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Article
Open AccessGermline TP53 mutations undergo copy number gain years prior to tumor diagnosis
Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) analysis of tumors from 22 patients with T...
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Article
Open AccessAuthor Correction: Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada
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Article
Open AccessEmergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada
The emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) was met with rapid development of robust molecular-based detection assays. Many SARS-CoV-2 molecular tests target multiple genetic re...
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Article
Open AccessImpact of neoadjuvant chemotherapy on somatic mutation status in high-grade serous ovarian carcinoma
Patients treated with neoadjuvant chemotherapy (NACT) for advanced high-grade serous ovarian carcinoma (HGSC) have a higher rate and shorter time to platinum-resistant recurrence compared to patients treated w...
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Article
Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes
The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify th...
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Article
Open AccessBPG: Seamless, automated and interactive visualization of scientific data
We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment.
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Article
Genomic hallmarks of localized, non-indolent prostate cancer
Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome sequences a...
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Article
Spatial genomic heterogeneity within localized, multifocal prostate cancer
Paul Boutros, Robert Bristow and colleagues report a molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer. They find that multifocal tumors are highly heterogeneo...
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Article
Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers
Adam Shlien, Peter Campbell, Uri Tabori and colleagues report genome and exome sequencing of biallelic mismatch repair deficiency cancer samples from 12 children, including 10 high-grade gliomas. The hypermuta...
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Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands
Jorge Reis-Filho and colleagues identify recurrent mutations in PRKD1 in 73% of polymorphous low-grade adenocarcinoma, a malignant tumor of the minor salivary glands. The mutations cause activation of the PRKD1 s...
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Article
SeqControl: process control for DNA sequencing
SeqControl uses 15 quality metrics of high-throughput sequencing experiments to predict how much sequencing is needed to reach a desired depth of coverage.
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Article
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 1...
