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<p>Ploidy determination across the genome has been challenging for low-pass-WGS tumor-only samples. We present BACDAC<b>,</b> 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<sup>+</sup>LOH, that when combined with ploidy better distinguishes near-diploid from high-ploidy tumors. Validated using TCGA, BACDAC had good agreement with other methods and 88% agreement with experimental methods. Discrepancies occur mainly when BACDAC predicts diploidy with subclones rather than high-ploidy. Applied to 653 low-pass-WGS samples spanning 12 cancer subtypes, BACDAC calls 40% as high-ploidy.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月20日

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

摘要

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 high-ploidy tumors. Validated using TCGA, BACDAC had good agreement with other methods and 88% agreement with experimental methods. Discrepancies occur mainly when BACDAC predicts diploidy with subclones rather than high-ploidy. Applied to 653 low-pass-WGS samples spanning 12 cancer subtypes, BACDAC calls 40% as high-ploidy.