Dataset Information

DIA analysis of paired primary and recurrent breast cancers

ABSTRACT: Molecular profiling of breast cancer has achieved great depth in defining the mutational landscapes and molecular profiles of primary tumors, though little is still known regarding cancer evolution into a recurrence. Proteogenomic workflows are particularly useful in defining the multi-layered biology of complex diseases by combining genomic, transcriptomic, and proteomic technologies so to inform not only on mutational processes, but also on their repercussion at the effector level, proteins. We employed our recently developed proteogenomic workflow to analyze a cohort of 27 primary breast cancers and their matched loco-regional recurrences by whole genome sequencing, RNA sequencing, and mass spectrometry.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast Epithelial Cell, Epithelial Cell

DISEASE(S): Breast Cancer

SUBMITTER: Tommaso De Marchi

LAB HEAD: Emma Nimeus

PROVIDER: PXD032266 | Pride | 2023-02-03

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	2017-06-12.uniprot.hsapiens.reviewed.DECOYed.fasta	Fasta
	2019-05-20.Subtypes.Merged.GTL.old.DIA.Scale.FDR.0.10.tr.3.to.100.lenient.Unimod.DECOY.PQP	Other
	BCLR_Full.run10.feature_alignment_matrix.Filtered.csv	Csv
	SMPL_NFO.xlsx	Xlsx
	TDM_M1912_226.raw	Raw

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Publications

Proteogenomics decodes the evolution of human ipsilateral breast cancer.

De Marchi Tommaso T Pyl Paul Theodor PT Sjöström Martin M Reinsbach Susanne Erika SE DiLorenzo Sebastian S Nystedt Björn B Tran Lena L Pekar Gyula G Wärnberg Fredrik F Fredriksson Irma I Malmström Per P Fernö Mårten M Malmström Lars L Malmstöm Johan J Niméus Emma E

Communications biology 20230202 1

Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic det ...[more]

PMID: 36732562

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