Sequenza

Overview

Sequenza is an R/Bioconductor tool for allele-specific copy-number analysis and loss-of-heterozygosity (LOH) inference from tumor/normal paired sequencing data. It jointly estimates tumor cellularity, ploidy, B-allele frequencies, and segmented copy-number states using depth ratio and B-allele frequency (BAF) information. LOH events are inferred from heterozygous germline SNP positions and are manually curated against depth ratio tracks.

Used by

  • Applied to 15 Korean vulvar SCC paired tumor/normal WES samples to infer LOH events including copy-neutral LOH (4 tumors: 1 HPV(+), 3 HPV(−)); results were manually curated using depth ratio and B-allele frequency in conjunction with nexus-copy-number PMID:29422544

Notes

  • Corpus-grown slug; not listed as a genePanelId in cBioPortal gene panels or as a molecularAlterationType in cBioPortal molecular profiles.
  • Operates on paired tumor/normal WES or targeted sequencing data; not suitable for tumor-only workflows.
  • Complementary to allele-specific CNA tools such as facets and ascat.

Sources

This page was processed by entity-page-writer on 2026-05-15.