Genomics


Director: David Symer, MD, PhD
Senior Faculty Advisor: Carlo Croce, MD
Technical director: Pearlly Yan, PhD

The Genomics Shared Resource (GSR) provides both Nucleic Acid services and Microarray services. It offers instrumentation and expertise for DNA and RNA analysis using sequencing, genotyping, real-time PCR, Affymetrix GeneChips, nCounter Analysis, next-generation sequencing, DNA synthesis support and genome-wide analysis using the Illumina NGS platform and Affymetrix and customizable gene chips.

Both OSUCCC member and non-member investigators have unlimited access to training, consultation, troubleshooting and assistance in experimental design.

Genomics Services

Genomics services provide substantial technical expertise and training for state-of-the-art genomic instruments to address fundamental cancer research questions. A variety of educational outreach activities are used to introduce OSUCCC members to new instrumentation, technology and methodologies developed at Ohio State and key allied organizations.

The microarray is a high-throughput technology that can monitor the entire transcriptome, including mRNA and lncRNA. A separate array is available for small RNA species, including microRNA, snoRNA and scaRNA. Additionally there is TAC 2.0 analysis software installed in the lab for users to explore pairwise comparisons and mRNA-miRNA interactions. The microarray service arm offers custom microarray design and fabrication, commercial microarrays (Affymetrix/Agilent/Nimblegen) and RNA/DNA quality/quantity analysis (Bioanalyzer, Qubit, NanoDrop).

Genomics Goals

  • Provide reliable, high-quality, affordable, low- and high-throughput standard user-level genomic and epigenomic support
  • Provide, optimize, develop and apply early access technologies relevant to cancer research
  • Provide and develop infrastructure and staff for progressive technologies for cancer research
  • Provide immediate access to data analysis and troubleshooting
  • Provide investigators with training in data analysis, data interpretation and experimental strategies, and provide assistance with investigator publication
  • Provide full service and support of genome-wide and targeted mRNA transcriptional profiling and SNP genotyping on Affymetrix and custom microarray platforms
  • Provide full service and support of genome-wide microRNA expression profiling using 10K human, canine and mouse microRNA expression arrays developed in-house, as well as other custom-built arrays
  • Provide quantitative measurement of RNA integrity for use with a multitude of downstream applications. Additionally, sizing analysis on small RNA species between 6 and 150nt is available. DNA analysis includes size and concentration information on DNA fragments between 60 and 12,000 bp and to improve the quality and reliability of expression analysis using Agilent Bioanalyzer.

Expertise

Director: David Symer, MD, PhD

  • Technical Director, Illumina HiSeq2500: Pearlly Yan, PhD
  • Laboratory Services Coordinator: Paolo Fadda, PharmD
  • Laboratory Services Coordinator: Christine Daugherty, MS
  • Laboratory Services Coordinator: Huabao Wang, BS
  • Laboratory Assistant: Cameron Stump, BS
  • Laboratory Assistant: Paige Stump, BS

David Symer, MD, PhD, is a faculty member in the Department of Molecular Virology, Immunology and Medical Genetics. His research has focused on impacts of human papillomavirus (HPV) and of endogenous transposable element (TE) insertions and on consequences of aberrant pre-mRNA splicing, each of which affect the expression, structure and function of genes. Dr. Symer has developed and uses state-of-the-art techniques and assays involving conventional and next generation sequencing, RNA-Seq, transcriptional analysis and molecular biology and bioinformatics tools, so he is well-qualified to provide expert assistance in designing genomics experiments and interpreting high-throughput datasets with GSR users.

Pearlly Yan, PhD, who serves as Technical Director for Illumina HiSeq 2500 Sequencing is also a Research Assistant Professor. Prior to joining the GSR, Dr. Yan was the deputy director for Ohio State’s NCI-Integrative Cancer Biology Program (OSU-ICBP). The OSU-ICBP program brings clinical and basic cancer researchers together with researchers from mathematics, physics, information technology, bioinformatics/biostatistics and computer science to work on key questions in cancer biology. Dr. Yan was responsible for establishing an Illumina sequencing sample submission contract with an external sequencing center. She established collaborations with Ohio State and non-Ohio State informatics scientists, biostatisticians, bioinformaticians and biologists to analyze, visualize and validate next-generation sequencing data. As the Genomics technical director, Dr. Yan is responsible for procurement, setup and managing the Illumina Core. She is an expert in working with high-volume, high-dimension, next-generation sequencing data, as well as with the diverse tools and viewpoints common to biologists and to computational scientists on the cancer genome. Dr. Yan works with OSUCCC – James principal investigators and their lab members to develop novel ways to use the Illumina HiSeq 2500 for integrating a specific region of genome interest. She has coauthored more than 100 publications.

Sarah Warner, Laboratory Supervisor, BS, is in Molecular Genetics at The Ohio State University. Warner is responsible for the tracking and processing of all the services the MASR offers. She works closely with Dr. Symer and Dr. Yan and in collaboration with other core labs to provide cost effective, high-quality data in a timely manner. Warner has received training on NGS from Applied Biosystems, and has used the technology extensively. She reduced microarray turnaround times 64 percent. With a background in Molecular Genetics, she has more than 12 years’ experience at Ohio State.

