CORE--MACROMOLECULAR ANALYSIS FACILITY

University Of Texas Md Anderson Can Ctr, Houston TX

Investigators

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Abstract

The Macromolecular Analysis Facility consists of three separate but related entities: the DNA Sequencing Facility (DSF), which performs automated DNA sequencing, automated microsatellite analysis, and single- strand conformation polymorphism (SSCP) analysis; the Computational Analysis Facility (CAF), which helps investigators with computational analysis of macromolecular structures; and the Nucleic Acid Core Facility (NACF), a centralized laboratory for standardized DNA extraction from various sources and genotyping of transgenic mice. These resources prepared DNA from blood, tumor samples, and paraffin-embedded or frozen sections (in the NACF); determine DNA sequences and perform microsattelite and SSCP analyses (in the DSF). DNA sequences are analyzed by the CAF. The DSF provides help to a wide range of investigators in basic, clinical and population-based research involved in studies of growth control, growth inhibition, commitment to specific cell lineages, cell adhesion and mobility, metastasis, angiogenesis, and other fields, as well as supports studies on the mapping and cloning of new cancer susceptibility genes and screening for tumor and constitutional mutations in known cancer susceptibility genes and screening for tumor and constitutional mutations in known cancer susceptibility genes and screening for tumor and constitutional mutations in known cancer susceptibility genes and oncogenes. The DSF provides fast and reliable sequence information to investigators in an efficient and cost-effective manner. The number of DNA sequences determined by the DSF increased 400% from about 1,500 in 1992 to over 6,000 between July 1, 1996 and June 1, 1997, and the length of readable sequences increased from about 300-350 to more than 650 bases per sample. To generate the DS sequences, the DSF currently uses on ABI 373 DNA sequencer equipped with stretch configuration and one recently acquired ABI 377 DNA sequencer. The resource provides investigators with the polymerase chain reaction (PCR)-generated DNAs, to produce the most accurate DNA sequences and expertise in primer design and maintain rigorous quality control to ensure consistency of service. A substantial effort of the facility is dedicated to determining optimal conditions for DNA sequencings with new and improved fluorescent dyes and more efficient enzymes. The facility recently began to use the ABI 377 DNA sequencer for automated analysis of the sizes and amounts of PCR products. The analysis detects SSCPs in PCR products and allows genetic linkage analysis by determining the sizes and amounts of specific microsatellite-containing PCR products. The 377 ABI DNA sequencer is also used to perform microsatellite analysis to evaluate constitutional and tumor-specific genomic instability.