Genomic Analysis Core

Director: Tapan Ganguly, PhD

The Genomic Analysis Core (GAC) of the Abramson Cancer Center (ACC) provides a spectrum of genomic and molecular biological services with a team of highly experienced and trained professionals. These services are essential to ACC members for studying the role of specific genes in normal or abnormal cellular processes found in cancer cells and tumors. Investigators can observe global gene expression patterns in a sample, and genetic variability in an unaffected or tumor genome. The GAC's configuration dates to 2014 when two Shared Resources — the DNA Sequencing Facility and the Genomics Facility — were consolidated under a single umbrella facility. The resulting Shared Resource was and continues to be directed by Dr. Tapan Ganguly, who directed the DNA Sequencing Facility since 2003.

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Major Services

The GAC utilizes state-of-the-art-technology and provides high quality services by employing multiple quality control checkpoints for all platforms, which are closely monitored and recorded by the staff. The sequencing and molecular profiling services enable basic, translational, clinical and population science researchers of ACC to use advanced molecular biology technologies.

Massively Parallel Sequencing (MPS; also known as NGS, next-generation sequencing). The GAC provides full service from library preparation to sequencing to data analysis on Ion Torrent and Illumina sequencers. For sequencing a custom panel of genes, the facility designs target amplicons or hybrid capture probes using manufacturer provided tools. Sequencing data analysis is performed by the Technical Director, Mr. Erik Toorens, using both custom and open source tools, and custom scripts. The Core also benefits from its close association with the PSOM Next Generation Sequencing Core (NGSC), which provides large scale MPS. With a newly acquired NovaSeq 6000, NGSC is well suited for ultra-high throughput sequencing and the ACC members are referred to the NGSC to sequence transcriptome, exome and whole genome in a cost-effective way. Sometimes MPS libraries are also made at the Core and sequenced at the NGSC. Dr. Ganguly and Mr. Toorens meet monthly with the NGSC leadership to coordinate these services.

Sanger Sequencing. The GAC provides long-read DNA sequencing with fast turnaround, and related support services. The investigators also submit full plates of plasmid DNA or PCR products for sequencing at significantly reduced user fees.

Microsatellite-based Genotyping and Fragment Analysis. The facility offers microsatellite-based genotyping, identification of VNTR (Variable Number of Tandem Repeats) alleles and other sizing applications. For human cell line authentication, the facility performs DNA fingerprinting (Short Tandem Repeat [STR] analysis) by using the Promega GenePrint kit.

Molecular Biological Services. Services include: vector construction, site-directed mutagenesis, cloning and sub-cloning, and plasmid DNA preparations at different scales. The facility provides a PCR-based mouse genotyping service with the Transgenic and Chimeric Mouse Facility, an ACC Shared Resource.

DNA and RNA Profiling. Genome-Wide or Targeted. Starting from DNA extraction, the GAC provides whole-genome SNP screening on an Affymetrix GeneChip system and high-throughput GeneTitan. Copy number variation (CNV) is analyzed using Agilent's aCGH platform. Small panels of SNPs are assayed on an ABI QS12. Larger panels (48-96 SNPs) are deployed in assays that genotype 24-48 samples on Fluidigm BioMark HD. Full service, RNA and microRNA extraction and transcriptome profiling are offered on the Affymetrix GeneChip and GeneTitan. The GAC supports Q-rtPCR for quantitation of single genes using the TaqMan assay on ABI QS12. Alternatively, panels of 24-48 genes can be combined in profiling assays using BioMark HD from Fluidigm.

Consultations. Dr. Ganguly and Mr. Toorens serve as a resource to investigators to address molecular biological approaches to scientific questions, providing consultation in experimental design, technology options and budgets. Dr. Ganguly assists investigators with writing manuscripts and grants involving GAC services. Quality control and assurance are primary concerns of the facility and are discussed during the initial consultation. Dr. Ganguly also connects investigators to the ACC Biostatistics and Bioinformatics Core (BBC) for data analysis. Dr. John Tobias, formerly in the GAC, moved to the BBC to join other bioinformaticians and provides the same level of service as before, a nice example of Shared Resource collaboration and synergy. He supports GAC services by providing consultations on experimental design, data analysis, and database development.

Education and Training. The GAC is deeply committed to education and training of ACC members and other potential users, as detailed in Shared Resources Management. The facility routinely presents posters or has talks at PSOM/ACC events, such as the annual PSOM Cores Fair. The GAC offers training in basic molecular biology techniques as well as the use of several data analysis software such as MacVector, Sequencher, Ingenuity Pathway Analysis (IPA), and data visualization with the Integrated Genome Viewer (IGV). The GAC also teaches users how to operate several instruments for self-service at reduced cost.

Technologies and Equipment

The GAC is fully equipped for state-of-the-art molecular biology work. It has one 96- and one 16-capillary ABI sequencer, and a Beckman FX Robot for Sanger sequencing and fragment analysis. Massively parallel sequencing is done on Ion Torrent PGM and S5, and Illumina MiSeq. For larger projects, the GAC, in collaboration with Dr. Kojo Elenitoba-Johnson (Hematologic Malignancies), has unlimited access to an Illumina NextSeq 500 located on the same floor. The molecular profiling services are performed on several platforms: Affymetrix GeneChip and high-throughput GeneTitan, medium-throughput profiling on Fluidigm BioMark HD, and low-throughput profiling on ABI QS12 real-time PCR instrument. Agilent aCGH platform offers CNV analysis. For data analysis, the GAC maintains two multi-core, high RAM desktop workstations, and integrates the PSOM HPC (High-Performance Computing Cluster) for compute-intensive analyses. Raw user data and the associated analysis files are stored on a fault-tolerant RAID. Backups of sequencing data are maintained on LTO5 data tapes in duplicate.

For more information, please visit the Core's website: http://www.med.upenn.edu/genetics/dnaseq