Mapping TCGA tumor codes to NCIT

Vincent J. Carey, stvjc at channing.harvard.edu

Contents

1 Introduction

The TCGA tumor types cover a collection of anatomical compartments. Organizing tumor types into groups of related compartments may be fruitful. We will use the oncotree OBO representation from an NCI thesaurus OBO distribution in the Bioc 3.9 version of ontoProc.

2 A table

This table was constructed by hand on Oct 10 2019 using materials in ontoProc package.

suppressPackageStartupMessages({
library(DT)
library(ontoProc)
library(magrittr)
library(dplyr)
library(BiocOncoTK)
otree = getOncotreeOnto()
})
data("map_tcga_ncit")
datatable(map_tcga_ncit)

3 Formal annotation of anatomic site

3.1 Expeditious mapping

We will drop the CNTL class, and use only the first NCIT mapping when two seem to match.

controlindex = which(map_tcga_ncit[,1]=="CNTL")
tcgacodes = map_tcga_ncit[-controlindex,1]
ncitsites = map_tcga_ncit[-controlindex,3]
ssi = strsplit(ncitsites, "\\|")
sites = sapply(ssi, "[", 1)
simpmap = data.frame(code=tcgacodes, oncotr_site=otree$name[sites], ncit=sites,
  stringsAsFactors=FALSE)
simpmap[sample(seq_len(nrow(simpmap)),5),]

##            code              oncotr_site       ncit
## NCIT:C3171  AML   Acute Myeloid Leukemia NCIT:C3171
## NCIT:C2919 PRAD  Prostate Adenocarcinoma NCIT:C2919
## NCIT:C3058  GBM             Glioblastoma NCIT:C3058
## NCIT:C9383 READ    Rectal Adenocarcinoma NCIT:C9383
## NCIT:C9325  ACC Adrenal Cortex Carcinoma NCIT:C9325

We now have a 1-1 mapping from TCGA code to NCIT site. These sites can be grouped according to organ system, using the knowledge that NCIT:C3263 is the ‘neoplasm by site’ (which really should be ‘system’) category.

poss_sys = otree$children["NCIT:C3263"][[1]] # all possible systems
allanc = otree$ancestors[simpmap$ncit]
specific = sapply(allanc, function(x) intersect(x, poss_sys)[1]) # ignore multiplicities
sys = unlist(otree$name[specific])
datatable(systab <- cbind(simpmap, sys=sys))

Neither thymoma nor mesothelioma have NCIT organ system mappings per se.

3.2 Aggregation

We now have 12 categories for 33 tumor types. A code pattern for finding the TCGA codes for a given system is:

systab %>% filter(grepl("Repro", sys))

##   code                   oncotr_site        ncit
## 1 CESC    Cervical Squamous Neoplasm NCIT:C40195
## 2   OV Ovarian Serous Adenocarcinoma  NCIT:C7550
## 3 PRAD       Prostate Adenocarcinoma  NCIT:C2919
## 4 TGCT    Testicular Germ Cell Tumor  NCIT:C8591
## 5  UCS        Uterine Carcinosarcoma NCIT:C42700
##                            sys
## 1 Reproductive System Neoplasm
## 2 Reproductive System Neoplasm
## 3 Reproductive System Neoplasm
## 4 Reproductive System Neoplasm
## 5 Reproductive System Neoplasm