Cancer Genomics Shared Resource

Overview of Services

The Sidney Kimmel Cancer Center Cancer Genomics Core Facility is a state-of-the-art, integrated, multi-site, shared resource consortium that was formed in 2016 through a merger of the SKCC Cancer Genomics Core (SCGC) located at Thomas Jefferson University and the conjoint omics capabilities of the Center for Genomic Sciences (CGS) and the Center for Advanced Microbial Processing (CAMP) both of which are located within the Institute for Molecular Medicine and Infectious Diseases (IMMID) at Drexel University College of Medicine.  The SKCC Meta-omics Core Facility merges the capabilities of the two core facilities, together with the CGS and CAMP under the direction of Professor Garth D. Ehrlich PhD continuing operation at Drexel, and the SCGC under the direction of Professor Paolo Fortina MD PhD continuing at TJU.  This unique shared resource provides a collaborative interdisciplinary teaching and service environment which employs scientists, bioinformaticians, and clinicians who provide consultative services in terms of experimental design and data analyses, as well as a very broad range of high-throughput and high-fidelity laboratory services. 

The laboratory technical services include genomics, transcriptomics, epigenetics, metabolomics, lipidomics, proteomics, and glycomics. 

These facilities are dedicated to meeting the current and future needs of both researchers and clinicians and regularly implement new technologies and methods to provide the highest level of service.  In addition, an integral role of the facility is to test new equipment and implement novel assays in collaboration with biotech companies.  Included in these offerings are leading-edge capabilities in ultra-long DNA sequencing, whole genome non-modified epigenetic analyses, ultra-precise nucleic acid quantification technologies, imaging mass spectroscopy (MS), and ion-mobility MS, all technologies that are rarely found in core facilities and which provide significant value-added to researchers with non-standard and complicated questions relating to oncogenesis. 

The integration of the multiple omics methodologies within the SKCC Cancer Genomics facility wherein all of the faculty providers are co-localized provides for exceptional interdisciplinary expertise for the development of cross-cutting, complementary, and confirmatory studies with orthogonal technologies.

Instruments:

1. Illumina Novaseq 6000
2. Illumina MiSeq
3. Illumina Nextseq
4. 10x genomics 

Services:

1.RNA sequencing : SKCC provides variety of bulk RNA sequencing services, such as stranded mRNA-seq, total RNA with Ribosomal depletion, small RNA-seq on Illumina instruments.

2.DNA sequencing: SKCC provides variety of DNA sequencing services, such as Whole Genome Sequencing, Whole Exome Sequencing, available or customized targeted Sequencing on Illumina instruments.

3.Single cell sequencing: SKCC utilize 10X genomics technology to provide variety of single cell services, such as 10x single cell RNAseq, 10X Linked Read Sequencing, 10x ATAC-Seq.

4.Spatial transcriptomics: SKCC provides variety of cutting-edge spatial services, such as Visium Spatial and Nanostring GeoMx samples sequencing

Thomas Jefferson University Core Staff

Andrew South, Ph.D., Director, andrew.south@jefferson.edu

Paolo Fortina, MD, Ph.D., Director (will step down in 2024), paolo.fortina@jefferson.edu

Sankar Addya, Ph.D., Research Associate, sankar.addya@jefferson.edu

Suhao Han, Ph.D., Research Associate, suhao.han@jefferson.edu

Emilie Lee, B.S., Research Assistant, Emilie.Lee@jefferson.edu

Drexel University Core Staff

Garth Ehrlich, Co-Director, ge33@drexel.edu 215-762-1878
Carol Hope, Business Manager,clh353@drexel.edu 215-762-2959
Joshua Mell Deputy, Director, Genomics jcm385@drexel.edu 215-762-1445
Joshua Earl, Deputy Director, Bioinformatics, jpe39@drexel.edu 215-762-8133
Joris Beld, Deputy Director, Metabolomics & Proteomics, jb3669@drexelmed.edu  215-762-1735
Azad Ahmed, Laboratory Manager, Genomics, aia38@drexelmed.edu  215-762-1958
Bhaswati Sen, Laboratory Technician, Genomics bs563@drexel.edu 
Rachel Ehrlich, Bioinformatician rle36@drexel.edu 

Hours of Operation and Location

Links and Resources

1. Center for Advanced Microbial Processing
2. Center for Genomic Sciences
3. Genomics Core Facility
4. Jefferson Website

Contacts