Background

In genomic research and medicine, it is often desirable to determine how many copies of a specific gene, or a specific set of genes, an individual has.

Existing methods, such as comparative genomic hybridization with arrays (aCGH), can qualitatively indicate these copy number variations but are not yet as precise as the innovation described below for definitive medical diagnosis using genomics alone.

The Innovation

Researchers at Children’s Mercy Hospitals and Clinics have developed a method to quantitatively determine genomic copy number variations for one specific gene or for several genes simultaneously.

In the quantitative microsphere hybridization (QMH) method, an entire target genome is amplified and densely tagged with biotin, which is then bound to a complex containing a bright fluorophore.

A probe specific to each target genomic region is labeled with a spectrally distinct microsphere and hybridized with target DNA. A two-laser flow cytometer then counts coincidences between microspheres and the bright fluorophore.

The ratio of the count for the target gene to the count for a gene that is known to have two copies and is identified with its own spectrally distinct microsphere gives the copy number value for the target gene: 1.0 for a gene present in the normal two copies, 0.5 for a gene with a single deletion, etc.

Quantitative determination of copy number for several target genes simultaneously is possible with additional spectrally distinct microspheres.

Applications

• Research: determine co-occurrence of a known genetic disorder and quantitative copy number variations in suspect genes
• Medicine: use quantitative copy number variations in one or several specific genes to identify or confirm a genetic disorder
• Calibration: Use QMH to calibrate other methods of determining copy number

Advantages

• General: can be applied to any gene for which the sequence is known
• Quantitative: copy number determined to relative accuracy of about ± 5%
• Multiplex: simultaneous determination of a wide range of targets, depending on availability and detection of spectrally distinct microspheres
• Uses common flow cytometry equipment and methods

Status

• Demonstrated in laboratory applications
• Newkirk HL, Rogan PK, Miralles M, Knoll JH. Hum Mut 27(4), 376-386, 2006
• Newkirk HL, Bittel DC, Butler MG. Am J Med Genet A. 2008 Sep 15; 146A(18):2346-54
• Non-provisional U.S. patent application
• Seeking partner to license, further develop, and market

File Number: 2006-001