Andrew Kernytsky Email & Phone Number

Cambridge, MA, US

• I provide consulting expertise to develop next generation gene and cell therapies: computational biology, gene therapy / gene editing, guide design, on- and off-target analysis, new company setup, and regulatory.
• Advising on overall off-target strategy from early research to clinic
• Regulatory submission of Investigational New Drug (IND) applications
• Implementing and improving gene editing off-target methods including Digenome-seq
• Epigenetic (ATAC-seq) and RNA-seq data analysis
• Setting up new computational infrastructure (AWS / cloud), computational biology groups and hiring new employees

Boston, MA, US

• Led gene editing characterization and regulatory submission for 10+ CRISPR-based clinical trials that are currently open
• Expanding the research platform by characterizing new Cas enzymes, Cas specificities, and other new editing modalities
• CRISPR screening for various cell traits and modifications that can improve outcomes in clinical trials

Boston, MA, US

• Started first company sponsored CRISPR clinical trials for CTX001 via submissions to European or American regulatory agencies for beta thalassemia and sickle cell disease(!)
• Created on- and off-target NGS assessment strategy for all CRISPR Therapeutics programs; presented and published about strategy to influence community conversation
• Work with multiple collaboration / alliance partners and contract research organizations on therapeutic programs
• Manage outsourced software development, research IT infrastructure maintenance
• Lead amazing team of over 10 computational and bench researchers

Boston, MA, US

• Predicted guide RNAs appropriate for therapeutic targets
• Sequenced edited DNA to asses guide efficiency on and off target
• Validated various methods for increasing guide screening capacity
• Computationally improved guide RNA effectiveness prediction and guide editing detection limit

Cambridge, MA, US

• Summary: Key early research put two drugs on the market - Idhifa (IDH2m inhibitor) and Tibsovo (IDH1m inhibitor) - and led to three ongoing clinical trials - Mitapivat (PKR activator), Vorasidenib (Pan-IDHm inhibitor).
• Showed first evidence that methylation reversal of leukemia pathways was the mechanism of action of Agios’ IDH2 small molecule inhibitor (Idhifa) by analyzing methylation microarray and sequencing data (Kernytsky et.
• Identified MAT2A in synthetic lethal shRNA screens as a target for AG-270 currently in clinical development (Marjon et al Cell Rep. 2016 15:575-587)
• Created the next generation of cancer metabolism drugs by creating and testing patient stratification and responder hypotheses and identifying new targets for personalized treatments.
• Inferred rare disease prevalence using NHLBI 6500 exome sequencing data
• Developed PCR and deep sequencing methods for phage display small peptide screening

Cambridge, MA, US

• Summary: Directed basic research decisions using genome-scale tumor data (gene expression, methylation, amplification/deletion, and mutation) from public sources including Gene Expression Omnibus (GEO), The Cancer.
• Built a framework for mining The Cancer Genome Atlas (TCGA) for recurrent gain-of-function point mutations that make ideal small molecule drug targets
• Created SNP imputation algorithm with a 60% accuracy to identify cell lines for a new program using public data and enabled stalled project to proceed

Cambridge, MA, US

• Contributed and evaluated core methods and algorithms for large-scale data integration and refinement project that produced leading DNA sequence variation detection engine (SNP and indel genotyping) for next-generation.
• Interacted closely with bench scientists to create, test, and approve new design for selectively sequencing whole exomes (all exons in a genome); design is currently in production on large fraction of the Broad’s 100.
• Created and developed reusable bioinformatics tools within a structured Java analysis framework to fulfill various projects’ analysis needs

New York, NY, US

• Integrated various genome-scale sources of sequence, structure, and function data and used genetic algorithms to automatically select appropriate input features for the training of machine learning algorithms including.
• Performed large-scale assessment of integral membrane protein structure prediction methods; created public web server to provide rigorous community benchmarking of methods
• Automated the creation and weekly updating of custom, in-house databases of protein structure and sequence from mirrored versions of public biological databases
• Optimized prediction of protein crystallizability for high-throughput crystallization consortium

Rahway, New Jersey, US

• Worked on design, implementation, and testing of gene expression microarray production facility
• Designed software to select the best group of oligonucleotides to detect a given gene with high sensitivity

• Performed gene expression experiments and analyzed results for disease relevance in collaboration with various research groups using Affymetrix GeneChip and proprietary microarray technology
• Implemented system for annotation and analysis of high-throughput expression data that interacted with SQL databases and Java-based analysis tools

Ph.D., Biochemistry And Molecular Biophysics

B.A., Chemistry, Biochemistry