Herbert Irving Comprehensive Cancer Center

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 Share 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 Genomic Shared Resources at HICCC (tp2151|_at_|columbia|_dot_|edu).
http://hiccc.columbia.edu/?page=research/sharedresources/genomics