Conference Day Two: Thursday, September 19

8 AM Check In, Coffee & Light Breakfast

8:50 AM Chair’s Opening Remarks

Leveraging the Latest Sequencing-Based Methods

9:00 am Large Serine Integrase Off-target Discovery and Validation for Therapeutic Human Genome Editing


  • Large serine integrases (LSIs) have emerged as an attractive therapeutic modality for the site specific genomic integration of DNA because they are sequence specific, size independent and do not rely on endogenous DNA repair mechanisms
  • New technologies and computational methods that account for all potential unintended genome editing related to LSIs are required to advance their clinical application for therapeutic gene integration
  • Compared to whole genome sequencing on a population of edited cells, the combination of fit-for-purpose discovery technologies and validation assays with hybrid capture sequencing is 45-fold more sensitive

9:30 am InferLOH: Assessing CRISPR-Induced Copy-Neutral Loss-of-Heterozygosity Prevalence Through Single-Cell RNA Sequencing

  • Haizi Zheng Principal Scientist - Bioinformatics, Regeneron Pharmaceuticals Inc


  • CRISPR-based genome editing may lead to copy-neutral loss-of-heterozygosity (LOH) occurring from the site of CRISPR editing to the telomere of the same chromosome arm. LOH could have serious health-related implications
  • Most existing LOH assessment methods rely on cell cloning, which may not be applicable for primary cells. In addition, the methods are usually labor- and time intensive
  • We have developed a single-cell RNA sequencing (scRNAseq) and machine learning based method that accurately predicts the zygosity of a genomic DNA region of interest of individual cells
  • This high-throughput method also allows us to assay large number of cells to reduce sampling error in the estimation of the LOH prevalence in a cell population

10:00 am Panel Discussion: Ensuring Orthogonal Validation of Unintentional Edits

  • Luca Pinello Associate Professor, Massachusetts General Hospital (MGH) and Harvard Medical School
  • TJ Cradick Chief Scientific Officer & Principal Consultant, Gene Editing Frontiers
  • Daniel O’Connell Senior Director, Genomics, Tome Biosciences


  • Benchmarking the benefits and limitations of key sequencing and PCR tools for determining on- and off-target editing outcomes
  • Assessing the latest technologies for detecting on- and off-targets
  • Case studies of effective use of NGS in the clinical setting
  • How do I effectively combine a range of these assays for a robust orthogonal approach?

10:45 AM Morning Refreshments & Speed Networking

Analytical Testing Requirements to Support an IND Filing

11:30 am Developing an Analytical Strategy to Successfully Enter the Clinic

  • Yune Kunes Vice President, Head of Analytical Development, Formulation and Early-Stage Quality Control, Prime Medicine


  • What level of product understanding do we need to establish when submitting an IND?
  • CQAs: How to understand, monitor, and link these to safety and efficacy profiles
  • Can platform understanding and data be leveraged for sound and faster development strategies?

12:00 pm Getting to Approval: Facilitating Agreements with the FDA


  • An overview of the analytical characterization pathway to the clinic
  • What really matters with off-targets: Number of sites, amount of off-target editing, oncogenesis?
  • How should we account for population diversity when quantifying gene therapies?

12:30 pm Roundtable Discussion: Successes and Setbacks with IND Submissions


Roundtable discussions place a larger focus on group discussion. A moderator will introduce the session topic and attendees then split into groups to discuss a series of assigned questions. At the end, all groups report back on their discussions, and findings are collated.

  • Highlighting areas of CMC and nonclinical testing most commonly met with regulatory feedback
  • Sharing experiences with on- and off- targeting assessment
  • What level of sensitivity and specificity do I need to demonstrate to the regulators?

1:15 PM Lunch & Networking

Key Analytical Considerations for the Delivery Method

2:15 pm Analytical Tools for Characterizing LNP-CRISPR Therapies

  • Bryant Chica Scientist II, Analytical Chemistry & Structural Biology, Editas Medicine


  • Evaluating the stability of gRNA and implications for in vivo editing
  • Characterizing targeted LNPs via LC-MS to evaluate conjugation efficiency
  • Biolayer interferometry to confirm retention of binding activity through bioconjugation process

2:45 pm Characterizing the Composition & Integrity of LNP-Based Gene Editing Therapies

  • Carl Co Senior Director - Analytical Sciences, Arbor Biotechnologies


  • Highlighting key physiochemical analytical challenges in LNP-mediated gene editing formulations
  • Analytical techniques for characterizing the DS and DP
  • Developing a toolbox to assess the stability of LNP-based gene editing cargo

3:15 pm Panel Discussion: AAV, LNP, and the Implications for In Vivo Delivery Analytical Testing Requirements

  • Kok Seong Lim Senior Director - Analytical Sciences & Quality Control, Metagenomi
  • Pete Cotter Director, Molecular Biology & Potency Analytics, Verve Therapeutics
  • Yune Kunes Vice President, Head of Analytical Development, Formulation and Early-Stage Quality Control, Prime Medicine


  • Generating robust analytical data for your delivery vehicle to bridge the gap between in vitro and in vivo studies
  • Highlighting key analytical challenges for AAV and LNP delivery of gene editing therapies
  • Developing an effective safety assessment to identify toxicities related to the delivery method

4 PM Chair’s Closing Remarks

4:10 PM End of Conference