David Neeley Email & Phone Number

United States

Woodland Hills, Ca

Led the development of an RNA-based fusion gene detection pipeline slated for commercial marketing.Key Accomplishments:• Developed an NGS data analysis pipeline using GPLv3 software tools; producing a CSS stylized PDF report containing all relevant assay findings.• Established CNV detection parameters using a bootstrap algorithm launched with assay-specific Rscript's.Principal data analyst for in-house NGS libraries:• Created Unix (shell) scripts and accompanying usage SOPs to streamline QC protocols for the Production Team's assessment of NGS assay component lots.• Conducted secondary analysis on data generated from an FDA-approved colorectal cancer diagnostic kit used as a comparator for the company's first FDA submission. o Generated stats, figures, and context to report discordant patient sample results.

Woodland Hills, Ca

Brought NGS data analysis in-house, organized validation study protocols, and collaborated cross-functionally with R&D and Product Validation teams.Key Accomplishments:• Implemented ad-hoc support scripts to identify assay components causing off-target effects for R&D and QC purposes.• Developed an analysis pipeline based on Illumina's DNA Amplicon Analysis Workflow to replicate mapping coverage, variant frequencies, and uniformity results for DNA-based NGS assays.• Completed validation studies and reports for a commercial IVD, RT-qPCR fusion gene assay. o Studies include LOB, LOD, Input Range, QC Transfer, and Closed & Open Vial Stability studies.

Greater San Diego Area

Utilized open-source tools and mined public databases to create homology models of uncharacterized plant protein structures, delivering two invention disclosures summarizing all relevant findings towards actionable gene editing targets.Key Accomplishments:• Modeled the interaction of a bacterial host protein with a disease-based plant effector protein. Developed an experiment plan to evaluate single point mutations of the hypothesized residues involved in this interaction.o Designed an NGS analysis pipeline to assess base pair mismatches in studies using a bacterial system.• Characterized the functional domains of a plant-based DNA repair protein and quantified its effects on CRISPR/Cas9 experimentation using NGS data.• Developed an NGS pipeline to quantify the 4 major stages of the precise editing pathway; included detection of initial blunt-end digestion (NHEJ events), alt-NHEJ analysis, imprecise edits (incorrect incorporation of donor template), and precise gene editing events.Coordinated the implementation of a MiSeq NGS screening platform, establishing protocols for weekly NGS library preparations and high-throughput data analysis methods. Key Accomplishments:• Established new NGS analysis pipelines to quantify gene editing markers by targeting key data points throughout the stages of product development across multiple plant species and gene targets.o Designed a universal NGS analysis template to analyze early time-point plant tissues.o Produced allele characterization pipelines for later stage plant tissues.o Created genotyping pipelines for high-throughput breeding programs. • Validated the NGS platform’s limit of detection at 0.01% for precise gene editing events leading to new library prep strategies and DNA isolation methods that reduced sample-to-sample variability by 50%.• Standardized NGS library prep QC requirements for all samples before final library pooling using both Bioanalyzer and TapeStation 4200 instrument metrics.

Greater San Diego Area

Established a high-throughput automated screening platform centered on two Hamilton MicroStar liquid handling workstations enabling processing of over 3,000 samples per week for routine qPCR-based screening assays. Key Accomplishments:• Optimized the primary qPCR screening assay for early plant tissues to perform at 50% routine master mix volume without comprising data integrity. • Integrated bulk NGS library preps into the automation platform, tripling the efficiency of plant breeding programs.• Designed a microbe assay to isolate a mutant yeast strain containing a single SNP enriched from an initial 1:500,000 mutant population.

Greater San Diego Area

I began my career as a Research Associate on a team of plant tissue culture researchers that used biolistic techniques to introduce nucleic acids and gene editing tools into plant cells. In conjunction with my main research duties I also maintained a sample catalog indicating qualitative and quantitative features of over 30 crop species to identify top producing varieties. I later served as a member of the newly formed yeast group developing gene editing techniques and protocols to be used on commercially available yeast strains. I was successfully implementen sensitive qPCR-based assays to detect a single-nucleotide polymorphism (SNP) mutant in a 1:10,000 cell population. The methodology was used to establish a markerless microbial isolation process designed to segregate a mutant yeast strain containing a single SNP from an initial 1:500K cellular population using an iterative screening and enrichment strategy.I also designed RT-qPCR gene expression assays to quantify the metabolic consequences of a successful mutagenic candidate post isolation.