ichorCNA

[PMID: 29109393] [Nature Communications]

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

“software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers.” Work from Gad Getz and Matthew Meyerson.

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Subclonal Evolution of Resistant Cancer Phenotypes

[PMID: 29093439] [Nature Communications]

Combating subclonal evolution of resistant cancer phenotypes

“track the genetic and phenotypic subclonal evolution of four breast cancers through years of treatment to better understand how breast cancers become drug-resistant. Recurrently appearing post-chemotherapy mutations are rare. However, bulk and single-cell RNA sequencing reveal acquisition of malignant phenotypes after treatment” “These findings highlight cancer’s ability to evolve phenotypically and suggest a phenotype-targeted treatment strategy that adapts to cancer as it evolves.”

Spatial-omic data in Early Breast Tumor

[PMID: 29093438] [Nature Communications]

Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma

“To address this we created a unique dataset of epithelial samples ductoscopically obtained from ducts leading to breast carcinomas and matched samples from ducts on the opposite side of the nipple. Here, we demonstrate that perturbations in mRNA abundance, with increasing proximity to tumour, cannot be explained by copy number aberrations. “

Hypermutation in Cancer

[PMID: 29056344] [Cell]

Comprehensive Analysis of Hypermutation in Human Cancer

“an extensive assessment of mutation burden through sequencing analysis of >81,000 tumors from pediatric and adult patients” “Mutation burden analysis reveals new drivers of hypermutation in POLE and POLD1.” “Replication repair deficiency was a major contributing factor. ” “Unbiased clustering, based on mutational context, revealed clinically relevant subgroups regardless of the tumors’ tissue of origin, highlighting similarities in evolutionary dynamics leading to hypermutation.” “The order of mutational signatures identified previous treatment and germline replication repair deficiency”

PancanQTL

[PMID: 29036324] [Nucleic Acids Research]

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types

“Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis.” “We developed PancanQTL, a user-friendly database, to store cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs to enable searching, browsing and downloading.”