Metadata and supplementary data supporting the published article: Using Whole Genome Seque

A cohort of familial breast cancer samples provides data for comparing Homologous Recombination Deficiency scores derived from DNA copy number arrays, whole genome sequencing, and downsampled low-coverage WGS. The data, supporting a published article by Xavier Marc De Luca, includes segmentation outputs, HRD score matrices, and performance metrics, all publicly available via multiple figshare repository links. This resource enables methodological comparison for inferring deficiencies in DNA damage repair pathways like BRCA1/BRCA2.

Use Cases

• Benchmarking HRD score calculation methods based on data from arrays, WGS, and downsampled WGS.
• Analyzing the impact of sequencing coverage on HRD score reliability using the provided 30X, 15X, and 10X downsampled data.
• Investigating GC bias and WGS performance metrics for samples with differential HRD score classification.
• Visualizing genomic alterations for specific tumor samples using the provided Circos plot data.

Strengths

• Publicly accessible data via persistent figshare DOIs for all components, including segmentation, HRD scores, and performance metrics.
• Includes data from multiple technological platforms (arrays, original WGS, and three levels of downsampled WGS) for direct comparison.
• Focuses on a specific, clinically relevant cohort of familial breast cancers.

Limitations

• Row count and dataset scale are unknown, which may limit suitability assessment for large-scale machine learning.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

figshare repository, supporting a published research article.

Collection Method

Derived from whole genome copy number data analysis of a familial breast cancer cohort using ASCAT and ascatNGS.