John F. Peden
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View article: A dedicated caller for<i>DUX4</i>rearrangements from whole-genome sequencing data
A dedicated caller for<i>DUX4</i>rearrangements from whole-genome sequencing data Open
Rearrangements involving the DUX4 gene ( DUX4- r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no ‘standard of care’ diagnostic method for their confident ident…
View article: Genome sequencing as a generic diagnostic strategy for rare disease
Genome sequencing as a generic diagnostic strategy for rare disease Open
Background To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increa…
View article: Genome sequencing as a generic diagnostic strategy for rare disease
Genome sequencing as a generic diagnostic strategy for rare disease Open
Background To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increa…
View article: Data from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
Data from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma Open
Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here, we report wide variation in the expression of the DNA cytosine deaminase APOBEC3B, with elevated expression…
View article: Supplementary Methods, Tables 1 - 6, Figures 1 - 5 from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
Supplementary Methods, Tables 1 - 6, Figures 1 - 5 from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma Open
PDF file - 481K, Table S1: Cell line information Table S2: Quantitative PCR primer and probe sequences. Table S3: Non-malignant tissues tested Table S4: Early stage serous ovarian tumors used in sequence analyses Table S5: Additional ovari…
View article: Data from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
Data from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma Open
Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here, we report wide variation in the expression of the DNA cytosine deaminase APOBEC3B, with elevated expression…
View article: Supplementary Methods, Tables 1 - 6, Figures 1 - 5 from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
Supplementary Methods, Tables 1 - 6, Figures 1 - 5 from APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma Open
PDF file - 481K, Table S1: Cell line information Table S2: Quantitative PCR primer and probe sequences. Table S3: Non-malignant tissues tested Table S4: Early stage serous ovarian tumors used in sequence analyses Table S5: Additional ovari…
View article: Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial.
Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial. Open
Incorporating genetics into risk-stratification for treatment of childhood B-progenitor acute lymphoblastic leukaemia (B-ALL) has contributed significantly to improved survival. In about 30% B-ALL (B-other-ALL) without well-established chr…
View article: Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia
Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia Open
Childhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations is challenging, due …
View article: Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 2011; 478: 103-109
Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 2011; 478: 103-109 Open
Blood pressure (BP) is a heritable trait1 influenced by multiple biological pathways and is responsive to environmental stimuli. Over one billion people worldwide have hypertension (BP ≥140 mm Hg systolic [SBP] or ≥90 mm Hg diastolic [DBP]…
View article: Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma Open
Concentrations of liver enzymes in plasma are widely used as indicators of liver disease. We carried out a genome-wide association study in 61,089 individuals, identifying 42 loci associated with concentrations of liver enzymes in plasma, …
View article: Familial congenital cataract, coloboma, and nystagmus phenotype with variable expression caused by mutation in <i>PAX6</i> in a South African family.
Familial congenital cataract, coloboma, and nystagmus phenotype with variable expression caused by mutation in <i>PAX6</i> in a South African family. Open
PAX6 is a highly conserved gene crucial for normal oculogenesis, and although mutations within the gene may cause an array of ocular developmental abnormalities, most are associated with aniridia and aniridia-related ocular defects. The ob…
View article: Causal Effect of Plasminogen Activator Inhibitor Type 1 on Coronary Heart Disease
Causal Effect of Plasminogen Activator Inhibitor Type 1 on Coronary Heart Disease Open
Background Plasminogen activator inhibitor type 1 ( PAI ‐1) plays an essential role in the fibrinolysis system and thrombosis. Population studies have reported that blood PAI ‐1 levels are associated with increased risk of coronary heart d…
View article: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes
The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes Open
The genomic landscape of breast cancer is complex, and inter- and intra-tumour heterogeneity are important challenges in treating the disease. In this study, we sequence 173 genes in 2,433 primary breast tumours that have copy number aberr…