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MOTIVATION Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and whole genome shotgun sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as(More)
The current paradigm of cancer care relies on predictive nomograms which integrate detailed histopathology with clinical data. However, when predictions fail, the consequences for patients are often catastrophic, especially in prostate cancer where nomograms influence the decision to therapeutically intervene. We hypothesized that the high dimensional data(More)
Next-generation sequencing is making sequence-based molecular pathology and personalized oncology viable. We selected an individual initially diagnosed with conventional but aggressive prostate adenocarcinoma and sequenced the genome and transcriptome from primary and metastatic tissues collected prior to hormone therapy. The histology-pathology and copy(More)
Complex Genomic Rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints, and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole genome shotgun sequencing (WGSS) is beginning to facilitate the(More)
BACKGROUND The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes. RESULTS In the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell(More)
Complex genome rearrangements are frequently observed in cancer but their impact on tumor molecular biology is largely unknown. Recent studies have identified a new phenomenon involving the simultaneous generation of tens to hundreds of genomic rearrangements, called chromothripsis. To understand the molecular consequences of these events, we sequenced the(More)
Castrate-resistant prostate cancer (CRPC) and neuroendocrine carcinoma of the prostate are invariably fatal diseases for which only palliative therapies exist. As part of a prostate tumor sequencing program, a patient tumor was analyzed using Illumina genome sequencing and a matched renal capsule tumor xenograft was generated. Both tumor and xenograft had a(More)
RNA editing modifies the sequence of primary transcripts, potentially resulting in profound effects to RNA structure and protein-coding sequence. Recent analyses of RNA sequence data are beginning to provide insights into the distribution of RNA editing across the entire transcriptome, but there are few published matched whole genome and transcriptome(More)
Complex genomic rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole-genome shotgun sequencing (WGSS) is beginning to facilitate the(More)
AIMS We tested whether urinary podocalyxin-positive element (PCX+EL) can be a marker of early stage of diabetic nephropathy (DN). METHODS DN patients (n=68) and health controls (n=28) were enrolled in this study. Patients were classified into three groups: normoalbuminuria, microalbuminuria and macroalbuminuria. Urinary PCX+EL, serum cystatin C (Scys C)(More)