High-Throughput Genotyping and Genetic Linkage Analysis Facility

University Of Tx Md Anderson Can Ctr, Houston TX

Investigators

Linked publications & trials

Abstract

The broad, long-term objectives of the High-Throughput Genotyping and Genetic Linkage Analysis Facility[unreadable] (Core E) are to provide the members of the program and their projects with a state-of-the-art facility for high-throughput,[unreadable] automated genotyping and genetic linkage analysis for the mutation epidemiology of childhood[unreadable] tumors. The objectives of Core E are: (1) to genotype constitutive DNA samples for genome-wide[unreadable] linkage and association studies, (2) to allelotype on a genome-wide or targeted basis matched[unreadable] normal/tumor DNA sample pairs for tumor-specific loss of constitutive heterozygosity (LOH), (3) to[unreadable] maintain a functioning genotype database, and (4) to conduct genetic analyses on the obtained[unreadable] genotype data. To this end, human genomic DNA samples of individuals from cancer families ascertained[unreadable] by Dr. Strong (Core B) segregating either soft tissue sarcomas (STS) or osteosarcomas (OST) and[unreadable] classified as having Li-Fraumeni syndrome (LFS) or one of its variants (Dr. Strong/Project 1 and Dr.[unreadable] Krahe/Project 2), or Wilms' tumor (Dr. Huff/Project 4) will be analyzed using various complementing high-throughput[unreadable] technologies integrating microsatellite and single nucleotide polymorphism (SNP) markers to[unreadable] identify genomic regions co-segregating with the disease (Projects 1 and 2) and to confirm regions of LOH[unreadable] (Projects 2 and 4). Genotyping platforms include fluorescent technology with highly informative[unreadable] microsatellite markers in optimized panels for genome-wide genotyping and custom markers using a[unreadable] universal primer approach for regional fine mapping (Projects 1, 2, and 4). High-density SNP microarrays[unreadable] (approximately 10,000 or about 100,000 SNPs) will be used to genotype individuals in both p53 and non-p53 families to identify modifier genes of tumor susceptibility (Projects 1 and 2) and to allelotype matched normal/tumor DNA[unreadable] sample pairs to identify regions of tumor-specific loss of constitutive heterozygosity (Projects 1 and 2).[unreadable] Pyrosequencing will be used to type additional SNP markers in targeted regions identified by the above[unreadable] approaches for fine mapping (Projects 1, 2, and 4). The obtained human genotype data will be analyzed for[unreadable] genetic linkage and association by complementing parametric and non-parametric analysis methods. For[unreadable] these analyses, Core E will interact closely with the Statistical Genetics and Bioinformatics Core (Core C)[unreadable] headed by Dr. Amos. The ultimate goals are to map major cancer susceptibility genes and modifier genes[unreadable] that underlie the observed increased segregation of certain cancers in the families studied by Drs. Strong[unreadable] (Projects 1, Core B), Krahe (Project 2), and Huff (Project 4), to map and identify modifiers of tumor[unreadable] susceptibility (Projects 1 and 2), and to identify additional genomic regions that may be involved in tumor[unreadable] development and/or progression by providing LOH information (Project 2).