A study published in GenomeBiology finds that human papillomavirus integration induces changes in local chromatin of the host and the local transcriptome which may contribute to tumorigenesis. More research may help develop therapies for HPV+ cancers.
$$\begin{aligned} \left\lvert {\log _2 \frac{\text {TPM}_{\text {HPV}^{+}}}{\langle \text {TPM}_{\text {other}} \rangle }}\right\rvert > 1 \text {.} \end{aligned}$$
$$\begin{aligned} \left\lvert{\text {TPM}_{\text {HPV}^{+}} - \left\langle \text {TPM}_{\text {other}} \right\rangle }\right\rvert > 2 \text {SD} \end{aligned}$$To estimate the background distribution of genomic signal or outlier expression of genes at a given genomic region, we performed permutation analysis.
To estimate the background distribution of allelic imbalance, we shuffled the cell type corresponding to each HPV integration. This matched each allelic imbalance value to a cell type with no HPV integration within the examined 500-kbp window. We performed 100 such permutations, and quantified theof this distribution. We counted the SNPs passing a cutoff on imbalance at a given distance from the HPV integration site.
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