Quality Control Pipelines for T cell and B cell AIRR-seq

Professors Encarnita Mariotti-Ferrandiz and Nina Luning Prak, members of the Adaptive Immune Receptor Repertoire (AIRR) Community Biological Resources Working Group, discuss quality control (QC) procedures for immune repertoire profiling. Dr. Mariotti-Ferrandiz describes QC pipelines for sequencing of T cell receptor gene rearrangements that are in use in her laboratory in the Department of Immunology, Immunopathology and Immunotherapy at the Sorbonne. Next, Dr. Luning Prak describes QC pipelines for sequencing of B cell receptor gene rearrangements that are in use in her laboratory and in the Human Immunology Core facility at the University of Pennsylvania. They then respond to questions posed by attendees during a Q&A period.
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About the speakers: Prof. Encarnita Mariotti-Ferrandiz, Prof. Nina Luning Prak
Nina Luning Prak is a Professor of Pathology and Laboratory Medicine at the University of Pennsylvania in Philadelphia, PA. In addition to running a research lab that studies B-cell repertoires in human health and disease, Dr. Luning Prak directs the Human Immunology Core at Penn, which has performed over 140 B and T-cell immune repertoire profiling projects. Dr. Luning Prak also has clinical duties as a pathologist at the Hospital of the University of Pennsylvania.
Prof. Luning Prak has been an active member of the AIRR community since its founding in 2015. She is very interested in both the generation and analysis of AIRRseq data. She served as Co-lead of the Minimal Standards Working Group with Steven Kleinstein and has served as Chair and Past Chair of the Executive Sub-committee. She currently serves as a member of the Biological Resources Working Group, the Standards Working Group and the Diagnostic Working Group. Dr. Luning Prak is also currently serving as an elected member of the Executive Sub-committee.
Prof. Encarnita Mariotti-Ferrandiz is an Associate Professor in Immunology from Sorbonne Université, working in the i3 lab directed by Prof. David Klatzmann, located at Pitié-Salpêtrière Hospital, in Paris. Since her PhD, she has been involved in deciphering the Adaptive Immune Receptor Repertoire (AIRR) diversity in health and pathology with a major focus on T-cell biology. From sample to statistical modelling, she is interested in 1) refining T cell differentiation and selection knowledge in health and disease, and 2) identifying biomarkers of diseases. Her main field of research in immunology focuses on the study of autoimmune in inflammatory diseases. T cells and the T-cell receptor being a part of a whole in T-cell biology, she uses the Systems Immunology approach to better characterize the immune system by coordinating the integration of multi-scale biological (deep cell phenotype, transcriptome, repertoire, microbiome) and clinical information. As an Associate Professor, she launched the “Integrative and Systems Immunology” Master 2 curriculum at Sorbonne Université in 2019, with the aim to promote and train the future research generation to Systems Immunology as a whole, including AIRR.
With this expertise, she joined the AIRR Community in 2016. Starting as a member of AIRR-C Standards Working Group, she then Co-led from 2017 to 2020 together with Maggie Bostick the AIRR-C Biological Resources Working Group. In 2020, she was elected as an AIRR-C Executive Sub-committee member. From 2020 to 2022, she Co-led the AIRR-C Meetings Sub-committee together with Pam Borghardt. She is now a member of the Biological Resources Working Group and the Chair-elect of the AIRR Community.