Cancer Institute

  • Molecular Genomics Services and Pricing

    The Molecular and Genomic Core facility provides a variety of genomics services, including sample processing, genotyping, sequencing, gene expression (microarray and real-time PCR) and early stage bioinformatics analysis. The general services offered by the Molecular and Genomics Core are briefly discussed below. For the current price of commonly used services, click here.

    Sample processing and storage

    The core will provide technical expertise and isolation services for DNA and RNA from blood, saliva, cell culture, animal or human tissue. The core will provide long-term storage of processed sample, if desired by center investigators.

    Genotyping

    Microsatellite-based genotyping can be performed via multiplexing (3-5 primer sets per PCR reaction) using a fluorescent-based approach on a Beckman Coulter CEQ8000 XL capillary sequencer. TaqMan® SNP Genotyping can also be performed. TaqMan genotyping provides an accurate and reliable method of genotyping single nucleotide polymorphism (SNP). Genotyping will be performed on Bio-Rad CFX96 real-time PCR machine to identify the presence of the SNPs of interest.

    Sequencing

    As technology for sequencing continues to improve and costs decrease there will be an increasing need to sequence. Consequently, DNA sequencing will continue to play a major role in molecular genetics. Currently, the core is capable of sequencing small to modest sized projects using 96-well reaction plate using Sanger sequencing. Sequencing will be performed by automated fluorescence-based DNA sequencing using Beckman Coulter CEQ8000XL. Sequencing reaction will be performed using modified protocol for DTCS Quick Start Kit (Beckman Coulter, Inc) using ¼ or ½ reactions to reduce cost. For large-scale sequencing projects, samples will be outsourced to commercial provider (Seqwright, Delwalch, etc.) to provide investigators a lower price.

    Microarray and quantitative real-time PCR:

    The core will provide technical support for study design, RNA extraction, assessment of RNA, labeling, hybridization, image collection, data analysis, and pathway analysis for data generated using Affymetrix GeneChip®, GeneAtlas or Agilent platforms. These systems provide diverse genomic platforms that can be useful for basic researchers studying animal models of disease (hypertension, diabetes, renal disease) and for clinical researchers looking to evaluate and characterize clinical samples, such as cancer and/or tumor biopsies. The specific array products for each platform can be found at Affymetrix's website (http://www.affymetrix.com/estore/) and Agilent's website (http://www.genomics.agilent.com). The core will also offer services to help investigators validate microarray data using quantitative real-time PCR.

    Bioformatics

    The core will perform a preliminary analysis of sequencing, genotyping, or microarray data. Sequencing reads will be assessed for quality and aligned to the reference gene sequence using DNASTAR's Lasergene v7.2 software package. All SNP and INDELS (insertion-deletions) will be visually confirmed in the trace files. To evaluate the functional significance of identified sequence variants several bioinformatics software packages are available.

    Microarray analysis will be performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software) and the commercially available GeneSifter™ software platform (http://www.genesifter.net). GeneSifter offers a robust statistical framework with 15 advanced options, including 2-way ANOVA, PCA, PAM, hierarchical clustering, CLARA, FDR, FWER, RMA, Max T and more. In addition, the UMMC Center for Biostatistics and Bioinformatics can provide more thorough analysis of microarray experiments. Gene networks and functional analysis will be evaluated through the use of Ingenuity Pathways Analysis (IPA, Ingenuity® Systems, http://www.ingenuity.com) or other web-based software.