Thomas G. Wood, Ph.D.

UTMB Genomics Core Facility

Publications (Pubmed)

Affiliations: Department of Biochemistry & Molecular Biology
Tel: (409) 747-0387
Fax: (409) 747-8608
tgwood@utmb.edu
Route: 1079
6.132 Blocker Medical Research Bldg.

Thomas G. Wood, Ph.D.

Professor

UTMB’s Next Generation Sequencing (NGS) Core utilizes an Illumina HiSeq 1500 sequencing system to perform massively parallel sequencing for genetic analysis. The NGS Core offers support in library construction from various template sources; RNA (total, poly A+, ncRNA and miRNA), chromatin immunoprecipitated DNA (ChIP-Seq) and DNA (genomic exome and amplicon-derived). Library complexity is assessed using qPCR prior to amplification. Illumina NGS technology uses adapter-ligated template molecules to populate a hollow glass flow cell; two lanes for Rapid Run flow cells and eight lanes for the High Capacity Flow Cells. Individual target molecules are then amplified to create template clusters. Templates are sequenced using reversible, fluorescent-tagged terminator nucleotides. The HiSeq 1500 has the capacity to create over 1.5 billion clusters across an 8-channel flow cell and 300 million clusters using the two lane flow cell. With the capability of either single-end or paired-end sequence reads and 50 to 150 base read lengths, the HiSeq 1500 can generate up to 300 Gb from a single sequence run. Costs are reduced by indexing (“bar coding”) individual template libraries, allowing multiple libraries to be sequenced in each of the flow cell lanes.

The Molecular Genomics (MG) Core provides technical support in both the design and performance of real time quantitative PCR (both Taqman and SYBR-based assays), SNP discrimination analysis and Sanger-based DNA sequence analysis. Confirmation of gene expression data is available using quantitative RT-PCR (Q-PCR) analysis (absolute or relative). Both Taqman (Applied Biosystems /Life Technologies) and SYBR Green-based assays are offered. In addition to commercial assays, the MG Core will design a custom assay for any target sequence. RNA samples are quantified using a Nanodrop Spectrophotometer (Nanodrop Technologies) and qualified by analysis on an RNA Nanochip using the Agilent 2100 Bioanalyzer (Agilent Technologies). Assays are analyzed on an ABI Prism 7500 Sequence Detection System (Life Technologies/ Applied Biosystems) or a model 480 Light Cycler (Roche). Data analysis is performed using the ΔΔ method for relative gene expression analysis.