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View article: Supplementary Table 9 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 9 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 9 summarizes the characterization of 16 SNPs associated with 23 concordant dQTLs.
View article: Data from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Data from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as tumor grade. To interrogate the evolutionary origin…
View article: Supplementary Table 2 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 2 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 2 displays results from driver selection, driver groupings and driver associations.
View article: Figure 5 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 5 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Mutational hallmarks of prostate cancer grade. A, A linear model was fit to relate each mutational density measure to ISUP GG using tumor and normal sequencing coverage as covariates. Dot size and color represents the effect size fo…
View article: Supplementary Table 7 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 7 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 7 provides summary statistics from distal dQTL associations
View article: Figure 7 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 7 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Characterization of dQTLs. A, Summary of all 35 dQTLs involving 25 unique SNPs. Dot size and color indicate the magnitude and direction of association (as OR), and background shading indicates dQTL discovered strategy. B, For…
View article: Figure 4 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 4 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Mutational subtypes of localized prostate cancer. A, Mutation densities (rows) differ by ETS fusion and NKX3-1 CNA status (columns). Dot size and color gives effect-size as a Z-score, scaled to ETS-negative, NKX3-1<…
View article: Supplementary Table 3 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 3 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 3 illustrates driver co-occurrence analysis, driver clusters, and associations of drivers with clinical features
View article: Supplementary Table 4 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 4 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 4 shows driver selection for dQTL nomination and prevalence of drivers in cohorts
View article: Supplementary Figures from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Figures from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Figures & Figure Legends. Supplementary Figure 1 | Cohort Structure and Analysis. Supplementary Figure 2 | CNA Evolution & Transcriptomic Effects. Supplementary Figure 3 | Properties of Driver Mutations. Supplementary Figure …
View article: Supplementary Table 8 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 8 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 8 shows summary statistics of 16 SNPs associated with 23 concordant dQTLs across cohorts
View article: Figure 3 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 3 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Functional characterization of driver mutations. A, Network diagrams represent multimodal pathway enrichment analysis of driver genes. Mutation types (i.e., the type of driver analysis) are indicated by shading of circles. Circle si…
View article: Figure 6 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 6 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
dQTLs bias somatic mutational landscape. A, Schematic of dQTL detection. The PRS used was by Schumacher and colleagues (16). Linear local dQTLs were assessed within ±500 kbp around a driver. Spatial local dQTLs were evaluated using …
View article: Supplementary Table 1 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 1 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 1 shows a feature-by-patient summary matrix. For each patient, this table provides version information of bioinformatics tools, summary sequencing statistics, mutational density metrics, clinical information and driver …
View article: Supplementary Table 5 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 5 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 5 displays summary statistics from PRS and HOXB13 associated with somatic drivers. β and P-value from logistic regression correcting for five genetic principal components, age and somatic mutation burden. FDR = false di…
View article: Supplementary Table 6 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 6 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 6 displays the number of dQTLs identified for each somatic driver in each analysis strategy. Summary statistics from local dQTL associations. Statistics from logistic regression correcting for five genetic principal com…
View article: Supplementary Table 10 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 10 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 10 lists dQTL SNPs identified as eQTLs in prostate tissue in GTEx.
View article: Supplementary Table 11 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Supplementary Table 11 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Supplementary Table 11 reports percentages of cross-individual contamination for each sample and sequencing lane.
View article: Figure 2 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Figure 2 from The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Somatic driver mutations in localized prostate cancer. Driver mutation discovery in 666 localized prostate tumors. The top barplot shows the distribution of the number of drivers in patients; the covariates on the left show the region type…
View article: The Germline and Somatic Origins of Prostate Cancer Heterogeneity
The Germline and Somatic Origins of Prostate Cancer Heterogeneity Open
Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as tumor grade. To interrogate the evolutionary origin…
View article: The Landscape of Prostate Tumour Methylation
The Landscape of Prostate Tumour Methylation Open
Prostate cancer is characterized by profound clinical and molecular heterogeneity. While its genomic heterogeneity is well-characterized, its epigenomic heterogeneity remains less understood. We therefore created a compendium of 3,001 mult…
View article: TAD boundary deletion causes PITX2-related cardiac electrical and structural defects
TAD boundary deletion causes PITX2-related cardiac electrical and structural defects Open
View article: Multimodality imaging and transcriptomics to phenotype mitral valve dystrophy in a unique knock-in Filamin-A rat model
Multimodality imaging and transcriptomics to phenotype mitral valve dystrophy in a unique knock-in Filamin-A rat model Open
Aims Degenerative mitral valve dystrophy (MVD) leading to mitral valve prolapse is the most frequent form of MV disease, and there is currently no pharmacological treatment available. The limited understanding of the pathophysiological mec…
View article: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter
DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter Open
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1<…
View article: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter
DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter Open
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1<…
View article: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter
DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter Open
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1<…
View article: DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter.
DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the <i>RB1</i> gene promoter. Open
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1<…
View article: Genome-wide germline correlates of the epigenetic landscape of prostate cancer
Genome-wide germline correlates of the epigenetic landscape of prostate cancer Open
View article: Widespread and Functional RNA Circularization in Localized Prostate Cancer
Widespread and Functional RNA Circularization in Localized Prostate Cancer Open
View article: Relaxed Selection During a Recent Human Expansion
Relaxed Selection During a Recent Human Expansion Open
Peischl et al. explore the way evolutionary forces shape genetic variability in expanding human populations. Over a few generations of separate evolution... Humans have colonized the planet through a series of range expansions, which deepl…