oncoscanR

oncoscanR uses copy number segments from a text file to identify globally altered chromosome arms and compute genome-wide scores including homologous recombination deficiency (HRD) metrics.

Key Features:

• Chromosome arm alteration identification: Detects all chromosome arms that are globally altered from copy number segment data.
• HRD score computation: Calculates LST, HR-LOH, nLST and gLOH scores characteristic of BRCA-mutated cancers.
• Oncoscan assay compatibility: Tailored for the ThermoFisher Oncoscan assay analyzed with Chromosome Alteration Suite (ChAS) but adaptable to any input format.

Scientific Applications:

• BRCA-mutated cancer characterization: Computes HRD scores to assess genomic instability patterns associated with BRCA deficiency.
• CNV secondary analysis: Performs downstream analysis of copy number variation data from microarray-based assays.

Methodology:

The software processes copy number segments from a text file to identify globally altered chromosome arms and compute genome-wide scores including LST, HR-LOH, nLST and gLOH.