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:C3326 PCPG Adrenal Gland Pheochromocytoma NCIT:C3326
## NCIT:C3411 THYM                        Thymoma NCIT:C3411
## NCIT:C3483 LCML               Chronic Leukemia NCIT:C3483
## NCIT:C3510 SKCM             Cutaneous Melanoma NCIT:C3510
## NCIT:C8294 PAAD      Pancreatic Adenocarcinoma NCIT:C8294

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