Prediction of breast cancer risk based on profiling with common genetic variants

BACKGROUND: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. METHODS: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. RESULTS: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. CONCLUSIONS: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.

Business Process Modelling based on formal temporal theory with an application to hospital patient flows

Existing Workflow Management Systems (WFMSs) follow a pragmatic approach. They often use a proprietary modelling language with an intuitive graphical layout. However the underlying semantics lack a formal foundation. As a consequence, analysis issues, such as proving correctness i.e. soundness and completeness, and reliable execution are not supported at design level. This project will be using an applied ontology approach by formally defining key terms such as process, sub-process, action/task based on formal temporal theory. Current business process modelling (BPM) standards such as Business Process Modelling Notation (BPMN) and Unified Modelling Language (UML) Activity Diagram (AD) model their constructs with no logical basis. This investigation will contribute to the research and industry by providing a framework that will provide grounding for BPM to reason and represent a correct business process (BP). This is missing in the current BPM domain, and may result in reduction of the design costs and avert the burden of redundant terms used by the current standards. A graphical tool will be introduced which will implement the formal ontology defined in the framework. This new tool can be used both as a modelling tool and at the same time will serve the purpose of validating the model. This research will also fill the existing gap by providing a unified graphical representation to represent a BP in a logically consistent manner for the mainstream modelling standards in the fields of business and IT. A case study will be conducted to analyse a catalogue of existing ‘patient pathways’ i.e. processes, of King’s College Hospital NHS Trust including current performance statistics. Following the application of the framework, a mapping will be conducted, and new performance statistics will be collected. A cost/benefits analysis report will be produced comparing the results of the two approaches.

A general framework for Business Process Modelling (BPM) based on Formal Temporal Theory with an application to Hospital Patient flows

Existing Workflow Management Systems (WFMSs) follow a pragmatic approach. They often use a proprietary modelling language with an intuitive graphical layout. However the underlying semantics lack a formal foundation. As a consequence, analysis issues, such as proving correctness i.e. soundness and completeness, and reliable execution are not supported at design level. This project will be using an applied ontology approach by formally defining key terms such as process, sub-process, action/task based on formal temporal theory. Current business process modelling (BPM) standards such as Business Process Modelling Notation (BPMN) and Unified Modelling Language (UML) Activity Diagram (AD) model their constructs with no logical basis. This investigation will contribute to the research and industry by providing a framework that will provide grounding for BPM to reason and represent a correct business process (BP). This is missing in the current BPM domain, and may result in reduction of the design costs and avert the burden of redundant terms used by the current standards. A graphical tool will be introduced which will implement the formal ontology defined in the framework. This new tool can be used both as a modelling tool and at the same time will serve the purpose of validating the model. This research will also fill the existing gap by providing a unified graphical representation to represent a BP in a logically consistent manner for the mainstream modelling standards in the fields of business and IT. A case study will be conducted to analyse a catalogue of existing ‘patient pathways’ i.e. processes, of King’s College Hospital NHS Trust including current performance statistics. Following the application of the framework, a mapping will be conducted, and new performance statistics will be collected. A cost/benefits analysis report will be produced comparing the results of the two approaches.