Garrett Cooper

Decoding pediatric cancer through omics and functional genomics to drive better diagnostics and therapies.

EDUCATION

  • PhD Genetics and Molecular Biology, Emory University – Nov 2025
  • BSc Genetics, University of Georgia – May 2020

RESEARCH

Doctoral Researcher, Hong Lab – Emory University (2021-2025), Atlanta, GA

  • Characterized SMARCB1 missense variants that mimic complete protein loss yet maintain detectable protein, using integrated multi-omics and NGS methods (RNA-seq, ATAC-seq, CUT&RUN, proteomics, and computational biophysical modeling).
  • Built scalable bioinformatics pipelines (R, Python, AWS) integrating multi-omic NGS data and applying statistical methods (R/Bioconductor) to reveal that pathogenic missense mutations destabilize the SWI/SNF chromatin remodeling complex.
  • Designed and executed end-to-end functional genomics workflows including plasmid design, lentiviral transduction, assay optimization, NGS library prep, and QC to generate sequencing data for chromatin remodeling studies.
  • Benchmarked machine learning variant prediction models against proliferation-based deep mutational scanning data, revealing functional-readout dependent limitations in variant predictions.
  • Co-led a study identifying XPO1 as a targetable vulnerability in Wilms tumor by analyzing CRISPR-Cas9/RNAi screening data and performing validation studies including knockout/knockdown cell lines, transcriptomic analysis, and drug synergy assays, contributing to the advancement of a Phase II clinical trial (NCT05985161).

Laboratory Research Intern, Assay Research – GRAIL, Inc. (2024), Menlo Park, CA

  • Conducted a platform transition study comparing WGBS sequencing performance between NovaSeq 6000 and NovaSeq X+, benchmarking key metrics including mapping efficiency, insert sizes, mapping CpG detection rates to validate the new platform for clinical-grade epigenomic assays.
  • Evaluated an updated conversion reagent in the WGBS sample preparation pipeline, performing end-to-end sample prep, sequencing, and characterization, to assess impact on sample quality.

Undergraduate Research Assistant, Kissinger Lab – University of Georgia (2018-2020), Athens, GA

  • Performed genome-wide SNV analysis of ~250 parasite genomes using BWA/GATK on HPC clusters, revealing population-level genetic diversity that challenged standard subtyping approaches.

GGBC Intern – Georgia Genomics and Bioinformatics Core (2018-2019), Athens, GA

  • Developed an automated rRNA library preparation workflow for microbial-based projects.

PUBLICATIONS

Cooper GW, et al. SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity. Research Square (2025). https://doi.org/10.21203/rs.3.rs-6018128/v1

Mitall KM*, Cooper GW*, Lee BP*, Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin. Communications Biology 7, 426 (2024). https://doi.org/10.1038/s42003-024-06140-6

Cooper GW, Hong AL. SMARCB1-deficient cancers: novel molecular insights and therapeutic vulnerabilities. Cancers 14, 3645 (2022). https://doi.org/10.3390/cancers14153645

Baptista RP, Li Y, Sateriale A, Sanders MJ, Brooks KL, Tracey A, Ansell BR, Jex AR, Cooper GW, et al. Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Research 32: 203-213 (2022). https://doi.org/10.1101/gr.275325.121

Jones RB, Farhi J, Adams M, Parwani KK, Cooper GW et al. Targeting MLL methyltransferases enhances the antitumor effects of PI3K inhibition in hormone receptor–positive breast cancer. Cancer Research Communications 2, 1569–1578 (2022). https://doi.org/10.1158/2767-9764.CRC-22-0158

Baptista RP, Cooper GW, et al. Challenges for Cryptosporidium Population Studies. Genes 12, 894 (2021). https://doi.org/10.3390/genes12060894

PRESENTATIONS

  • Poster Presentation, American Association for Cancer Research Annual Meeting, April 2025. “SMARCB1 missense mutants destabilize SWI/SNF complex stability and remodeling activity”, doi: https://doi.org/10.1158/1538-7445.AM2025-986
  • Poster Presentation, Advances in Pediatric Cancer Research AACR Special Conference, September 2024. “Deep mutational scanning of SMARCB1 identifies missense mutants that destabilize SWI/SNF complex stability and diminish remodeling activity”, doi: https://doi.org/10.1158/1538-7445.PEDIATRIC24-B028
  • Poster Presentation, Gordon Research Conference Human Genetics and Genomics, July 2023. “Elucidating loss-of-function mutations in the RPT2 domain of SMARCB1”
  • Poster Presentation, Southeastern Annual Pediatric Research Conference, June 2023. “Elucidating loss-of-function mutations in the RPT2 domain of SMARCB1”
  • Oral Presentation, DSAC Student Research Symposium, March 2023. “Deep Mutational Scanning Reveals a Role of DPF2 in SMARCB1-deficient Cancers”
  • Oral Presentation, Aflac Cancer and Blood Disorders Center Advances in Research, Nov 2022. “The Role of DPF2 Stability in SMARCB1-Deficient Cancer”
  • Poster Presentation, 29th Annual Molecular Parasitology Conference, May 2019. “Catch Me If You Can: Identifying Fast-evolving Genes in the Genus Cryptosporidium”

TEACHING AND ACTIVITIES

  • Emory BIOL 250 – Cell Biology, Graduate TA (Fall 2021)
  • President – Graduate Student in Genetics (Sep 2020–Aug 2023)
  • Polygence Student Mentor (Oct 2022–May 2025)
  • Office of Postdoctoral Education Mentoring Certificate (Fall 2023)

AWARDS

  • NCI F31 Ruth L. Kirschtein NRSA for Individual Predoctoral Fellowship (2023-2026)
  • NRSA T32 Institutional Training Grant (2021-2022)
  • Phi Beta Kappa Honor Society (2020)
  • CURO Research Assistantship (2018-2019)

SKILLS

Computational biology & bioinformatics:

  • NGS pipeline development (AWS, R, Python, Bash, git/GitHub)
  • Multi-omics data integration (ATAC-seq, CUT&RUN, RNA-seq, WGBS, WES, and proteomics)
  • Variant interpretation and classification using deep mutational scanning
  • Machine learning model evaluation (REVEL, CADD, AlphaMissense)
  • Statistical analysis and data visualization
  • Molecular dynamic simulation to interpret biophysical variant effects

Functional genomics & Assay Development:

  • Lentiviral production and transduction (CRISPR-Cas9, shRNA, overexpression)
  • Cell-based functional assay development (proliferation, viability, drug response)
  • NGS library preparation and QC (Qubit, Bioanalyzer, qPCR)
  • Experimental design for NGS assay validation, including controls, replicates, and statistical analysis

Molecular Biology:

  • Immunoblotting; immunoprecipitation; proteomics; qRT-PCR; molecular cloning (restriction enzyme and Gateway); knockout/knockdown cell line generation