Detect Canonical IGH Translocations in Multiple Myeloma

Identifies one of the five canonical IGH translocations in multiple myeloma: t(11;14), t(4;14), t(14;16), t(14;20), and t(6;14). Analyzes structural variant BEDPE data to detect translocations involving the IGH locus on chromosome 14 and canonical partner chromosomes.

Breakpoint capture regions are GRCh38 genomic coordinates based on the panel regions defined in https://github.com/parvathisudha/Targeted-Panel-Analysis/blob/v1/BED_files/hg38/v22/MyelomaPanel2Translocationsv2_hg38.bed from https://pmc.ncbi.nlm.nih.gov/articles/PMC9250632/

Usage

get_igh_trx_subtype(bedpe_file_path, region_flank = "500Kb", verbose = TRUE)

Arguments

bedpe_file_path

Character, path to BEDPE file containing structural variants

region_flank

Character, flank size to use for partner regions. Default: "500Kb"

verbose

Logical, whether to print progress messages. Default: TRUE

Value

Character vector of detected translocation subtype(s) or "Not Detected"