The evolutionary dynamics of human colorectal cancer using single-gland spatial multi-omic profiling of DNA, RNA and chromatin.

Deciphering the mechanisms of colorectal cancer growth, progression and dissemination in each individual patient.

3 Datasets 3 Publications

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
EGAD00001007828	661 bam files generated from high-throughput RNAseq of tumour biopsies from colorectal cancer patients	NextSeq 500	661
EGAD00001008140	ATAC-seq profiling bam files from colorectal carcinoma and adenoma.	NextSeq 500	1207
EGAD00001008642	Primary tumour tissue and matched normal samples were prospectively collected from patients undergoing curatively-intentioned surgery at University College London Hospital (UCLH). All patients gave informed consent for collection of their materials to the UCLH Cancer Biobank (REC approval 15/YH/0311). Four regions of each primary cancer were sampled by punch biopsy or scalpel dissection, at 12, 3, 6 and 9 o’clock positions around the tumour periphery. Tissue pieces were manually dissociated under the microscope using two 16 G needles, where individual glands were pulled away from the tissue mass. Sequencing and mutation calling DNA fractions were extracted using the Zymo QuickDNA Microprep plus kit according to the manufacturer’s instructions. Only samples with a total DNA yield higher than 10 ng were taken forward for WGS library preparation. Libraries were prepared using the NEBnext Ultra II FS kit according to manufacturer’s instructions. Samples with sufficient library DNA yield and characteristic fragment size distribution (~200-500 bp) were further subjected to deep (~35x coverage) WGS. Sequence libraries were multiplexed and sequenced on an Illumina Novaseq.	Illumina NovaSeq 6000	609

Publications	Citations
The co-evolution of the genome and epigenome in colorectal cancer. Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. Nature 611: 2022 733-743	40
Phenotypic plasticity and genetic control in colorectal cancer evolution. Househam J, Heide T, Cresswell GD, Spiteri I, Kimberley C, Zapata L, Lynn C, James C, Mossner M, Fernandez-Mateos J, Vinceti A, Baker AM, Gabbutt C, Berner A, Schmidt M, Chen B, Lakatos E, Gunasri V, Nichol D, Costa H, Mitchinson M, Ramazzotti D, Werner B, Iorio F, Jansen M, Caravagna G, Barnes CP, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Sottoriva A, Graham TA. Nature 611: 2022 744-753	52
Contribution of pks<sup>+</sup> E. coli mutations to colorectal carcinogenesis. Chen B, Ramazzotti D, Heide T, Spiteri I, Fernandez-Mateos J, James C, Magnani L, Graham TA, Sottoriva A. Nat Commun 14: 2023 7827	12