Biology subjects

Jones, M. R.

Publications and source records attributed to Jones, M. R..

3 recordsLinked to original sources

bioRxiv2018

CancerMine: A literature-mined resource for drivers, oncogenes and tumor suppressors in cancer

Understanding a mutation in cancer requires knowledge of the different roles that genes play in cancer as drivers, oncogenes and tumor suppressors. We present CancerMine, a high-quality text-mined knowledgebase that catalogues over 856 genes as drivers, 2,421 as oncogenes and 2,037 as tumor suppressors in 426 cancer types. We compile 3,485 genes that are not in the IntOGen resource of drivers and complement the Cancer Gene Census with 3,136 new genes identified as oncogenes and tumor suppressors. CancerMine provides a method for gene-centric clustering of cancer types illustrating genetic similarities between cancer types of different organs and was validated against data from the Cancer Genome Atlas (TCGA) project. Finally with 178 novel cancer gene mentions in publications each month, this resource will be updated monthly, pre-empting the need to manually curate the ever-increasing number of novel cancer associated genes. CancerMine is viewable through a web portal (http://bionlp.bcgsc.ca/cancermine/) and available for download (https://github.com/jakelever/cancermine).

bioinformatics↗

bioRxiv2018

Large-Scale Genome-Wide Meta Analysis of Polycystic Ovary Syndrome Suggests Shared Genetic Architecture for Different Diagnosis Criteria.

Polycystic ovary syndrome (PCOS) is a disorder characterized by hyperandrogenism, ovulatory dysfunction and polycystic ovarian morphology. Affected women frequently have metabolic disturbances including insulin resistance and dysregulation of glucose homeostasis. PCOS is diagnosed with two different sets of diagnostic criteria, resulting in a phenotypic spectrum of PCOS cases. The genetic similarities between cases diagnosed with different criteria have been largely unknown. Previous studies in Chinese and European subjects have identified 16 loci associated with risk of PCOS. We report a meta-analysis from 10,074 PCOS cases and 103,164 controls of European ancestry and characterisation of PCOS related traits. We identified 3 novel loci (near PLGRKT, ZBTB16 and MAPRE1), and provide replication of 11 previously reported loci. Identified variants were associated with hyperandrogenism, gonadotropin regulation and testosterone levels in affected women. Genetic correlations with obesity, fasting insulin, type 2 diabetes, lipid levels and coronary artery disease indicate shared genetic architecture between metabolic traits and PCOS. Mendelian randomization analyses suggested variants associated with body mass index, fasting insulin, menopause timing, depression and male-pattern balding play a causal role in PCOS. Only one locus differed in its association by diagnostic criteria, otherwise the genetic architecture was similar between PCOS diagnosed by self-report and PCOS diagnosed by NIH or Rotterdam criteria across common variants at 13 loci.

genetics↗

bioRxiv2017

P-values and confidence intervals: not fit for purpose?

DeclarationsCompeting interests: All authors have completed theunified competing interest form and declare: no support from any organisation for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years, no other relationships or activities that could appear to have influenced the submitted work.\n\nThe lead author (the manuscripts guarantor) affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted.\n\nEthical approval: not required\n\nDetails of funding: Not applicable\n\nStatement of independence of researchers from funders: Not applicable\n\nPatient involvement statement. Not applicable.\n\nData sharing statement: Not applicable.

scientific communication and education↗