Danielle Vasquez

Translational Genomics Research Institute

Collaborative Sequencing Center

· Experience using and maintaining Illumina NovaSeq, MiSeq, NextSeq, and MiniSeq

· Operating and performing regular maintenance on in-house sequencing instruments

· Identifying the probable source of data quality issues (in-house error or instrument malfunction)

· Library preparations of DNA and RNA

· Evaluating protocols for potential issues to produce better outcomes

· Understanding of sequencing bandwidth and flow cell chemistry for the purpose of obtaining desired data quantity

· Development and optimization for assay catalog: PCR free workflows

· Managed complex databases to ensure accuracy and accessibility of critical information.

High Throughput Research Team

· Ability to process large sample volumes for whole genome preparation and next generation sequencing · Quick turnaround times (

· Statewide Group A Strep surveillance via whole genome sequencing

· Statewide genomic surveillance program for COVID tracking using amplicon sequencing\ · Extraction of SARS-CoV2 viral RNA and RT-qPCR testing

Public Health Core

· Successfully prepared microbial WGS libraries for use on Illumina platforms

· Bacterial isolations and DNA extractions from: Escherichia coli, Cryptococcus spp., Salmonella spp., Campylobacter spp., Listeria monocytogenes, MRSA, Mycobacterium kansasii, Coccidiodes spp.

· Biowatch surveillance: processed air filters to test for the presence of Coccidiodes

· Train interns on molecular technique and specific common protocols.

· Assign tasks, review work, and supervise daily activities

Factorial Biotechnologies

R&D

· Development and optimization of high-throughput, single-cell NGS library prep

· Experience using both human and yeast cells in a single-cell assay

· Tasked with the application of new techniques and uses for novel single-cell assay

· Project lead for key partnership to identify uses for dPCR in current workflow

· Experience and comfort with dynamic goals and unique problem solving for a new technology

Laboratory Skills

• Knowledge and experience with many commercial library preparation kits, including PCR free workflows and ones relating to RNA
• Experience using Agilent Bioanalyzer/Tapestation, Applied Biosystems QuantStudio7, VarioSkan plate reader, Qubit, Nanodrop and EGel platform to assess the quality of samples and libraries
• Experience using Qsonica and Covaris E220 for DNA shearing
• Familiar Nexcelom and Countess for cell counting
• Experience with low quality and complex samples, including those with low concentrations
• Knowledge of common failures in WGS preparations, ability to identify problems and solutions
• Bacterial isolation, culture/enumeration
• DNA and RNA extractions
• BSL2 level training
• Macrodissection of FFPE slides

Organization and Management

• Experienced in complex record keeping of sample data using LIMS
• Maintaining an organized laboratory notebook
• Organization of large data sets using Microsoft Excel
• Managed early stages of high throughput lab with supervision responsibility of interns in various stages of sample preparation