PREDICT___Whole_Genomes

PREDICT/Predicting individual response and resistance to VEGFR/mTOR pathway therapeutic intervention using biomarkers discovered through tumour functional genomics.

Type: Cancer Genomics
Archiver: EGA European Genome-Phenome Archive

2 Datasets 2 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
EGAD00001003445	Clear cell renal cancer is characterized by near-universal loss of the short arm of chromosome 3 (3p). This event arises through unknown mechanisms, but critically results in the loss of several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with clear cell renal cancer (ccRCC) recruited into the Renal TRACERx study. We find novel hotspots of point mutations in the 5'-UTR of TERT, targeting a MYC-MAX repressor, that result in telomere lengthening. The most common structural abnormality generates simultaneous 3p loss and 5q gain (36% patients), typically through chromothripsis. Using molecular clocks, we estimate this occurs in childhood or adolescence, generally preceding emergence of the most recent common ancestor by years to decades. Similar genomic changes recent common ancestor by years to decades. Similar genomic changes are seen in inherited kidney cancers. Modeling differences in age-incidence between inherited and sporadic cancers suggests that the number of cells with 3p loss capable of initiating sporadic tumors is no more than a few hundred. Targeting essential genes in deleted regions of chromosome 3p could represent a potential preventative strategy for renal cancer.	HiSeq X Ten	164
EGAD00001004774	We investigated the somatic genetic basis of Wilms’ tumour and found complex phylogenetic relations between tumours.	HiSeq X Ten	203

Publications	Citations
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal. Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O'Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR, Butler AP, Raine K, Stewart GD, Challacombe B, Fernando A, Lopez JI, Hazell S, Chandra A, Chowdhury S, Rudman S, Soultati A, Stamp G, Fotiadis N, Pickering L, Au L, Spain L, Lynch J, Stares M, Teague J, Maura F, Wedge DC, Horswell S, Chambers T, Litchfield K, Xu H, Stewart A, Elaidi R, Oudard S, McGranahan N, Csabai I, Gore M, Futreal PA, Larkin J, Lynch AG, Szallasi Z, Swanton C, Campbell PJ, TRACERx Renal Consortium. Cell 173: 2018 611-623.e17	226
Embryonal precursors of Wilms tumor. Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW, Oostveen M, Collord G, Tarpey PS, Cagan A, Hooks Y, Brougham M, Reynolds BC, Barone G, Anderson J, Jorgensen M, Burke GAA, Visser J, Nicholson JC, Smeulders N, Mushtaq I, Stewart GD, Campbell PJ, Wedge DC, Martincorena I, Rampling D, Hook L, Warren AY, Coleman N, Chowdhury T, Sebire N, Drost J, Saeb-Parsy K, Stratton MR, Straathof K, Pritchard-Jones K, Behjati S. Science 366: 2019 1247-1251	42

Publications

Citations

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal.
Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O'Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR, Butler AP, Raine K, Stewart GD, Challacombe B, Fernando A, Lopez JI, Hazell S, Chandra A, Chowdhury S, Rudman S, Soultati A, Stamp G, Fotiadis N, Pickering L, Au L, Spain L, Lynch J, Stares M, Teague J, Maura F, Wedge DC, Horswell S, Chambers T, Litchfield K, Xu H, Stewart A, Elaidi R, Oudard S, McGranahan N, Csabai I, Gore M, Futreal PA, Larkin J, Lynch AG, Szallasi Z, Swanton C, Campbell PJ, TRACERx Renal Consortium. Cell 173: 2018 611-623.e17

226

Embryonal precursors of Wilms tumor.
Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW, Oostveen M, Collord G, Tarpey PS, Cagan A, Hooks Y, Brougham M, Reynolds BC, Barone G, Anderson J, Jorgensen M, Burke GAA, Visser J, Nicholson JC, Smeulders N, Mushtaq I, Stewart GD, Campbell PJ, Wedge DC, Martincorena I, Rampling D, Hook L, Warren AY, Coleman N, Chowdhury T, Sebire N, Drost J, Saeb-Parsy K, Stratton MR, Straathof K, Pritchard-Jones K, Behjati S. Science 366: 2019 1247-1251