Bioinformatic Tools for Genomic DNA Sequence Dimorphisms (Indels)

Background:
The National Cancer Institute, Center for Cancer Research, Mouse Cancer Genetics Program is seeking statements of capability or interest from parties interested in collaborative research to further develop, evaluate, or commercialize identification and use of such genomic DNA sequence insertion/deletion dimorphisms (indels). Applications include:

• A new bioinformatics software tool that can easily identify dimorphisms and can help create a searchable database and graphical interface containing sites of dimorphisms and information regarding functional effects of dimorphisms.
• Low cost, high-throughput PCR based methods to identify dimorphic repetitive elements from any eukaryotic genome including individual tissue specimens.
• Methods to determine functional consequences of dimorphisms (indels).

Technology:
This invention describes new methods to identify genomic DNA sequence dimorphisms called indels and to determine their biological consequences. "Indels" refers to large insertions and deletions, a form of variation in DNA sequences, that can cause genotypic and phenotypic differences between cells, tissues, individuals, populations or species. The technology describes new bioinformatic tools and high-throughput methods to identify such dimorphisms. Additionally, the technology provides new assays to distinguish genomic sequences by genotyping, understand the role of such indels in altering gene expression, for example in disease pathogenesis, develop new models for variation in genomes and in gene expression, and improve methods for the molecular diagnosis and treatment of disease.

Development Status:

• Bioinformatics software tools are ready for use.
• High-throughput PCR methods have been validated.
• Annotated mouse genes whose expression is altered by dimorphic indels have been identified.

IP Status:
U.S. Provisional Application No. 60/841,089 filed 29 Aug 2006

Contact Information:
John D. Hewes, Ph.D., NCI Technology Transfer Center
Phone: 301-435-3121
E-mail: Hewesj@mail.nih.gov

Reference:  #480 JH

Updated 10/24/2007