Harvard Chan Bioinformatics Core

Location: Harvard T. H. Chan School of Public Health
Associated Core Faculty participating on this Training Grant: Peter Kraft (Core Scientific Director), David Christiani, David Hunter, Nan Laird, Christoph Lange, Xihong Lin (PI/Co-Director)

The SPH Bioinformatics Core (HBC) was established in 2003 by Dr. Barry Bloom, then-Dean of the Harvard School of Public Health to aid researchers at SPH with the management, integration, and contextual analysis of biological high-throughput data. It provides researchers with consulting, training, tools, databases and best practices. It fosters collaboration and a community of bioinformatics activities by working closely with other Cores and centers in the Longwood community and across Harvard. The HBC also builds a unified infrastructure supporting a diverse set of experimental systems and high-throughput biological data. The HBC, now led by Scientific Director Dr. Peter Kraft and overseen by Associate Director Dr. Oliver Hofmann, is integral to the Program for Quantitative Genomics (PQG). It provides a single point of contact for computational biology, applying genomic approaches together with established and developing Public Health methodologies, including the integration of basic biology, epidemiology, environmental health, biostatistics and bioinformatics to develop novel approaches to improve human health. The Core allows SPH to exploit data-driven research, providing a training venue and improving grant funding opportunities, which are becoming increasingly computational. By providing access to bioinformatics expertise for researchers at SPH, the HBC opens new areas of research, enhances the quality and consistency of high-throughput data analysis and improves the school’s ability to support research in this “mission-critical” area.

High-Throughput Polymorphism Detection Core
(Dana-Farber/Harvard Cancer Center)

Location: Harvard T. H. Chan School of Public Health and Harvard Medical School
Associated Faculty participating on this training grant: Peter Kraft, 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 wet laboratory environment includes two PCR workstations, six Perkin-Elmer 9600 PCR machine, two MJ Research Tetrad Thermal Cyclers. An AB1377 DNA sequencer is also available with a molecular Dynamics DNA 96-well quantitator. The Whole Genome Amplification lab consists of a closed area with more limited access and low traffic. Equipment includes two new Qiagen robots equipped with computer barcode readers for accurate logging and tracking of samples.

Harvard Partners Center for Genetics and Genomics

HPCGG Bioinformatics Core

Location: Harvard Partners Center for Genetics and Genomics and Harvard Medical School
Associated Faculty participating on this Training Grant: Peter Park

The HPCGG Bioinformatics Core recognizes that quantitative analytic methods are now central to the pursuit of biomedical research. The intersection of information science, biostatistics, biology and clinical medicine requires multidisciplinary collaborative efforts that the Bioinformatics Core is designed to nurture. Whether it is expression microarrays, proteomic experiments, or populations-wide linkage studies, the HPCGG Bioinformatics Core works with investigators across the Harvard Medical community including affiliated hospitals. Activities of the Bioinformatics Core range from the provision of services to fully-collaborative grant-funded investigations.

HPCGG Microarray Core
Location: Harvard Partner Center for Genetics and Genomics & Harvard Medical School
Associated Faculty participating on this Training Grant: Peter Park

HPCGG operates a full service facility dedicated to providing analysis for DNA or RNA samples. The Core provides support for high density microarrays to the Harvard Medical Community, including affiliated hospitals and the School of public health. The unit specializes in microarray analysis using Affymetrix, Agilent and other microarray platforms. We have experience with large, medium, and small project needs. Equipment comprising the available technology includes automation, the Axon Scanner, Maui Hybridization stations, Agilent 2100 bioanalyzer, and the Affymetrix GeneChip® System. The GeneChip® System includes all of the hardware necessary for running and analyzing high-density Affymetrix arrays for expression analysis and SNP mapping arrays. The facility also offers various levels of bioinformatics support for comparative analysis projects.

