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BIOINFORMATICS CORE

Location: Harvard School of Public Health
Associated Core Faculty participating on this Training Grant: LJ Wei, Xin Lu, Peter Kraft, Cheng Li, Xiaole Shirley Liu, Dyann Wirth, Dieter Wolf

The Bioinformatics Core is designed to help faculty, researchers and students develop and implement methods for designing and analyzing studies with large scale, high-throughput datasets (including microarrays, proteomics, genomic variation data sets, etc.) Specifically, the core will provide consulting services to biological/clinical studies regarding experimental design and data analysis, coordinate Bioinformatics activities and promote collaborative research within HSPH, and provide training environment for graduate students in bioinformatics/biostatistics/computational biology at HSPH.

MICROARRAY FACILITY CORE

Location: Dana-Farber Cancer Institute
Associated Faculty participating on this Training Grant: Cheng Li, Xiaole Shirley Liu

The Microarray Core carries out gene expression profiling, Single Nucleotide Polymorphism (SNP), Comparative Genomic Hybridization (CGH), and Chromatin ImmunoPrecipitation localization (ChIP-on-Chip), all determinations using oligonucleotide microarrays, and provides biostatistical support to assist in analyzing the data. The services of the Core are available to DFCI investigators and to investigators outside of DFCI. The laboratory analyses begin with RNA or DNA, provided by investigators, and produce scan data along with quality control data. These data are available via password-protected accounts accessible through this web site. Biostatistical support is available at the facility to educate investigators about approaches and tools for microarray data analysis. Assistance with concepts and software related to image analysis, statistical methods, clustering, supervised learning and other aspects of microarray data analysis is offered.

HIGH-THROUGHPUT GENOTYPING CORE

Location: Harvard School of Public Health
Associated Faculty participating on this training grant: David Hunter

This Core/Laboratory offers SNP (single nucleotide polymorphism) genotyping using Taqman allelic discrimination assays and MALDI-TOF (Matrix-assisted laser desorption ionization - time of flight) mass spectrometry as primary techniques. The facility can also perform custom microsatellite genotyping. The core director Dr. Hunter provides mentoring, guidance and advice to those interested in haplotyping and genotyping analysis of large numbers of samples. He directs an active Program in Molecular and Genetic Epidemiology, helps faculty and students keep abreast of technological advances and genomics applications to epidemiological research through a core-sponsored seminar and lecture series.

PROTEOMICS CORE FACILITY

Location: Harvard School of Public Health
Associated Core Faculty participating on this training grant: Dieter Wolf, Marianne Wessling-Resnick, Dyann Wirth

Services currently provided through the HCPF include protein profiling to identify known markers that uniquely define a particular functional state of cells, organs and whole organisms. Routine technologies offered by HCPF include biochemical prefractionation of complex protein samples, comparative analysis of analysis of fractions by two-dimensional gel electrophoresis (2D-PAGE), and protein identification by nano-flow liquid chromatography and electrospray ionization tandem mass spectrometry (nano-LC ESI MS/MS) followed by database search. The spectrum of samples amenable to this routine analysis is diverse, ranging from microorganisms to human cells and fluids. Recently Dr. Wolf has been working with several other HSPH faculty members to develop high throughput methods to quantitatively analyze proteins and small peptides present in human and animal blood plasma (Plasma Proteomics). To achive this goal, the Core Facility is in the process of acquiring the capacity for multidimensional liquid chromatography coupled to highly sensitive mass spectrometry (nano flow LC/LC/MS/MS).