Penn Genomic Analysis Core

The Penn Genomic Analysis Core is home to two facilities specializing in genomic services, the DNA Sequencing Facility & the Molecular Profiling Facility.

DNA Sequencing Facility

The DNA Sequencing Facility provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. It performs sequencing services on three different platforms: gold standard Sanger sequencing on ABI sequencers, and next generation sequencing (NGS) on Ion Torrent platform PGM and S5, and Illumina MiSeq and Next-Seq. The NGS service includes full service from project design, library preparation to sequencing and data analysis. 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 using both custom and open source tools, and custom scripts. In addition, if offers microsatellite-based genotyping and fragment analysis, and cell line authentication. The molecular biological 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 working with the Transgenic and Chimeric Mouse Facility.

The range of services along with the expertise of the facility personnel enables this core to provide full support for investigators at Penn, who can easily obtain fast, reliable data on genes of interest, whether they are doing targeted or exome sequencing, small genome sequencing, searching for mutations in specific genes, screening clones for sequences of interest, or establishing the identity of new clones.

Molecular Profiling Facility

The Facility provides an integrated set of services for molecular profiling of DNA and RNA. These services are performed by experienced genomics professionals, including bioinformatics support staff. The investigators benefit from consultations and training available throughout their projects, including during experimental design and budget development, sample accrual, quality control assays and lab work, data management and analyses, and manuscript preparation.

Starting from DNA extraction from various sources, the Facility 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 and microRNA profiling are offered on the Affymetrix GeneChip and GeneTitan. The Facility 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.

Penn Genomics Analysis Core is an Abramson Cancer Center Shared Resource that is approved and partially funded by the National Cancer Institute.