New method for DNA breakpoint detection

Many diseases, including some cancers, are associated with specific chromosomal trans-locations, and a technique reported in Genome Medicine provides a new way to detect these anomalies. The presence or absence of a translocation may have implications for diagnosis,  prognosis, and therapy.

The BCR-ABL1 fusion gene is a marker of chronic myeloid leukaemia. Anindya Dutta and colleagues used BCR-ABL1 as a model to test their novel high-throughput technique for interrogation of a specific chromosomal region, which uses DNA capture and enrichment of the region of interest, followed by multiplexed paired-end sequencing.  They were able to detect the BCR-ABL1 breakpoint to base-pair resolution in cell lines and clinical samples, and also showed that for formaldehyde-fixed cells and nucleic acids released from dying cells, the sensitivity was higher than that of an RNA biomarker.  This technique, called Anchored ChromPET, has the potential to facilitate patient
management by identifying a specific translocation even
when the currently-used clinical methods cannot detect the chimeric RNA transcript.

Shibata, Y., Malhotra, A., & Dutta, A. (2010). Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET Genome Medicine, 2 (9) DOI: 10.1186/gm191

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