Gene essentiality in cancer cell lines is modified by the sex chromosomes

Identification of sex chromosome dosage in cancer cell lines. (A) The relative DNA copy number of Y-linked genes for the Y⁺ and Y⁻ cell lines. (B) The expression of Y-linked genes for the Y⁺ and Y⁻ cell lines. (C) The gene expression is plotted as a function of the relative DNA copy number of Y-linked genes. (D) The relative DNA copy number of X-linked genes for the XX, X0, and XXdup cell lines. (E) The proportion of heterozygote SNPs across the X Chromosomes for the female XX, X0, and XXdup cell lines (based on 17,463 high-confidence SNPs with minor allele frequency > 10%). (F) The proportion of heterozygote SNPs as a function of the relative DNA copy number of X Chromosome genes in female cell lines. DNA copy number values are log₂(relative to ploidy + 1), and gene expression values are log₂(TPM + 1). For the DNA copy number, a log ratio of one indicates that copy number is unchanged relative to a normal diploid sample (n = 2). The black lines are the mean value for each group. (Chr) Chromosome; (XXdup) cell lines with duplication of the active X Chromosome.