Graham G. Giles
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View article: Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study
Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study Open
Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection withi…
View article: Social relationships and epigenetic markers of aging in middle-aged and older adults: cross-sectional and prospective analyses
Social relationships and epigenetic markers of aging in middle-aged and older adults: cross-sectional and prospective analyses Open
Objectives Social relationships play an important role in maintaining physical and psychological health. Epigenetic age is a potential mechanism underlying health-related aspects of social relationships. We aimed to assess the cross-sectio…
View article: Predictive prioritization of enhancers associated with pancreatic disease risk
Predictive prioritization of enhancers associated with pancreatic disease risk Open
Genetic and epigenetic variation in enhancers is associated with disease susceptibility; however, linking enhancers to target genes and predicting enhancer dysfunction remain challenging. We mapped enhancer-promoter interactions in human p…
View article: Genetically determined body mass index is associated with diffuse large B‐cell lymphoma in polygenic and Mendelian randomization analyses
Genetically determined body mass index is associated with diffuse large B‐cell lymphoma in polygenic and Mendelian randomization analyses Open
Obesity has been associated with non‐Hodgkin lymphoma (NHL), but the evidence is inconclusive. We examined the association between genetically determined adiposity and four common NHL subtypes: diffuse large B‐cell lymphoma (DLBCL), follic…
View article: Genome-wide analysis highlights causal epigenetic link to age at menarche
Genome-wide analysis highlights causal epigenetic link to age at menarche Open
Age at menarche, a key milestone in female reproductive development, has declined globally and is associated with cancer and other health outcomes. We investigated epigenetic mechanisms underlying pubertal timing by analysing genome-wide D…
View article: Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue
Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue Open
Objective The performance of FFPE tissue-derived DNA on the MethylationEpicV1.0 array can be unpredictable as the protocol only has two quality checks; checkpoint 1 for DNA quantity and checkpoint 2 for DNA quality assessment. We sought to…
View article: Cancer control measures have prevented 230,000 deaths in Australia since the mid-1980s
Cancer control measures have prevented 230,000 deaths in Australia since the mid-1980s Open
These estimates demonstrate the value of sustained cancer control investment, particularly in primary and secondary prevention.
View article: Smart Nonuniformity for Calibrating Sequencing Depth of a Targeted Gene Panel to Simultaneously Detect Somatic and Germline Variants
Smart Nonuniformity for Calibrating Sequencing Depth of a Targeted Gene Panel to Simultaneously Detect Somatic and Germline Variants Open
Targeted gene panel sequencing that measures genomic variation at different depths has potential diagnostic application. A targeted gene panel, smart nonuniformity sequencing, was developed to detect somatic variants associated with clonal…
View article: Association of Epigenetic Markers of Aging With Prevalent and Incident Type 2 Diabetes
Association of Epigenetic Markers of Aging With Prevalent and Incident Type 2 Diabetes Open
Background Type 2 diabetes (T2D) is characterized by elevated levels of metabolic and inflammatory markers but less is known about other molecular alterations that occur with aging. We aimed to assess the associations of DNA methylation-ba…
View article: Mammographic density, pathogenic breast cancer susceptibility gene variants and breast cancer risk
Mammographic density, pathogenic breast cancer susceptibility gene variants and breast cancer risk Open
Importance Mammographic density (MD) and pathogenic variants (PVs) in breast cancer susceptibility genes are major determinants of breast cancer risk, but their association and joint effects on breast cancer risk are unclear. Objective To …
View article: Central and peripheral adiposity and premenopausal breast cancer risk: a pooled analysis of 440,179 women
Central and peripheral adiposity and premenopausal breast cancer risk: a pooled analysis of 440,179 women Open
Our analyses did not support an association between central adiposity and overall premenopausal breast cancer risk after adjustment for BMI. However, our findings suggest associations might differ by breast cancer hormone receptor and intr…
View article: Supplementary Table S6 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S6 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S6 shows the DEPTH posterior log odds in favour of association (PLO) score and the logistic regression p-value of the lowest p-value variant for each of the 34 known glioma risk regions using GliomaScan (S6a), AGOG (S6b…
View article: Supplementary Table S9 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S9 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S9 shows the generalised Berk-Jones statistic (GBJ) p-values for the potential novel glioma susceptibility regions by study, glioma type and sex.
View article: Supplementary Figure S2 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Figure S2 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Figure S2 shows the estimation of genetic ancestry of AGOG, GliomaScan and GICC samples by way of scatter plot of PC1 versus PC2.
View article: Supplementary Figure S1 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Figure S1 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Figure S1 is a stylised illustration of DEPTH’s use of sliding windows to identify genomic susceptibility regions.
View article: Supplementary Table S8 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S8 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S8 summarizes the supporting evidence for the potential novel glioma susceptibility regions.
View article: Supplementary Table S2 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S2 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S2 shows the number of samples excluded from the GliomaScan data and reasons for exclusion.
View article: Supplementary Table S1 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S1 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S1 shows the age characteristics of the UCSF/Mayo data (validation data).
View article: Supplementary Table S5 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S5 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S5 shows the generalised Berk-Jones statistic (GBJ) p-values for the candidate novel susceptibility regions for glioma by study and sex.
View article: Supplementary Table S3 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S3 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S3 shows the number of samples excluded from the AGOG autosomal data (S3a) and X-chromosome data (S3b) and reasons for exclusion.
View article: Supplementary Table S7 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S7 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S7 shows the DEPTH posterior log odds in favour of association (PLO) score and generalised Berk-Jones statistic (GBJ) p-value for TERT, EGFR, CCDC26, CDKN2BAS, TP53 and RTEL regions.
View article: Supplementary Table S4 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma
Supplementary Table S4 from Region-Based Analyses of Existing Genome-Wide Association Studies Identifies Novel Potential Genetic Susceptibility Regions for Glioma Open
Supplementary Table S4 shows the number of samples excluded from the GICC data and reasons for exclusion.
View article: Diet and survival after a diagnosis of ovarian cancer: a pooled analysis from the Ovarian Cancer Association Consortium
Diet and survival after a diagnosis of ovarian cancer: a pooled analysis from the Ovarian Cancer Association Consortium Open
Adherence to a more healthy, less-inflammatory diet may confer a survival benefit for individuals with early-stage ovarian cancer.
View article: Categorising reported errors and incidents from morbidity and mortality meetings (M&Ms) in a small animal multi‐specialty veterinary teaching hospital
Categorising reported errors and incidents from morbidity and mortality meetings (M&Ms) in a small animal multi‐specialty veterinary teaching hospital Open
Background Errors in veterinary clinical settings can lead to patient harm. Morbidity and mortality meetings (M&Ms) are forums to discuss errors and incidents that can lead or have led to adverse outcomes, potential harm or unsafe conditio…
View article: Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours
Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours Open
Our study highlights that common clustering strategies involving an arbitrary choice of algorithm, number of clusters and number of methylation sites are likely to identify different DNA methylation-based breast tumor subtypes.