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TransNEO neoadjuvant breast cancer study

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

1 Dataset 5 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
EGAD00001008269	Whole exome, shallow whole genome, and RNA-sequencing data from a cohort of 168 women with breast cancer receiving neoadjuvant chemotherapy.	Illumina HiSeq 4000	336

Publications	Citations
Multi-omic machine learning predictor of breast cancer therapy response. Sammut SJ, Crispin-Ortuzar M, Chin SF, Provenzano E, Bardwell HA, Ma W, Cope W, Dariush A, Dawson SJ, Abraham JE, Dunn J, Hiller L, Thomas J, Cameron DA, Bartlett JMS, Hayward L, Pharoah PD, Markowetz F, Rueda OM, Earl HM, Caldas C. Nature 601: 2022 623-629	345
Residual cancer burden after neoadjuvant chemotherapy and long-term survival outcomes in breast cancer: a multicentre pooled analysis of 5161 patients. Yau C, Osdoit M, van der Noordaa M, Shad S, Wei J, de Croze D, Hamy AS, Laé M, Reyal F, Sonke GS, Steenbruggen TG, van Seijen M, Wesseling J, Martín M, Del Monte-Millán M, López-Tarruella S, I-SPY 2 Trial Consortium, Boughey JC, Goetz MP, Hoskin T, Gould R, Valero V, Edge SB, Abraham JE, Bartlett JMS, Caldas C, Dunn J, Earl H, Hayward L, Hiller L, Provenzano E, Sammut SJ, Thomas JS, Cameron D, Graham A, Hall P, Mackintosh L, Fan F, Godwin AK, Schwensen K, Sharma P, DeMichele AM, Cole K, Pusztai L, Kim MO, van 't Veer LJ, Esserman LJ, Symmans WF. Lancet Oncol 23: 2022 149-160	308
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics. Hoang DT, Dinstag G, Shulman ED, Hermida LC, Ben-Zvi DS, Elis E, Caley K, Sammut SJ, Sinha S, Sinha N, Dampier CH, Stossel C, Patil T, Rajan A, Lassoued W, Strauss J, Bailey S, Allen C, Redman J, Beker T, Jiang P, Golan T, Wilkinson S, Sowalsky AG, Pine SR, Caldas C, Gulley JL, Aldape K, Aharonov R, Stone EA, Ruppin E. Nat Cancer 5: 2024 1305-1317	59
Detecting homologous recombination deficiency for breast cancer through integrative analysis of genomic data. Zhu R, Eason K, Chin SF, Edwards PAW, Manzano Garcia R, Moulange R, Pan JW, Teo SH, Mukherjee S, Callari M, Caldas C, Sammut SJ, Rueda OM. Mol Oncol 19: 2025 3613-3633	0
Path2Omics Enhances Transcriptomic and Methylation Prediction Accuracy from Tumor Histopathology. Hoang DT, Shulman ED, Dhruba SR, Nair NU, Barman RK, Cantore T, Biswas S, Lalchungnunga H, Singh O, Chung Y, Lee JS, Nasrallah MP, Stone EA, Aldape K, Ruppin E. Cancer Res 85: 2025 5098-5112	2