HPCGG High-Throughput Genotyping Core

Location: Harvard Partners Center for Genetics and Genomics
Associated Faculty participating on this training grant: David Hunter, Scott Weiss, David Christiani

The HSPH and Harvard Partners Genotyping Facilities provides flexible, high quality, high throughput SNP genotyping to researchers. The portfolio of Genotyping methods at HPCGG now includes Affymetrix, Illumina, Sequenom, and TaqMan. Services provided by the core include:

  1. Taqman SNP allelic discrimination: Performed on the ABI7900. In this method, specialized probe oligonucleotides are used to distinguish the SNPs during or at the end of a PCR reaction. Depending upon a number of factors, including previous implementation of the method for a particular SNP, this method will be the first approach for genotyping in some cases.
  2. Sequenom genotyping: Performed using MALDI-TOF (Matrix-assisted laser desorption ionization – time of flight) mass spectrometry. This method is suitable for small numbers of SNPs, from 2 to 300 SNPs. The service includes primer and assay design through to production of genotypes. All steps involved are highly automated and are tracked using a laboratory management system with bar coding. An average of 34 SNPs can be plexed into a single well of a 384 well plate using Sequenom iPLEX chemistry, with a maximum of 40 SNPs per plex. Specialized equipment for this work includes a Biomek multi-pipettor robot, a Multimek multi-pipettor robot, a nanoliter plotting robot for spotting the extension products onto chips, and the mass spectrometer.
  3. Affymetrix Whole Genome Genotyping: The Illumina Bead Station GoldenGate assay system for SNP genotyping is a platform most suitable for researchers engaged in large scale association studies: whole genome linkage mapping panels and large scale fine mapping panels. The genotyping is carried out in 384 plex reactions then in multiples of 96 SNPs up to 1536 SNPs using Illumina custom SNP panels. Many standard panels are also available from Illumina. The Illumina Bead Station Infinium assay system is also available for Whole Genome Genotyping. Genotyping is carried out on standard chips containing up to 1 million SNPs. Custom genotyping of large numbers of SNPs is also available using the iSelect system. Several standard chips allow the addition of iSelect custom SNP sets to allow customization of the chip for the researchers specific aims. The facility can also perform custom fragment analysis genotyping for users who wish to use microsatellites, VNTR’s and insertion deletion polymorphisms in their research.

HPCGG Sequencing Core

Location: Harvard Partners Center for Genetics and Genomics & Harvard Medical School
Associated Core Faculty participating on this training grant: David Hunter, Scott Weiss

The Sequencing Group currently supports three sequencing platforms: ABI 3730xl Analyzers for fluorescence-based DNA sequencing and cycle sequencing with di-deoxynucleotide terminator chemistry, and Illumina Genome Analyzers, employing the Solexa sequencing technology.
The DNA Sequencing Group at the Harvard Partners Center for Genetics and Genomics has a strong history of producing high quality, dependable and informative results for researchers. The Core participated in the Human Genome Project, building the STS-Based BAC map for Human Chromosome 12, and providing Chromosome 12 tiling path clones to the Baylor Human Genome Sequencing Center for sequencing. They also sequenced 113 BACs for the Mouse Genome Project, contributing 24 megabases of finished mouse sequence to the published Mouse Genome. We have provided draft sequences for unique strains of several bacterial genomes, including Pseudomonas aeruginosa, and Vibrio cholerae. More recently, Core members participated in identifying mutations linked to numerous diseases by providing researchers with full service resequencing and analysis.

Dana-Farber Cancer Institute

DFCI Microarray Core Facility

Location: Dana-Farber Cancer Institute
Associated Faculty participating on this training grant: Xiaole Shirley Liu, John Quackenbush, GC Yuan

The Microarray Core carries out gene expression profiling on 3′ arrays, Exon 1.0 ST arrays, and on Gene 1.0 ST arrays; genotyping and comparative genomic hybridization both on single nucleotide polymorphism (SNP) arrays, and Chromatin ImmunoPrecipitation localization (ChIP-on-Chip). All services use oligonucleotide microarrays. The Core also provides biostatistical support to assist in analyzing the data, along with educating investigators about approaches and tools for microarray data analysis 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 the core web site. The Core also provides assistance with concepts and software related to image analysis, statistical methods, clustering, supervised learning and other aspects of microarray data analysis is offered. The DFCI Microarray Core recently added an ABI SOLiD sequencer to its cadre of instruments, allowing researchers to generate ultra-high-throughput sequence data for a wide range of projects, including human genome re-sequencing, ChIP-Seq, RNA-Seq, and metagenomics.