Code availability for research paper:

Identification of genes associated with testicular germ cell tumor susceptibility through a transcription wide association study. Ugalde-Morales E. et al. emilio.ugalde.morales@ki.se

DESCRIPTION

The present repository contains computer code used to perform Transcriptome Wide Association Study (TWAS) on TGCT risk, following FUSION methodology (Gusev et al. 2016)¹, as well as complementary analysis on external gene expression data sets related to normal testis embryonal development (Human gonadal development)², pre-malignant tissue (i.e GCNIS, germ cell neoplasia in situ)³, and TGCT tumor tissue⁴.

Code regarding data preparation 1.GWAS_imputation, data analysis on TWAS 2.FUSION_TWAS and expression data sets 3.Gene_expression, and generation of tables and figures for publication Tables_and_figures, is provided.

Modified version of FUSION software (R scripts) are located under 2.FUSION_TWAS/Software folder.

Detailed methodology is described in Methods section of the manuscript.

DATA SOURCES

GWAS summary statistics

TGCT GWAS meta-analysis summary statistics (Pluta et al. 2021)⁵ at availabe at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001349.v2.p1. Summary-GWAS harmonization and imputation was done to improve SNP overlap with prediction models (see documentation under the 1.GWAS_imputation folder).

TWAS analysis

Visit FUSION website for software installation and documentation FUSION. Pre-computed prediction models on testis tissue (GTExv8.ALL), TGCT (TCGA), and cross-tissue (GTExv8) were download as follow:

mkdir -p ./Data/WEIGHTS
cd ./Data/WEIGHTS
wget https://s3.us-west-1.amazonaws.com/gtex.v8.fusion/ALL/GTExv8.ALL.Testis.tar.gz
wget http://gusevlab.org/projects/fusion/weights/TCGA-TGCT.TUMOR.tar.bz2
wget http://gusevlab.org/projects/fusion/weights/sCCA_weights_v8_2.zip
tar xzf GTExv8.ALL.Testis.tar.gz
tar xjf TCGA-TGCT.TUMOR.tar.bz2
unzip sCCA_weights_v8_2.zip

Gene expression analysis

Data sets can be obtained from:

• Human gonadal development The Reproductive Cell Atlas.
• Pre-malignan tissue GCNIS data set.
• TGCT tumor samples TGCA data set.

To download single-cell gonadal data on developmental germ cells human_germcells.h5ad and male germ cells human_germcells.h5ad:

mkdir - Data/Gonads
cd Data/Gonads
wget https://cellgeni.cog.sanger.ac.uk/vento/reproductivecellatlas/gonads/human_main_male.h5ad
wget https://cellgeni.cog.sanger.ac.uk/vento/reproductivecellatlas/gonads/human_germcells.h5ad

References

Footnotes

1. Gusev A., et al. Nat Genet. 2016 Mar;48(3):245-52. doi: 10.1038/ng.3506. Epub 2016 Feb 8. ↩

2. Garcia-Alonso L., et al. Nature. 2022 Jul;607(7919):540-547. doi: 10.1038/s41586-022-04918-4. ↩

3. Sonne S. B. et al. Cancer Res. 2009 Jun 2. doi: 10.1158/0008-5472.CAN-08-4554. ↩

4. Shen H., et al. Cell Reports. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039. ↩

5. Pluta J., et al. Nat Commun. 2021 Jul 23;12(1):4487. doi: 10.1038/s41467-021-24334-y. ↩