TS7B: Next-Generation Sequencing for Antibody Discovery and Engineering
DAY 1, WEDNESDAY, 14 NOVEMBER, 2018: 08:30 - 19:45 HRS
DAY 2, THURSDAY, 15 NOVEMBER, 08:30 - 12:45 HRS
Room Location: Room 5B
Instructors:
Sai Reddy, Ph.D., Assistant Professor, Biosystems Science and Engineering, ETH Zurich, Switzerland
Simon Friedensohn, MSc, Research Assistant; Biosystems Science and Engineering, ETH Zurich, Switzerland
In this training seminar, participants will learn about Next-Generation Sequencing (NGS) of antibody repertoires. Part 1 will provide an introduction to the antibody repertoires, consisting of genetic background, generation of diversity, sequencing technologies and a hand-on session on the computational tools available for the analysis antibody repertoire NGS data. Part 2 will focus on the pre-processing and analysis of data. Each step of the preprocessing will be elucidated using the programming language R along with existing bioinformatics pipelines available. Repertoire analysis content will provide statistical quantification and visualization of high-dimensional data. The course will be fully interactive with case studies, participants will be able to download data and example scripts. Please bring your computer.
Topics Include:
PART I: Introduction to NGS of Antibody Repertoires and Bioinformatics Tools
Antibody repertoires
- Antibody responses: cells, biological function and applications
- Genetic background and basis of diversity
Introduction to NGS of antibody repertoires
- Sequencing platforms: advantages and disadvantages
- Single-cell and paired variable region sequencing
Experimental design and considerations
- Cell isolation and selection
- Sampling depth
- Library preparation methods
- Error and bias correction strategies
Data analysis overview
- Data formats and preprocessing
- Antibody sequence annotation
Hands-on session: Introduction of common computational tools
- Introduction to programming with the language R
- Data preprocessing
- Errors and Quality control
- Assembly of paired-end reads
- Bioinformatics tools for antibody repertoire annotation
- IMGT
- MiXCR
- In-house aligner (MAF)
- Single-cell sequencing software
- R packages for data analysis
PART II: Preprocessing and Analysis of Antibody Repertoire NGS Data
Hands-on session: Preprocessing data in R
- Additional data sources
- Common databases and repositories
- Guide to data retrieval and download
- Explore annotated reads
- IMGT – V(D)J germline segment assignment, CDR1/2/3, FW1/2/3/4
- Filtering and cleaning
- Filtering CDR3 singletons, short CDR3s, remove unproductive sequences
Hands-on session: Immune repertoire analysis
- Determine clonal variants
- Global characterization of immune repertoires
- Diversity, somatic hypermutations (SHM) distribution, CDR3 length distribution, V(D)J gene and allele frequency
- Extraction of monoclonal antibody (mAb) candidates and somatic variants
- Based on CDR3s, SHM, Germlines, repertoire frequencies
- Data visualization
- Saving output and reproducibility
Advanced topics & case studies
- Identification of biologically relevant sequences from NGS data using machine learning
- Phylogenetic trees of clonal lineages
- In-silico modelling of novel antibody sequences based on antibody repertoires
- Single-cell sequencing
Instructor Biographies:
Sai Reddy, Ph.D., Assistant Professor, Biosystems Science and Engineering, ETH Zurich, Switzerland
Sai Reddy is a tenure-track Assistant Professor (since 02.2012) in the Dept. of Biosystems Science & Engineering, ETH Zurich, Switzerland. His research group uses methods in systems and synthetic biology to study and manipulate immune responses for applications in biotechnology, vaccination, and immunotherapy. Sai Reddy holds B.S. (2003) and M.S. (2004) in Biomedical Engineering from Northwestern University (Evanston, IL, USA). He completed his Ph.D. thesis at Ecolé Polytechnique Féderale de Lausanne (EPFL, Switzerland) in Bioengineering and Biotechnology (2008). Sai Reddy did post-doctoral research at the University of Texas, Austin (2008-2011).
Simon Friedensohn, MSc, Research Assistant; Biosystems Science and Engineering, ETH Zurich, Switzerland
Simon Friedensohn is a Ph.D. candidate in Sai Reddy’s Laboratory of Systems and Synthetic Immunology at ETH Zurich (since 02.2015). His research work focuses on developing both experimental as well as computational methods for high-throughput immune repertoire sequencing in order to improve antibody discovery and engineering from NGS datasets. He holds a B.Sc. and M.Sc. in Biotechnology from ETH Zurich. Previous to joining the Reddy lab, he completed a scientific internship at Roche where he worked on high-throughput (mi)RNA profiling for comparative genomics.
Training Seminar Information
Each CHI Training Seminar offers 1.5 days of instruction with start and stop times for each day shown above and on the Event-at-a-Glance published in the onsite Program & Event Guide. Training Seminars will include morning and afternoon refreshment breaks, as applicable, and lunch will be provided to all registered attendees on the full day of the class.
Each person registered specifically for the training seminar will be provided with a hard copy handbook for the seminar in which they are registered. A limited number of additional handbooks will be available for other delegates who wish to attend the seminar, but after these have been distributed, no additional books will be available.
Though CHI encourages track hopping between conference programs, we ask that Training Seminars not be disturbed once they have begun. In the interest of maintaining the highest quality learning environment for Training Seminar attendees, and because Seminars are conducted differently than conference programming, we ask that attendees commit to attending the entire program, and not engage in track hopping, as to not disturb the hands-on style instruction being offered to the other participants.