Subclonal evolution of four ER+ breast cancers determined by WGS and scRNA-Seq

We analyzed the subclonal evolution of four ER+ breast cancers over 2-15 years using whole-genome sequencing (WGS) and single-cell RNA-Seq (scRNA-Seq). For each patient we analyzed 2-6 cancer samples, generally metastatic pleural effusions or ascites, by WGS, along with germline DNA. Two of the samples per patient were selected for single-cell RNA-Seq.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 5 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001003303	The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.		16

Publications	Citations
Combating subclonal evolution of resistant cancer phenotypes. Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Nat Commun 8: 2017 1231	89
Mobile element insertions and associated structural variants in longitudinal breast cancer samples. Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB. Sci Rep 11: 2021 13020	3
Phylogenetic inference from single-cell RNA-seq data. Liu X, Griffiths JI, Bishara I, Liu J, Bild AH, Chang JT. Sci Rep 13: 2023 12854	2
A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT. Genome Res 34: 2024 94-105	2
Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Biomark Res 12: 2024 107	0