Paolo Fadda, PharmD, laboratory services coordinator, earned a PharmD degree from Sassari University (Italy) and brings more than three years of research experience in molecular biology to the shared resource. Dr. Fadda has experience in gene expression analysis, including TaqMan gene expression assays, TaqMan Low Density Array (TLDA), TaqMan microRNA assays, high-throughput gene expression analysis using the nCounter System from NanoString Technologies, SYBR Green chemistry and data analysis.

Christine Daugherty, MS, laboratory services coordinator, earned her MS in Molecular Genetics from Ohio State. She has more than 19 years of experience in molecular biology, sequencing, and genotyping research and analysis. Her expertise includes Sanger-based DNA sequencing and genotyping on ABI PRISM 3730 DNA Analyzers, and Next-generation Sequencing (Ion PGM Sequencer).

Huabao Wang, BS, has over 7 years of experience in preparing several forms of barcoded sequencing libraries for the ABI SOLID platform, including whole transcriptome, miRNA and targeted genomic DNA libraries. She also has generated custom miRNA microarrays in the core laboratory. More recently, she has been trained to run multiple platforms in the GSR including the Affymetrix microarray loader and plate reader, the NanoString, the ABI PRISM Sanger sequencing instrument and the QuantStudio high throughput PCR machine. Currently she is developing new expertise in using robotic instruments to prepare custom libraries for diverse sequencing projects including targeted genomic sequencing using the Illumina HiSeq2500 sequencing instrument. 

Cameron Stump, BS, received his degree from the Ohio State University and is taking a research leave from University of Cincinnati College of Medicine. He is responsible for all types of Illumina sequencing library generation, including transcriptome profiling, exome and smRNA-seq. Most importantly, Stump is responsible for quantifying and characterizing sequencing libraries, pooling them by barcode compatibility, and targeting a predetermined amount to yield the desired reads counts.

Paige Stump, BS, received her degree from the Otterbein University. Her expertise is in characterizing and quantifying user-submitted nucleic acid samples for Illumina library generation, coordinating library generation schedules to fit upcoming sequencing format. Stump is responsible for the bulk of the diverse library types produced from the core. She also coordinates with the computation team members to generate and distribute sequencing data QC reports to OSUCCC users.

Cross-Institutional Work

  • Next-generation sequencing services to:
    • The Cleveland Clinic
    • Nationwide Child’en's Hospital
    • Indiana University, Bloomington
    • Indiana University-Purdue University in Indianapolis
    • Case Western University
    • Miami University
    • Various institutions in Taiwan
  • Quantitative real-time PCR services to:
    • MedImmune Inc., Gaithersburg
    • Moffitt Cancer Center, Florida
    • NIH
    • Thomas Jefferson University, Philadelphia
  • Organized and hosted the First Illumina North Central User Group Meeting, which involved five sites from Ohio, Iowa, Wisconsin, Michigan and Indiana.
    • Indiana University – Purdue University, Indianapolis
    • Sapienza University of Rome
    • University of Ferrara

Contact Us

OSUCCC – James Genomics Shared Resource


Biomedical Research Tower
460 W. 12th Ave.
2nd Floor BRT283
Columbus, OH 43210

Phone: 614-685-2224

Email: David.Symer@osumc.edu

Email: Pearlly.Yan@osumc.edu

Email: Sarah.Warner@osumc.edu

Availability: Monday – Friday
Hours:  8:30 a.m. – 5 p.m. or by appointment

Next-Generation Sequencing, The Ion Personal Genome Machine Sequencer (Ion PGM), Sanger-Based DNA Sequencing, Genotyping


Biomedical Research Tower
460 W. 12th Ave.
Rooms 285 and 291
Columbus, OH 43210

Phone: 614-685-2224
Phone: 614-685-9254

Email: David.Symer@osumc.edu

Email: christine.daugherty@osumc.edu

Availability: Monday – Friday
Hours:  8:30 a.m. – 5 p.m. 

Next-Generation Sequencing, HiSeq 2500


Biomedical Research Tower
460 W. 12th Ave., Room 291
Columbus, OH 43210

Phone: 614-685-9164
614-685-2224

Email: pearlly.yan@osumc.edu

Email: David.Symer@osumc.edu

Availability: Monday – Friday
Hours: 8:30 a.m. – 5 p.m.

Quantitative Real-Time PCR/Gene Expression


Biomedical Research Tower
460 W. 12th Ave., Room 236
Columbus, OH 43210

Phone: 614-685-2224
614-688-5810

Email: David.Symer@osumc.edu

Email: Paolo.Fadda@osumc.edu

Availability: Monday – Friday

Please enter a keyword (i.e. Name, Research Interest) or choose a Research Program

OR

Please enter a keyword (i.e. Name, Cancer Type) or choose a Principle Investigator

OR

Search for Clinical Trials

Find a Scientific Publication