Genomics Technologies
Teresa Palomero, Ph.D., Director
Murty Vundavalli, Ph.D., Co-Director
The Genomics Technologies Shared Resource, consisting of the Microarray and Molecular Cytogenetics facilities, provides access to specialized instrumentation and technical expertise in high-throughput genomic technologies and molecular cytogenetics for use in individual and collaborative research programs.
Together the Microarray and Cytogenetics facilities and services provide an integrated platform for basic and translational genomics research in cancer biology.
Microarray Service
The microarray component of the Genomics Shared Resource provides a comprehensive set of integrated genomic analysis tools and services that facilitate the high throughput analysis of genetic and epigenetic alterations in human cancer in basic and translational research programs. These services focus on procedures with different microarray platforms from Affymetrix and Agilent, with ancillary methods including real-time PCR and Phosphorimaging, are closely linked to those provided by the Biomedical Informatics Shared Resource.
The Shared Resource offers investigators education and consultation on how to adopt genome-wide profiling and molecular cytogenetics into their cancer research.
Microarray and related services are:
- Microarray based genome-wide analysis of gene expression, genetic markers, and DNA copy number aberrations
- Microarray based genome-wide analysis of chromatin modifications
- Validation of microarray and other data by high-throughput quantitative PCR
DNA Sequencing
The ultradeep (high throughput) sequencing capabilities of the Genomics Shared Resource Facility include a 454 FLX system, currently operational, and an ABI SOLiD™ 3 system, which will be open for service in the late summer 2009. The Ultradeep Sequencing Facility is operated by the Herbert Irving Comprehensive Cancer Center (HICCC) with support from the Systems Biology and Stem Cell Initiatives, and HICCC.
The Genome Sequencer 454 FLX Instrument, powered by GS FLX Titanium and Standard series reagents, features long reads (average 350-400 bp for the Titanium platform), exceptional accuracy and high throughput. This platform accommodates a wide number of applications including de novo sequencing, resequencing of whole genomes and target DNA regions, metagenomics and RNA analysis.
The SOLiD™ System is a massively-parallel, next-generation sequencing platform that supports a wide range of applications, including de novo sequencing, targeted resequencing, whole genome resequencing, gene expression profiling, small RNA analysis, whole transcriptome analysis, epigenome, chromatin immunoprecipitation (ChIP) and methylation analysis. The SOLiD™ 3 System, which will be available in the Genomics Shared resource facility, can generate over 400M tags (20 Gbp) per run with an average read length of 50 bp. SOLiD™ 3 is currently the leading platform for expression, resequencing, ChIP and methylation analyses due to its higher accuracy and throughput. Its use of sequencing by ligation and the two-base encoding ensures 99.94% read accuracy.
The SOLiD™ 3 platform can simultaneously process 2 slides and each slide can be partitioned into 1, 2, 4 and 8 regions that allow processing independent samples. Additionally, the SOLiD™ 3 barcoding system allows multiplexing of up to 256 samples per slide.
Services provided by the sequencing facility include the preparation of genomic clonal PCR libraries and their ultradeep sequencing. Basic bioinformatic analysis, with scope defined per application, is also included in the cost of the project. Advanced bioinformatic support, requiring significant customization of the standard set of analyses that is provided by the facility, is provided by the Cancer Center Biomedical Informatics Shared Resource (BISR) as a fee service.
Initially, SOLiD™ services will be limited to the preparation and sequencing of fragment libraries; mate-paired sequencing applications will be available in the Fall 2009.
For detailed project-specific scoping and pricing of each procedure, and for custom design of deep sequencing projects please contact: Dr Teresa Palomero, Director of the Genomics Shared Resource at HICCC (tp2151@columbia.edu).
Molecular Cytogenetics Service
The second major component of the Genomics Shared Resource, molecular cytogenetics facility, provides karyotypic (G-banding) and molecular cytogenetic (SKY and FISH) characterization of human and mouse tumor cells with efficient turnaround times, utilizing state-of-the-art technologies.
Services include:
- G-banded karyotyping of human cancer and non-cancer cells
- FISH analysis using a variety of DNA probes (locus and gene specific, region-specific, and chromosome painting) on a variety of human and mouse cell types and tissue samples, including cell lines, primary tissues from frozen or paraffin section, and tissue microarrays.
- Spectral karyotype (SKY) analysis of human and mouse primary tumors and cell lines.
These services are provided to the researchers after initial discussions regarding the requirements for cell and tissue specimen preparations to best facilitate the required testing. The molecular cytogenetics service also provides technical assistance on custom design and preparation of probes for FISH.