on the complexity in handling personalised germline reference sets. Our guests are both active members of the Germline Database Working Group and have a long standing interest in developing reference sets for adaptive immune receptors. |
| S02 E04 | Jul 2023 | On AIRR 14: Data protection and data sharing Guest: Alexander Bernier Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding We discuss the risk of identifying individuals in a biological data set, how this is approached differently in different countries, and possible strategies to ensure data privacy. Our guest is Alexander Bernier BCL, JD, LLM, a lawyer with expertise in biological data sharing designs. |
| S02 E03 | Jun 2023 | On AIRR 13: Disease diagnostics using machine learning Guests: Maxim Zaslavsky and Dr. Scott D. Boyd Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding We discuss the preprint “Disease diagnostics using machine learning of immune receptors”, available at BioRxiv. The work is led by Maxim Zaslavsky with Scott Boyd the corresponding author. In the manuscript, the authors demonstrate how AIRR-seq and machine learning can be used in disease diagnostics |
| S02 E02 | May 2023 | On AIRR 12: T-cell receptor-mimetic antibodies and immunoinformatics Guest: Prof. Charlotte Deane Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Prof. Charlotte Deane’s research merges statistics, immunoinformatics, protein structure and small molecule drug discovery. We discuss the relevance of including protein structure to study and design antibodies, and the availability of such data. |
| S02 E01 | Apr 2023 | On AIRR 11: Software as a Medical Device (SaMD) Guest: Dr. Xenophon Papademetris Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Dr. Papademetris provides an overview of the typical regulatory process for software classified as a medical device. We draw from his experience in the medical image field to design a high level route map for an imaginary company bringing to the market software to diagnose minimal residual disease. |
| S01 E10 | Nov 2022 | On AIRR 10: Characterising B Cell Lymphomas or Profiting from a Focus on B Cells in Health and in Disease Guest: Dr. Ralf Küppers Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Building upon Ralf’s background in B cell differentiation in health and pathogenesis of human B cell lymphomas, we discuss how micro-dissection and Sanger sequencing is still the method of choice when analysing Hodgkin lymphoma and the V-gene usage and mutations in CLL as prognostic indicators before talking about tracking pathogenic clones when surveying for relapse during clinical follow up. |
| S01 E09 | Oct 2022 | On AIRR 9: The ImmunoMind or wielding an AI for repertoire insights Guest: Vadim Nazarov Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Vadim Nazarov is Co-Founder & CEO of the startup ImmunoMind. The company focuses on improving the design of adoptive T-cell therapies using multi-omics technologies. Vadim's career began at Dr. Dmitry Chudakov’s Laboratory of Adaptive Immunity, where he developed the now discontinued R-package TcR. The replacement package ‘immunarch’ is continuously developed by ImmunoMind. |
| S01 E08 | Sep 2022 | On AIRR 8: Engineering B cells or Giving the immune System an Optimal Starting Point Guest: Dr. Adi Barzel Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Following Adi’s long standing interest in gene editing, we discuss the therapeutic potential based on Adi’s recent paper “In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice” (Nat Biotechnol.; 2022; https://doi.org/10.1038/s41587-022-01328-9). We also briefly touch on a second paper on some of the problems with CRISPR-Cas9 gene editing (“Frequent aneuploidy in primary human T cells after CRISPR-Cas9 cleavage”; Nat Biotechnol.; 2022; https://doi.org/10.1038/s41587-022-01377-0) |
| S01 E07 | Aug 2022 | On AIRR 7: Quality Controls in AIRR-Seq Assays or Handling the Catastrophe Guest: Dr. Encarnita Mariotti-Ferrandiz Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding The discussion focuses on sample quality and how to assess this. We draw on two papers during the discussion: “Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases” (Nature Biotechnology; 2021; https://doi.org/10.1038/s41587-020-0656-3) and “Biological controls for standardisation and interpretation of adaptive immune receptor repertoire profiling” (eLife; 2021; https://doi.org/10.7554/eLife.66274). |
| S01 E06 | Jul 2022 | On AIRR 6: Data Sharing or Finding Glory, Fame and a Big Pile of Gold Guests: Dr. Brian Corrie and Dr. Scott Christley Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding In this episode we discuss possibilities for sharing AIRR-Seq data - repositories and metadata standards describing the samples and experimental process. We discuss AIRR Standards which includes MiAIRR Standard for dataset metadata and AIRR Data Commons, which is an API to query and download data from AIRR-Seq repositories. Complete and proper data annotation will bring fame and glory. |
| S01 E05 | May 2022 | On AIRR 5: Machine learning and AIRR or Looking for the needle in a needle stack Guests: Dr. Lindsay Cowell and Dr. Victor Greiff Hosts: Dr. Ulrik Stervbo and Dr. Zhaoqing Ding Today we discuss machine learning with Dr. Lindsay Cowell and Dr. Victor Greiff. Machine learning is about pattern recognition and in AIRR-seq these patterns link repertoires to diseases and antigen binding. AIRR is nearly a perfect machine learning problem because the underlying patterns are unclear and complex - it is essentially looking for the needle in a needle stack. |
| S01 E04 | Apr 2022 | On AIRR 4: Understanding and engineering immune repertoires Guest: Dr. Jacob Glanville Hosts: Ulrik Stervbo and Zhaoqing Ding Dr. Jacob Glanville is founder and CEO of Centivax and founder of Distributed Bio, acquired by Charles River in 2021. His work focuses on understanding and engineering the repertoires of T and B cells to improve the response to pathogens. In this episode we discuss how to analyze receptor specificity and use this to create therapeutic antibodies and optimize vaccine response. |
| S01 E03 | Mar 2022 | On AIRR 3: Outlining chronic lymphocytic leukemia Guest: Dr. Anton Langerak Hosts: Ulrik Stervbo and Zhaoqing Ding Anton Langerak is Professor and head of Laboratory Medical Immunology at Erasmus MC in Rotterdam, Netherlands and chair of coordination of the EuroClonality-NGS working group. He has been working on chronic lymphocytic leukemia (CLL) for many years and in this episode we discuss the signatures of B cell receptors in CLL. |
| S01 E02 | Feb 2022 | On AIRR 2: Establishing an AIRR-Seq framework Guest: Dr. Lindsay Cowell, PhD., Division of Biomedical Informatics, University of Texas Southwestern Medical Center at Dallas Hosts: Ulrik Stervbo and Nidhi Gupta In this episode, we discuss the interest of Lindsay Cowell from UT Southwestern in creating a framework to enable deeper understanding of AIRR-Seq in health and disease. |
| S01 E01 | Jan 2022 | On AIRR 1: MRD Guest: Dr. Eline T. Luning Prak, MD, PhD. Professor of Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania Hosts: Ulrik Stervbo and Nidhi Gupta We talk a bit about the AIRR-Community but mostly we discuss diagnosis of B or T cell malignancies and minimal residual disease evaluation and tracking of B cell clones in autoimmunity. |
