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# oncoscanR author: Yann Christinat date: 9th of August 2022 version: 1.1.0 ## Description OncoscanR is an R package to handle Copy Number Variation analyses originating from the Oncoscan assay (Affymetrix). It allows computation of different homologous recombination deficiency (HRD) scores and 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 (e.g. 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). Any text file that complies with this structure should work equally well. 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 this package. ### Computation of arm-level alteration An arm is declared globally altered if more than 90% of its bases are altered with a similar CNV type (amplifications [5 copies or more], gains [1-2 extra copies], losses or copy-neutral losses of heterozygozity [LOH])[Christinat, J Mol Diagn 2021; PMID: 34454110]. For instance, "gain of 3p" indicates that there is more than 90% of arm with 3 copies but less than 90% 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. ### HRD scores #### Score nLST HRD score developed at HUG and based on the LST score by Popova et al. but normalized by an estimation of the number of whole-genome doubling events.Of note, copy-neutral LOH segments are removed before computation. `nLST = LST - 7*W/2` where `W` is the number of whole-genome doubling events. The score is positive if there are at least 15 nLST. #### 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 gLOH The percentage genomic LOH score is computed as described in the FoundationFocus CDx BRCA LOH assay; i.e. the percentage of bases covered by the Oncoscan that display a loss of heterozygosity independently of the number of copies, excluding chromosomal arms that have a global LOH (>=90% arm length). To compute with the armlevel_alt function on LOH segments only). 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 assay will most likely miss this second category. Nonetheless it is reported by the function but not by the standard workflow. ## Installation There are three options to install the package: 1. Install via bioconductor (nightly build): ```{r} if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("oncoscanR") ``` 2. Download the `oncoscanR_1.1.0.tar.gz` file (stable version). Then in R, set the working directory to where the compressed package is and run `install.packages('oncoscanR_1.1.0.tar.gz', repos=NULL, type='source')`. 3. 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`. ```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GenomicRanges") install.packages(c("magrittr", "jsonlite", "readr")) ``` ## Testing the installation Open R and type the following commands: ```{r} library(oncoscanR) segs.filename <- system.file("extdata", "chas_example.txt", package = "oncoscanR"), "M") ``` If everything is setup fine, it should return a list with no arm-level alterations and a negative HRD score (nLST=1). ## Usage The main workflow can be launched either in R via the `` function or via the script `bin/run_oncoscan_workflow.R`: Usage: `Rscript path_to_oncoscanR_package/scripts/run_oncoscan-workflow.R CHAS_FILE` - `CHAS_FILE`: Path to the text export file from ChAS or a compatible text file. The script will output a JSON string into the terminal with all the computed information. : ```{json} { "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": { "HRD": "Negative, nLST=12", "TDplus": 22, "avgCN": "2.43" } "file": "path/to/original_ChAS_file.txt" } ``` Please read the vignette for more details and 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). 5. "Absolute quantification of somatic DNA alterations in human cancer", S. Carter et al., Nat Biotech, 2012 volume 30(5). 6. "Automated Detection of Arm-Level Alterations for Individual Cancer Patients in the Clinical Setting", Y Christinat et al., J Mol Diagn 2021, Dec;23(17):1722-1731.