Platform for the High Throughput Screening of Single Nucleotide Polymorphisms and Small Insertions and Deletions
Description of Invention:
Available for licensing and commercial development is an oligoarray-based process for gene-specific single nucleotide polymorphism (SNP) genotyping based on comparative hybridization. This process can detect, even in heterozygous conditions, known and potentially flag unknown variants (point mutations, base insertion or deletion) along the complete sequence of a given gene while drastically cutting the time and costs compared to high-throughput direct sequencing without affecting sensitivity and specificity. The accuracy and efficiency of the invention was validated based on the BRCA-1 breast and ovarian cancer predisposing gene. This process can easily be custom designed to include within the same platform a relatively large number of genes relevant to a specific clinical condition and it is particularly useful for the screening of long genomic region with relatively infrequent but clinically relevant variants.
More specifically, the invention is made reliable by the development of two tailored algorithms: the first automatically designs the complete data set of gene-specific probes starting from the genomic sequence according to the user specification (size of the probes, relative position, etc.); and the other is based on an algorithm that flags gene variants in the test sample. This allows detecting unknown variants in the region in which only the reference hybridizes to the probes. These features drastically reduce the amount of sequencing (the gold standard for SNP detection) to small regions in which a discrepancy between test signal and reference signal is found. Moreover, there is no limit, other than the physical area of the slide, to the number of probes that can be added to the array and the number of genes that can be queried simultaneously. Thus, a repertoire of considerable size can be scanned in a single test for each sample with sensitivity and specificity comparable to direct sequencing.
Applications:
The immediate clinical applications of this platform is a remarkable improvement of genetic testing by increasing the number of target genes that can be screened in a short time, at a minimal cost using an automated simplified analysis, such as the sequencing-grade screening for BRCA-1 variants and the detection of mutations in cancerous tissues. The method can be also applied to other human genes (coding and non-coding sequences), and other sequences from animals, bacterial and viruses.
Development Status:
Method fully developed and validated.
Inventors:
Ena Wang (CC) Alessandro Monaco (CC) Francesco M Marincola (CC) et al.
Patent Status:
DHHS Reference No. E-082-2008/0 --
U.S. Provisional Application No. 61/068,182 filed 05 Mar 2008
Licensing Status: Available for non-exclusive or exclusive licensing.
Portfolios: Internal Medicine Devices/Instrumentation Cancer
Cancer -Diagnostics-In Vitro-DNA Based Cancer -Diagnostics Devices/Instrumentation-Diagnostics Internal Medicine-Diagnostics
For Additional Information Please Contact: Cristina Thalhammer-Reyero PhD MBA
NIH Office of Technology Transfer
6011 Executive Blvd, Suite 325
Rockville, MD 20852-3804
Phone: (301) 435-4507
Email: thalhamc@mail.nih.gov
Fax: (301) 402-0220
