Anch_chromPETs
Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET
Illumina paired end data (42bp) from two lanes of the Illumina sequencing platform
Background  Chromosomal aberrations, such as translocations or chromosomal inversions, are a major cause of acquired or inherited genetic disease in humans. Next-generation, ultra high-throughput sequencing coupled with paired-end DNA mapping is a powerful technique to obtain information on chromosomal aberrations. However, genome-wide sequencing to obtain information for a specific locus is expensive.  Method  We developed a novel technique, Anchored Chromosomal Paired End Tags (Anchored ChromPET), by combining three steps: enrichment of the chromosomal region of interest, ChromPET sequencing, and bar-coding to multiplex multiple samples into a single ultra high-throughput sequencing run. Anchored ChromPET was used to detect the DNA breakpoint at the BCR-ABL1 translocation in two Philadelphia chromosome positive (Ph(+)) cell lines and two chronic myeloid leukemia patients using M-bcr as an anchor. We also compared PCR detection efficiency of the DNA translocation junction to that of the RNA translocation junction in formaldehyde-fixed cells or in nucleic acids released from dying cells into the serum-containing culture medium.  Results  The BCR-ABL1 breakpoints detected by Anchored ChromPET in K562 and KU812 cells completely agreed with the breakpoint reported by others. We also identified the unknown ABL1-BCR reciprocal translocation in KU812 cells. The approach was also successful in detecting the BCR-ABL1 and ABL1-BCR translocation breakpoints in DNA from blasts in peripheral blood from two Ph(+) patients. In all cases we could validate the DNA breakpoints by PCR using primer sets that amplified the junctional fragments. The sensitivity for the detection of the DNA junction by PCR was significantly higher than the RNA biomarker currently in use, both in formaldehyde-fixed cells and in nucleic acids released from dying cells into the serum-containing cell culture medium.  Conclusions  Anchored ChromPET is a powerful technique with high sensitivity, high resolution, and good throughput for identifying disease-specific DNA translocations. It yields a patient-specific DNA biomarker that is useful for molecular follow-up after treatment. The DNA-based junctional fragment can be detected using samples from which it is hard to obtain RNA or from cells where the fusion RNA expression has been silenced.