oncoscanR

Description

OncoscanR is an R package to handle Copy Number Variation analyses originating from the Oncoscan assay (Affymetrix). It allows computation of two homologous recombination default (HRD) scores, LST and HR-LOH as defined by Telli et al. [Clin Cancer Res 2016], along with the tandem duplication plus score (TDplus) to identify CDK12-mutated tumors [Popova et al., Cancer Res 2016]. The package also allows for identification of arm-level alterations (i.e. gain of chromosome arm 1p).

IMPORTANT: The package expects as input the text exported file from ChAS (Chromosome Analysis Suite; the Affymetrix software to identify CNV segments from the Oncoscan Assay). The package assumes that all segments given in the file are correct and true. The ChAS text file has to contain the columns Type, CN State and Full Location (to setup in ChAS).

Note that the Oncoscan does not cover the p arms of chromosome 13, 14, 15 and 22. The coverage on the p arm of chromosome 21 is only partial and is not included in the workflow (function workflow_oncoscan.run or script bin/oncoscan-workflow.R).

Computation of arm-level alteration

An arm is declared globally altered if more than 80% of its bases are altered with a similar CNV type (amplifications [3 extra copies or more], gains [1-2 extra copies], losses or copy-neutral losses of heterozygozity [LOH]). For instance, "gain of 3p" indicates that there is more than 80% of arm with 3 copies but less than 80% with 5 (otherwise it would be an amplification). Prior to computation, segments of same copy number and at a distance <300Kbp (Oncoscan resolution genome-wide) are merged. The remaining segments are filtered to a minimum size of 300Kbp.

Score LST

Procedure based on the paper from Popova et al, Can. Res. 2012 (PMID: 22933060). First segments smaller than 3Mb are removed, then segments are smoothed with respect to copy number at a distance of 3Mb. The number of LSTs is the number of breakpoints (breakpoints closer than 3Mb are merged) that have a segment larger or equal to 10Mb on each side. This score was linked to BRCA1/2-deficient tumors.

Score LOH

Procedure based on the paper from Abkevich et al., Br J Cancer 2012 (PMID: 23047548). Number of LOH segments larger than 15Mb but excluding segments on chromosomes with a global LOH alteration. This score was linked to BRCA1/2-deficient tumors.

Score TDplus

Procedure based on the paper from Popova et al., Cancer Res 2016 (PMID: 26787835). The TDplus score is defined as the number of regions larger than 1Mb but smaller or equal to 10Mb with a gain of one or two copies. This score was linked to CDK12-deficient tumors. They also identified as second category of tandem duplication whose size is smaller or equal than 1Mb and around 300Kb but could not link it to a phenotype. Note that due to its resolution the Oncoscan assaywill most likely miss t his second category. Nonetheless it is reported by the function but not by the standard workflow.

Installation

There are two options to install the package:

1. Download the oncoscanR_0.1.0.tar.gz file (stable version). Then in R, set the working directory to where the compressed package is and run install.packages('oncoscanR_0.1.0.tar.gz', repos=NULL, type='source').
2. In R, install the devtools package (install.packages('devtools')), load it (library(devtools)), then run install_github('yannchristinat/oncoscanR').

The package requires the prior installation of the packages GenomicRanges (bioconductor), magrittr, jsonlite and readr.

Testing the installation

Open R and type the following commands:

• library(oncoscanR)
• segs.filename <- system.file("extdata", "chas_example.txt", package = "oncoscanR")
• workflow_oncoscan.run(segs.filename, "M")

If everything is setup fine, it should return a list with no arm-level alterations and all scores at 0 except LST=1.

Usage

The main workflow can be launched either in R via the workflow_oncoscan.run(chas.fn, gender) function or via the script bin/run_oncoscan_workflow.R:

Usage: Rscript path_to_oncoscanR_package/bin/oncoscan-workflow.R CHAS_FILE GENDER

• CHAS_FILE: Path to the text export file from ChAS or a compatible text file.
• GENDER: Gender of the sample (used to handle sex chromosomes). Has to be M (male) or F (female).

The script will output a JSON string into the terminal with all the computed information. :

{ "armlevel": { "AMP": [], "LOSS": ["17p", "2q", "4p"], "LOH": ["14q", "5q", "8p", "8q"], "GAIN": [19p", "19q", "1q", "20p", "20q", "3q", "5p", "6p", "9p", "9q", "Xp", "Xq"] }, "scores": { "LST": 12, "LOH": 10, "TDplus": 66 }, "gender": "F", "file": "H19001012_gene_list_full_location.txt" }

Please read the manual for a description of all available R functions.

References

1. "Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer.", M. Telli et al., Clin Cancer Res volume 22(15), august 2016.
2. "Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications.", T. Popova et al., Cancer Res volume 76(7), april 2016.
3. "Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation.", T. Popova et al., Cancer Res volume 72(21), november 2012.
4. "Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer.", V. Abkevich et al., Br J Cancer. 2012 Nov 6;107(10).