Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics

Translating genomics: cancer genetics, public health and the making of the (de)molecularised body in Cuba and Brazil

This article examines how cancer genetics has emerged as a focus for research and healthcare in Cuba and Brazil. Drawing on ethnographic research undertaken in community genetics clinics and cancer genetics services, the article examines how the knowledge and technologies associated with this novel area of healthcare are translated and put to work by researchers, health professionals, patients and their families in these two contexts. It illuminates the comparative similarities and differences in how cancer genetics is emerging in relation to transnational research priorities, the history and contemporary politics of public health and embodied vulnerability to cancer that reconfigures the scope and meaning of genomics as “personalised” medicine

Public Awareness of Genetic Influence on Chronic Disease Risk: Are Genetic and Lifestyle Causal Beliefs Compatible?

Background/Aims: There is concern that raising awareness about the role of genetics in chronic disease etiology could undermine public belief that lifestyles are important, leading to adverse effects on public health. We tested the hypothesis that people who believe genetics influence chronic disease risk are less likely to believe lifestyles play a role. Methods: Open-ended questions about cancer and heart disease risk factors were included in a population-based survey of 1,747 British adults. Responses were coded for causal beliefs about genetics and lifestyle (smoking, diet, alcohol, exercise). Results: One third of the respondents identified genetic factors as influencing cancer (35%) and heart disease (36%) risk. Identifying genetic risk was associated with female gender, older age and education for both diseases, as well as with family history for heart disease. Individuals identifying genetic influences on cancer risk were more likely to identify diet (p < 0.001) and exercise (p < 0.05), and mentioned more lifestyle factors overall (p < 0.05), independent of demographics and family history. Patterns were similar for heart disease. Conclusion: People who recognize that genetics influence chronic disease risk appear more, not less, likely to recognize the role of lifestyles, contradicting suggestions that the public takes an 'either/or' view of the etiology of these potentially preventable diseases. Copyright (C) 2010 S. Karger AG, Base

National evaluation of NHS genetics service investments: emerging issues from the cancer genetics pilots

In seeking to fulfil the ambition of the 2003 genetics white paper, Our Inheritance, Our Future, to ‘mainstream’ genetic knowledge and practices, the Department of Health provided start-up funding for pilot services in various clinical areas, including seven cancer genetics projects. To help to understand the challenges encountered by such an attempt at reconfiguring the organization and delivery of services in this field, a programme-level evaluation of the genetics projects was commissioned to consider the organizational issues faced. Using a qualitative approach, this research has involved comparative case-study work in 11 of the pilot sites, including four of the seven cancer genetics pilots. In this paper, the researchers present early findings from their work, focusing in particular on the cancer genetics pilots. They consider some of the factors that have influenced how the pilots have sought to address pre-existing sector, organizational and professional boundaries to these new ways of working. The article examines the relationship between these factors and the extent to which pilots have succeeded in setting up boundary-spanning services, dealing with human-resource issues and creating sustainable, ‘mainstreamed’ provision which attracts ongoing funding in a volatile NHS commissioning environment where funding priorities do not always favour preventive, risk-assessment services

Penalized EM algorithm and copula skeptic graphical models for inferring networks for mixed variables

In this article, we consider the problem of reconstructing networks for continuous, binary, count and discrete ordinal variables by estimating sparse precision matrix in Gaussian copula graphical models. We propose two approaches: $\ell_1$ penalized extended rank likelihood with Monte Carlo Expectation-Maximization algorithm (copula EM glasso) and copula skeptic with pair-wise copula estimation for copula Gaussian graphical models. The proposed approaches help to infer networks arising from nonnormal and mixed variables. We demonstrate the performance of our methods through simulation studies and analysis of breast cancer genomic and clinical data and maize genetics data

Linking genetics with biology in disease research: an interview with Nick Hastie

Professor Nick Hastie is Director of the MRC Human Genetics Unit in Edinburgh, a centre originally famous for early studies of chromosome biology. He is also Director of the newly formed Institute of Genetics and Molecular Medicine, which includes the Human Genetics Unit. In addition to overseeing the work on cancer and developmental genetics in his own lab, he is involved in a number of large-scale genetic studies aimed at uncovering genetic risk factors for various human diseases

Outcomes of Genetic Testing in a Genitourinary Genetics Clinic

Several known hereditary cancer syndromes confer an increased risk for genitourinary (GU)related malignancies. Various guidelines indicate when to refer patients to genetic counseling for GU-related hereditary cancer syndromes but there is limited research on the clinical picture of these patients, including their cancerous and non-cancerous features, the genetic testing strategy for this population, and the probability of having a positive germline mutation if testing is performed. The purpose of this study is to determine the most common indications for ordering genetic testing in a GU Genetics Clinic and evaluate whether there is a relationship between the indication for genetic testing and genetic testing outcome. An institutional review board-approved retrospective chart review was performed for 220 patients seen in the GU Genetics Clinic at M.D. Anderson Cancer Center. Patients were stratified into groups based on their indication for genetic testing and an exact binomial test was used to compare the proportion of patients with a positive genetic test from various groups. The majority of patients (92%) were seen for genetic evaluation related to either renal cell carcinoma (RCC) or prostate cancer. Among patients seen for RCC-related evaluation (N=107), meeting published clinical criteria for a hereditary RCC syndrome significantly predicted positive genetic testing (

Psychological care of women with a family history of breast cancer

In parallel to the development of clinical cancer genetics services for women with a significant history of breast cancer, there has been a growing need to identify the psychological sequelae to risk ascertainment, predictive genetic testing and preventive breast surgery. The organisation and structure of cancer genetics clinics vary widely both nationally and across Europe, as does the level of integration of psychological care: available research shows little variation in psychosocial outcomes but cultural factors affect attitudes to and uptake of predictive testing and preventive surgery. There is general agreement that risk counselling can be beneficial without inducing or increasing psychological morbidity. Health professionals in cancer genetic counselling, testing and risk management services increasingly use clinical protocols and professional guidelines.Routine psychological support is not required for the majority of women with a family history of breast cancer, but access to psychological services should be in place for women with high distress relating to the family history or those undergoing predictive testing or preventive surgery. Genetics staff should be aware of potential adverse psychological consequences of risk assessment and risk management interventions, and be adequately trained to elicit women´s concerns and involve psychosocial colleagues where appropriate

A randomised controlled trial of breast cancer genetics services in South East Scotland:Psychological impact

This study compared the psychological impact of two models of breast cancer genetics services in South East Scotland. One hundred and seventy general practices were randomised to refer patients to the existing standard regional service or the novel community based service. Participants completed postal questionnaires at baseline (n¼373), 4 weeks (n¼276) and 6 months (n¼263) to assess perceived risk of breast cancer, subjective and objective understanding of genetics and screening issues, general psychological\ud distress, cancer worry and health behaviours. For participants in both arms of the trial, there were improvements in subjective and objective understanding up to 4 weeks which were generally sustained up to 6 months. However, improvements in subjective understanding for the women at low risk of breast cancer (i.e. not at significantly increased risk) in the standard service arm did not reach statistical significance. Cancer worry was significantly reduced at 6 months for participants in both arms of the trial. The two models of cancer genetics services tested were generally comparable in terms of the participants’ psychological outcomes. Therefore,\ud decisions regarding the implementation of the novel community-based service should be based on the resources required and client satisfaction with the service