Description:
Executive Summary
Researchers at the University of Virginia have developed a method for high-throughput detection of disease-specific genomic rearrangements and have validated this method using chronic myeloid leukemia patient samples. This detection system can be utilized to provide clinical diagnosis, disease monitoring and treatment efficacy information.
Background
Chromosomal translocations, deletions and amplifications play a major role in many cancers. One such translocation is the Philadelphia chromosome, which has been linked to chronic myeloid leukemia (CML). In this case, the translocation results in the constitutive expression of an abnormal BCR-ABL1 fusion gene. CML has an incidence of about two cases per 100,000 people and constitutes 15–20 percent of all adult leukemias.
Two forms of cytogenetics are considered the gold standard for diagnosing CML and evaluating response to therapy, karyotyping and fluorescent in situ hybridization (FISH). Karyotyping involves the painful harvesting of bone marrow aspirates and requires several days of cell culture. FISH can be applied to cells isolated from blood to detect translocation directly with fluorescent-labeled DNA probes. However, neither method yields a patient-specific molecular biomarker that can be used to monitor the effectiveness of a treatment.
An alternative to karyotyping and FISH in the detection of chromosomal abnormalities are paired-end tags. These are short sequences of DNA that are mapped to the genome and can be used to identify structural variations such as fusion transcripts. This genome-wide approach to detect genetic aberrations is currently too costly in both time and money to be utilized as a clinical diagnostic.
Invention Description
Anindya Dutta, M.D., Ph.D., and colleagues at the University of Virginia have developed anchored chromosomal paired-end tag (ChromPET), a molecular and bioinformatic method to capture and identify chromosomal aberrations and to define DNA breakpoints at high resolution.
- capturing a selectively enriched target genomic region
- ChromPET sequencing
- bar coding to multiplex samples into a single high-throughput sequencing reaction
This method produces a patient-specific DNA biomarker that can be used to detect and monitor diseases caused by specific chromosomal translocations, such as in CML. The researchers have validated the ChromPET technique by defining the BCR-ABL1 translocation to base-pair resolution in CML patient samples.
A detailed description of this method and its validation can be found in the following inventor publications:
Advantages
This method of analysis:
- detects molecular biomarkers in blood or other body fluid samples, thus bypassing the need for bone marrow samples or cell culture
- rapidly identifies patient-specific genomic abnormalities at base pair-resolution
- produces patient-specific PCR primers for validating diagnoses and monitoring both disease progression and treatment efficacy
Applications
This method could be applied to any cancer or genetically-based disease to provide personalized medicine to afflicted patients. Further, this method can be used to detect specific genomic structural variations in any organism. For example, the researchers used ChromPET to identify genetic rearrangements in S. cerevisiae including expected events during strain construction and unannotated Ty element insertions.
