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Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region.

Authors

Zhou W, Huang WY, Freedman ND, Machiela M

Affiliations

  • Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA. zhouw@mail.nih.gov.
  • Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.

Abstract

BACKGROUND: Mosaic loss of the Y chromosome (mLOY) in circulating leukocytes is the most frequently detected age-related chromosomal mosaic event in men. Current mLOY detection approaches use genotyping arrays and employ a phase-based approach that identifies B allele frequency (BAF) deviations in the pseudo-autosomal region (PAR) shared between the X and Y chromosome. As some widely used genotyping arrays lack sufficient probe coverage of the PAR, methods for accurately measuring mLOY utilizing the median log2 R ratio across the male-specific region of Y chromosome (mLRR_Y) are needed for detecting mLOY on these platforms.

RESULTS: We derived a formula from mLRR_Y to estimate the cellular fraction (CF) of cells with Y loss and validated the approach, finding high alignment with the CF estimation from female data and lab-generated qPCR data (R2 = 0.98). Additionally, we compared the correlation between phase-based BAF and mLRR_Y methods for CF estimation, achieving a high correlation with R2 > 0.80.

CONCLUSION: Although mLRR_Y is a noisier metric for mosaic chromosomal alteration detection relative to BAF, we demonstrate mLRR_Y across non-PAR variants can accurately estimate mLOY CF, especially for high CF mLOY.

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Publication Details

PubMed ID
39972265

Digital Object Identifier
10.1186/s12859-025-06076-6

Publication
BMC Bioinformatics. 2025 Feb 19; Volume 26 (Issue 1): Pages 60

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