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Shallow Whole Genome Sequencing of Patient Derived Xenografts

Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we leveraged a comprehensive collection of 27 molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. Genetic analyses revealed that treatment sensitivity was marked by genomic scars indicative of BRCAness, suggesting homologous recombination (HR) deficiency as a key determinant. Accordingly, we surveyed a manually curated panel of 44 genes with a documented role in HR for the potential presence of pathogenic mutations. We did not observe a specific enrichment of HR gene mutations based on response to FOLFIRI. This result, combined with the absence of widespread biallelic inactivation of the analyzed genes and the predominance of mutations categorized as variants of unknown significance, suggests that FOLFIRI sensitivity is not primarily governed by underlying mutations in HR genes responsible for mitigating the genotoxic effects of this therapeutic regimen.

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General policy for IRCC datasets

Translational Cancer Medicine laboratory of Candiolo IRCC institute. Dataset available on request

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000000191 Whole Genome Sequencing

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF50000084741 fastq.gz 925.6 MB
EGAF50000084742 fastq.gz 952.4 MB
EGAF50000084743 fastq.gz 905.8 MB
EGAF50000084744 fastq.gz 938.6 MB
EGAF50000084745 fastq.gz 963.5 MB
EGAF50000084746 fastq.gz 984.2 MB
EGAF50000084747 fastq.gz 996.9 MB
EGAF50000084748 fastq.gz 1.0 GB
EGAF50000084749 fastq.gz 958.6 MB
EGAF50000084750 fastq.gz 980.3 MB
EGAF50000084751 fastq.gz 847.6 MB
EGAF50000084752 fastq.gz 869.6 MB
EGAF50000084753 fastq.gz 900.7 MB
EGAF50000084754 fastq.gz 927.3 MB
EGAF50000084755 fastq.gz 995.7 MB
EGAF50000084756 fastq.gz 1.0 GB
EGAF50000084757 fastq.gz 966.5 MB
EGAF50000084758 fastq.gz 990.7 MB
EGAF50000084759 fastq.gz 962.9 MB
EGAF50000084760 fastq.gz 987.7 MB
EGAF50000084761 fastq.gz 970.8 MB
EGAF50000084762 fastq.gz 938.5 MB
EGAF50000084763 fastq.gz 846.8 MB
EGAF50000084764 fastq.gz 876.4 MB
EGAF50000084765 fastq.gz 1.0 GB
EGAF50000084766 fastq.gz 1.0 GB
EGAF50000084767 fastq.gz 936.2 MB
EGAF50000084768 fastq.gz 962.2 MB
EGAF50000084769 fastq.gz 946.0 MB
EGAF50000084770 fastq.gz 964.4 MB
EGAF50000084771 fastq.gz 1.0 GB
EGAF50000084772 fastq.gz 1.0 GB
EGAF50000084773 fastq.gz 962.4 MB
EGAF50000084774 fastq.gz 979.5 MB
EGAF50000084775 fastq.gz 950.1 MB
EGAF50000084776 fastq.gz 982.3 MB
EGAF50000084777 fastq.gz 1.0 GB
EGAF50000084778 fastq.gz 1.0 GB
EGAF50000084779 fastq.gz 908.1 MB
EGAF50000084780 fastq.gz 880.6 MB
EGAF50000084781 fastq.gz 924.3 MB
EGAF50000084782 fastq.gz 893.7 MB
EGAF50000084783 fastq.gz 928.7 MB
EGAF50000084784 fastq.gz 969.0 MB
EGAF50000084785 fastq.gz 986.7 MB
EGAF50000084786 fastq.gz 1.0 GB
EGAF50000084787 fastq.gz 984.2 MB
EGAF50000084788 fastq.gz 995.4 MB
EGAF50000084789 fastq.gz 889.7 MB
EGAF50000084790 fastq.gz 909.6 MB
EGAF50000084791 fastq.gz 992.3 MB
EGAF50000084792 fastq.gz 1.0 GB
EGAF50000084793 fastq.gz 943.7 MB
EGAF50000084794 fastq.gz 978.5 MB
54 Files (51.8 GB)