Primary vs Metastasis Analysis (Head & Neck Cancer)

Introduction

This vignette demonstrates comparison between primary tumor and lymph node metastasis using head and neck squamous cell carcinoma (HNSCC) data from GSE10332.

Load Data

# Load HNSCC26 data (Primary and Lymph Node)
load(url("https://www.dropbox.com/s/6zns12amobs39g8/HNSCC26_data.RData?raw=1"))

# Examine structure
names(listCountMtx)
sapply(listCountMtx, ncol)

Run Multi-Sample Comparison

library(SCEVAN)

multiSampleComparisonClonalCN(
  listCountMtx,
  analysisName = "HNSCC26",
  organism = "human",
  par_cores = 20,
  plotTree = TRUE
)

Biological Questions

This analysis helps answer:

  1. Clonal evolution: Which alterations are present in both primary and metastasis?
  2. Metastasis drivers: What new alterations appeared in the lymph node?
  3. Lost alterations: Which primary alterations are absent in metastasis?

Output Files

  • HNSCC26_allOncoHeat.png - Combined OncoPrint
  • HNSCC26_CloneTree.png - Phylogenetic tree
  • Individual sample segmentation files

Summary

Primary vs metastasis comparison reveals:

  • Clonal alterations maintained during metastasis
  • Metastasis-specific alterations (potential drivers)
  • Evolutionary trajectory of the tumor

Session Info

sessionInfo()
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] rmarkdown_2.31
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## loaded via a namespace (and not attached):
##  [1] digest_0.6.39    R6_2.6.1         fastmap_1.2.0    xfun_0.59       
##  [5] maketools_1.3.2  cachem_1.1.0     knitr_1.51       htmltools_0.5.9 
##  [9] buildtools_1.0.0 lifecycle_1.0.5  cli_3.6.6        sass_0.4.10     
## [13] jquerylib_0.1.4  compiler_4.6.1   sys_3.4.3        tools_4.6.1     
## [17] evaluate_1.0.5   bslib_0.11.0     yaml_2.3.12      otel_0.2.0      
## [21] jsonlite_2.0.0   rlang_1.2.0