Ashoka University, in collaboration with the Council of Scientific and Industrial Research–Institute of Genomics and Integrative Biology (CSIR–IGIB), organized a 2-day hands-on workshop on DNA sequencing on August 29th and 30 th at IGIB. The workshop was carried out as part of the Rockefeller Foundation-Alliance for Pathogen Surveillance Innovations-India (RF-APSI-India) program.

Mandate


1. The workshop covered a range of topics, including:

Introduction to DNA Sequencing: Overview of sequencing technologies available and their application

Next-Generation Sequencing (NGS) Techniques: Principles of NGS, platforms used, and the advantages of high-throughput sequencing.

Sample Preparation and Quality Control: Detailed demonstration of DNA extraction, quantification, and quality assessment for sequencing.

Library Preparation: Hands-on session on preparing sequencing libraries.

Data Generation and Analysis: A walkthrough of sequencing data generation, quality control, and preliminary data analysis using bioinformatics tools.

Participants

This 2-day workshop at CSIR-IGIB included participants such as clinicians, clinical researchers, path lab technicians, pharmacists mainly from the Delhi-NCR and adjoining states. The workshop featured an introduction to pathogen sequencing, hands-on demonstrations, interactive sessions, and talks from experts. Discussions centered around integrating sequencing in clinical settings, particularly for the detection of Antimicrobial resistance.

Program

The workshop was led by Dr. Rajesh Pandey, Principal Scientist at CSIR-IGIB and Dr Shraddha Karve, Faculty Fellow at Ashoka.

On the first day, August 29th, the event began with an introduction by Dr. Aradhita Baral, Senior Program Manager at Ashoka University, followed by a detailed overview of DNA sequencing and its importance by Dr. Rajesh Pandey . Dr Shraddha Karve, Faculty Fellow at Ashoka University demonstrated introduced the importance of DNA extraction andDr. Rajesh Pandey provided insights into Nanopore sequencing. Dr Jitendra Narayan, Senior Scientist at CSIR-IGIB discussed the AMR Bioinformatics Workflow, and Dr Jaisri Jagannadham Project Lead at Ashoka University taught the analysis module for building genomic assembly from raw data.

The workshop included presentations on technical and theoretical aspects of DNA sequencing by experts from Ashoka University and IGIB.

Hands-on training of genomic DNA extraction:

Dr. Shraddha Karve and her team initiated the hands-on DNA extraction protocol using. Qiagen DNEasy Blood and Tissue kit, a silica column based DNA extraction method. This is a standardized a protocol to extract DNA from bacterial culture. It is a reasonably priced but highly efficient kit and requires basic laboratory equipment which can easily be found in most routine laboratories.

Hands-on Demonstration of Nanopore Sequencing:

Dr. Rajesh Pandey and his team initiated the hands-on training on Sequencing on Day 1, covering multiple steps such as library preparation, priming, and sample loading on Nanopore. The participants were trained in WGS Library Preparation using the Native Barcoding Kit 24 V14. They were also taken on a Sequencing facility visit to shaow the different types of sequencer available and their usage.

On the second day, 30 th August, participants continued with library preparation training and further analysis.

The final session of the workshop was led by Dr. Jaisri Jagannadham, who taught participants how to build a genomic assembly from raw data and perform downstream analysis to determine genes that confer resistance.

Learning through interactive sessions:

The workshop concluded with an engaging session in which Dr. Rajesh Pandey addressed general and technical queries from the participants. Certificates were given to participants who attended all sessions on both days.

1. Key Outcomes

Increased Competence in Sequencing Techniques: Participants trained and hence gained confidence in performing key steps of the sequencing process, including DNA extraction, library preparation, and data interpretation.

Understanding Clinical Relevance: Attendees better understood how sequencing technologies can be applied in clinical set up, particularly in identifying pathogen genomes.

Collaboration and Networking: The workshop fostered provided an opportunity for prospective collaborations.

Feedback: Participants valued the opportunity to work directly with sequencing equipment and software. They appreciated the availability of experts to clarify their doubts

Dr. Aradhita Baral,
Sr Program Manager,
Ashoka University and Abha Tiwari,
Project Manager,
Ashoka University.