zhangkaicr / depth2

DEPTH2

An mRNA-based algorithm to evaluate intratumor heterogeneity (ITH) without reference to normal controls.

Description

DEPTH2 evaluates the ITH level of each bulk tumor sample based on gene expression profiles.

Details

DEPTH2 calculates a tumor’s ITH level based on the standard deviations of absolute z-scored expression values of a set of genes in the tumor. In a tumor, if most genes show close absolute z-scored expression values, the tumor will likely have a low DEPTH2 score, namely low ITH level; otherwise, the tumor will have a relatively high ITH level. Input data are gene expression profiles in bulk tumor samples (microarray or RNA-Seq data, normalized), and output data are DEPTH2 ITH scores for each bulk tumor. The following tables illustrate an example of input data (Table 1) and an example of output data (Table 2).

Table 1. Gene expression matrix

Entrez ID	sample1	sample2	sample3	sample4	sample5
57505	8.23	8.68	8.19	9.06	8.70
80755	9.82	8.50	8.82	8.78	9.73
16	11.78	12.42	11.98	11.42	11.55
60496	10.52	9.68	10.03	9.21	9.99
132949	6.68	7.97	7.69	8.52	8.09
10157	9.89	7.53	8.25	9.33	7.57
26574	10.30	10.05	9.81	9.09	10.14
9625	4.85	10.08	6.55	8.82	5.50
18	10.63	10.53	9.88	9.29	9.19
10349	6.16	3.41	5.24	4.96	4.20

Table 2. DEPTH2 scores of tumors

Sample	DEPTH2_score
sample1	0.40
sample2	0.47
sample3	0.28
sample4	0.44
sample5	0.28

Installation

A user can install the released version of DEPTH2 with:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("XS-Wang-Lab/DEPTH2/DEPTH2")

Example

## Calculate ITH based on the gene expression profiles in tumors
library(DEPTH2)
path <- system.file("extdata", "example_DEPTH2.txt", package = "DEPTH2", mustWork = TRUE)
input_data <- read.table(path, stringsAsFactors = FALSE, header = TRUE, check.names = FALSE, sep = "\t", quote = "", row.names = 1)
DEPTH2(input_data)

Citation

Song D, Wang X. DEPTH2: an mRNA-based algorithm to evaluate intratumor heterogeneity without reference to normal controls. J Transl Med. 2022 Apr 1;20(1):150. doi: 10.1186/s12967-022-03355-1. PMID: 35365157; PMCID: PMC8974098.