Facility Details

The Biomedical Genomics Core (BGC) is a nationally recognized provider of expertise in multiple aspects of genomics data generation and analysis. The services include consultation and assistance with experimental design, quality control of starting material (DNA or RNA), microarray and next-generation sequencing data generation, bioinformatics, statistical analysis and interpretation. The core is comprised of three units:

BGC Microarray Unit: In 2009, the BGC Microarray Unit was awarded with “Certified Service Provider” status by Agilent Technologies, the first academic laboratory in the US to have achieved this. This certification ensures that our clients receive superior microarray processing and data with regards to quality, reproducibility, and reliability. Specific services include custom array design, gene expression analysis for eukaryotes and prokaryotes, array comparative genomic hybridization (aCGH) to detect genomic aberrations and copy number variants (CNVs), splice variant analysis and comprehensive microRNA profiling of the entire miRNome.

BGC Sequencing Unit: We have over seven years of experience with next-generation sequencing data generation and analysis and we have been providing Sanger sequencing services for over ten years. The BGC Sequencing unit assists the investigators with multiple aspects of next-generation sequencing, including library preparation, sequence generation and data analysis. We provide advanced bioinformatics support to analyze the complex sequencing datasets generated on the next generation sequencing platforms. The core is equipped with Illumina HiSeq 2500 sequencing system which is capable of producing 600 billion base pairs (600 GB) of sequence data, enabling us to sequence 5 human genomes at 30X coverage in a single 14 day instrument run or 1 human genome in 40 hours utilizing RAPID Mode. For smaller genomes the core utilizes the Illumina MiSeq Personal Sequencer which has an 8.5 Gb output in under 40 hours. These technologies are being utilized for multiple applications including human genome re-sequencing studies for rare variant discovery and structural variation analysis (both targeted capture and whole genome), gene expression and transcriptome analysis (RNA-Seq and miRNA-Seq of both eukaryotes and prokaryotes), epigenomic studies including DNA-Protein interaction analysis (ChIP-Seq) and methylation analysis (Methyl-Seq), and de novo genome assembly of both bacterial and viral genomes. The BGC Sequencing unit is a certified service provider for SureSelect capture technology, a genome partitioning strategy that allows investigators to target their sequencing strategies to defined regions of the genome or the entire human exome. We also provide Sanger sequencing services for routine sequencing of plasmid and PCR templates through ABI 3130xL Genetic Analyzer.

BGC Bioinformatics Unit: The Bioinformatics Unit is comprised of a dynamic team of six computational biologists, with the substantial technical and bioinformatics expertise required to oversee the multiple platforms that acquire, store and analyze large and complex data sets generated by the BGC Microarray and Sequencing Units. Integration of this team within the BGC is critical to its success, ensuring that team members are able to learn new methodologies and develop novel analysis approaches in pace with the technological growth that has become a primary driving force for biological discovery. The bioinformatics unit provides services on a collaborative basis and serves as an interface between the research investigator and the multiple domains that are required to handle the size and complexity of genomic data. With our high performance compute cluster and 700TB of clustered high performance disk space we are able to support the analysis of both large and small scale sequencing projects. We are uniquely positioned to adapt and develop new computational tools in a manner that is driven by the demands of our research community as it utilizes new technologies. As a part of Dr. Peter White’s research group, BGC Bioinformatics Unit also focuses on the development of analytical pipelines for human genome resequencing, exome capture and the identification of disease causing genetic variants. The unit also evaluates and supports multiple software products for genomics applications that are designed to make data analysis tools accessible to biologists.