Control samples, breast cancer clinical samples and matched patient-derived tumour xenografts (PDTXs) to develop and test a computational approach to discriminate human and mouse sequences in PDTXs

Study ID Alternative Stable ID Type
EGAS00001002445 Other

Study Description

Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. In this study we generated Whole Exome Sequencing (WES) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA.

Study Datasets 1 dataset.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
Whole Exome Sequencing was performed in a dilution series containing known amounts of human and mouse DNA, 3x 100% human 0% mouse, 2x 90/10, 3x 50/50, 2x 25/75 and 3x 0/100. A set of breast cancer clinical samples, matched normal tissue and matched PDTXs (total number = 14) were also analysed. Paired-end 75bp sequences for the dilution series and paired-end 125bp for the clinical samples were obtained on Illumina HiSeq2500; fastq files are provided. A triplicate analysis of the transcriptome ... (Show More)
Illumina HiSeq 2500,Illumina HiSeq 4000 12

Who archives the data?