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Article

Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.

Genome biology - 20 May 2025

Johnson Sarah H, Smadbeck James B, Zenka Roman M, Barrett Michael T, Gaitatzes Athanasios, Solanki Arnav, Florio Angela B, Borad Mitesh J, Cheville John C, Vasmatzis George

Abstract excerpt

Ploidy determination across the genome has been challenging for low-pass-WGS tumor-only samples. We present BACDAC, a method that calculates tumor ploidy down to 1.2X effective tumor coverage. Allele fraction patterns displayed in the Constellation Plot verify tumor ploidy and reveal subclonal populations. BACDAC outputs a metric, 2N+LOH, that when combined with ploidy better distinguishes near-diploid from...

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Topics

Humans
Ploidies
Neoplasms
Whole Genome Sequencing
Alleles
DNA Copy Number Variations

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Identifiers

PMID: 40394578
DOI: 10.1186/s13059-025-03599-2
PMCID: PMC12090563

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