Bioinformatics

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The mission of the Bioinformatics Shared Resource (BISR) is to provide bioinformatic and biostatistical collaboration, consultation, and quantitative research resources to clinical, laboratory, and prevention scientists engaged in the planning, conduct, analysis, and interpretation of research studies that use modern high-throughput technologies from molecular biology. Additionally, members of the BISR collaborate with oncology research scientists to develop bioinformatic and biostatistical methods to improve the efficiency of current and future basic science, therapeutic, diagnostic, prevention, and intervention studies. Members of the BISR have experience with mRNA expression microarrays from Affymetrix, Agilent, and Illumina, proteomics using mass spectrometry or two-dimensional polyacrylamide gel electrophoresis; serial analysis of gene expression; tissue microarrays; array comparative genomic hybridization; single nucleotide polymorphism chips; methylation arrays; microRNA arrays; exon tiling arrays; real-time polymerase chain reaction; and reverse-phase protein lysate arrays. The BISR provides advice on choosing technology platforms, experimental design, sample size and power computations, data preprocessing, statistical analysis, and bioinformatic interpretation. The services of the resource are directed toward three goals: (1) to ensure that all high-throughput experiments at M.D. Anderson are properly analyzed and interpreted, (2) to play a direct role in the planning and design of experiments that use these technologies, and (3) to provide educational programs in bioinformatics methods. During the previous funding period, the BISR assisted 244 investigators from 20 different programs. Use of the BISR doubled during the previous five years, and the number of publications by users of the BISR grew from 33 during the first year to 65 during the most recent year. In the future, we remain committed to providing support for the design and analysis of experiments using cutting-edge technologies and will work with M.D. Anderson researchers to understand the nature of the data generated from novel technologies. Where possible, we are standardizing our analyses and report generation by developing templates in Sweave, a tool that enhances the reproducibility of statistical analyses. We also plan to enhance our ability to offer sequence-based bioinformatics services such as ChlP-on-chip and motif finding. Finally, we are exploring innovative ways to integrate data, algorithms, and reports.