translocationscan

Translocationscan is a term used to describe high-throughput, sequencing-based approaches designed to identify chromosomal translocations—rearrangements where segments of non-homologous chromosomes exchange places. It encompasses a class of computational pipelines and laboratory workflows rather than a single standardized assay. It is used in research and clinical settings to detect clinically relevant gene fusions and structural rearrangements.

Most translocationscan workflows analyze DNA sequencing data or RNA sequencing data. In DNA-based approaches, the workflow aligns reads to a reference genome and searches for discordant read pairs, split reads, and abnormal read-depth patterns that indicate a breakpoint. In RNA-based approaches, it focuses on fusion transcripts arising from translocations. Long-read sequencing can improve resolution across complex breakpoints.

Outputs typically include the genomic coordinates of breakpoints, the genes involved, fusion transcripts, and the number of supporting reads, along with confidence scores. Some pipelines annotate potential functional impact and whether the event preserves reading frame.

Applications include cancer genomics to identify oncogenic fusions (for example, BCR-ABL, EWSR1-FLI1), developmental disorders, and prenatal diagnostics. It complements traditional karyotyping and fluorescence in situ hybridization by providing higher resolution and the ability to detect novel rearrangements.

Limitations include dependence on data quality, library design, and genome complexity; false positives may arise from repetitive regions; validation with orthogonal methods is common; interpretation requires clinical or biological context.

See also: karyotype analysis, fluorescence in situ hybridization, structural variant detection, fusion transcript analysis, long-read sequencing.