Flexible positions, managed hopes: the promissory bioeconomy of a whole genome sequencing cancer study

Unsettling the treatment imperative? Chemotherapy decision-making in the wake of genomic techniques

Social scientists have argued that a treatment imperative shapes experiences of biomedicine. This is evident within oncology, where discourses of hope are tempered by persistent fears surrounding cancer. It is within this context that genomic decision-making tools are entering routine care. These may indicate that a treatment is not appropriate for a particular disease profile. We draw on qualitative interviews and observations centred on gene expression profiling to consider the implications of this technique for the treatment imperative in early breast cancer. Influenced by sociological perspectives on medical technologies, we discuss how fallibilities of established tools have forged a space for the introduction of genomic testing into chemotherapy decision-making. We demonstrate how high expectations shaped patients' interpretations of this tool as facilitating the 'right' treatment choice. We then unpick these accounts, highlighting the complex relationship between gene expression profiling and treatment decision-making. We argue that anticipations for genomic testing to provide certainty in treatment choice must account for the sociocultural and organisational contexts in which it is used, including the powerful entwinement of chemotherapy and cancer. Our research has implications for sociological perspectives on treatment decision-making and clinical expectations for genomic medicine to resolve the 'problem' of overtreatment.

Kernel Fusion Method for Detecting Cancer Subtypes via Selecting Relevant Expression Data

Recently, cancer has been characterized as a heterogeneous disease composed of many different subtypes. Early diagnosis of cancer subtypes is an important study of cancer research, which can be of tremendous help to patients after treatment. In this paper, we first extract a novel dataset, which contains gene expression, miRNA expression, and isoform expression of five cancers from The Cancer Genome Atlas (TCGA). Next, to avoid the effect of noise existing in 60, 483 genes, we select a small number of genes by using LASSO that employs gene expression and survival time of patients. Then, we construct one similarity kernel for each expression data by using Chebyshev distance. And also, We used SKF to fused the three similarity matrix composed of gene, Iso, and miRNA, and finally clustered the fused similarity matrix with spectral clustering. In the experimental results, our method has better P-value in the Cox model than other methods on 10 cancer data from Jiang Dataset and Novel Dataset. We have drawn different survival curves for different cancers and found that some genes play a key role in cancer. For breast cancer, we find out that HSPA2A, RNASE1, CLIC6, and IFITM1 are highly expressed in some specific groups. For lung cancer, we ensure that C4BPA, SESN3, and IRS1 are highly expressed in some specific groups. The code and all supporting data files are available from https://github.com/guofei-tju/Uncovering-Cancer-Subtypes-via-LASSO.

Accomplishing an adaptive clinical trial for cancer: Valuation practices and care work across the laboratory and the clinic

A new generation of adaptive, multi-arm clinical trials has been developed in cancer research including those offering experimental treatments to patients based on the genomic analysis of their cancer. Depending on the molecular changes found in patients’ cancer cells, it is anticipated that targeted and personalised therapies will be made available for those who have reached the end of standard treatment options, potentially extending survival time. Results from these trials are also expected to advance genomic knowledge for patients in the future. Drawing on data from a qualitative study of one such trial in the UK, comprising observations of out-patient clinic appointments, out-patient biopsy procedures, laboratory work, and interviews with practitioners, this paper explores how the clinical and research value of one such trial was accomplished in everyday practice by focussing on the work of clinical trials and laboratory staff across recruitment, laboratory analysis, and results management. In the face of numerous potential set-backs, disappointments and failure, we explore how practitioners worked to balance the need to meet established measures of value such as numbers of patients recruited into the trial, alongside cultivating the value of positive affects for patients by managing their expectations and emotions. This care work was performed primarily by practitioners whose roles have historically been devalued in healthcare practice and yet, as we show, were critical to this process. We conclude by arguing that as complex multi-arm adaptive trials become more commonplace, we need to attend to, and render visible, the dynamic and care-full valuation practices of backstage practitioners through which experimental biomedicine is accomplished, and in doing so show that care both achieves clinical and research value, and is also a series of practices and processes that tends to tissue, patients and staff in the context of ever-present possibility of failure.

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Experimental genomic based trials are difficult to accomplish in practice.

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Valuation practices happen throughout recruitment and trial participation.

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Value was made via coordinative practices of care in the context of failure.

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Staff balance clinical and research value alongside expectations and emotions.

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Vital backstage practices of care were performed by devalued healthcare staff.

Psychological adaptation to diagnostic genomic sequencing results: The role of hope fulfillment

OBJECTIVE

Psychological adaptation is an important but understudied outcome among patients who undergo DNA evaluation to identify a cause of an unexplained health condition. This longitudinal study examines the relationship between the degree to which participants' hopes for diagnostic genomic sequencing were fulfilled and their psychological adaptation to their sequencing results over time.

METHOD

Secondary analyses were conducted on data from a subset of adult participants from the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing study with physical health conditions of suspected genetic etiology (such as neurological disorders or cancer; n = 192). Hope fulfillment and type of hope (hopes related to personal-family health implications vs. hoping to help others-advance science) were assessed as predictors of change in psychological adaptation (Psychological Adaptation Scale) and 4 subscales (coping efficacy, self-esteem, social integration, spiritual-existential well-being), from 2 weeks to 6 months after disclosure of genomic sequencing results.

RESULTS

Controlling for covariates, degree of hope fulfillment was associated with increased general psychological adaptation (β = .14, p = .02), social integration (β = .17, p = .01), and spiritual-existential well-being (β = .15, p = .02). Type of hope did not modify effects of degree of hope fulfillment on adaptation outcomes.

CONCLUSIONS

The degree to which patients' genomic sequencing-related hopes are fulfilled may be an important driver of long-term psychological adaptation after genomic sequencing. Evaluating the degree to which patients' hopes are fulfilled may allow clinicians to gain insight into the likely trajectory for patient adaptation after learning their results from genomic sequencing. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Genomic research and the cancer clinic: uncertainty and expectations in professional accounts

This paper explores clinicians' and scientists' accounts of genomic research in cancer care and the complexities and challenges involved with delivering this work. Contributing to the sociology of (low) expectations, we draw on sociological studies of uncertainty in medicine to explore their accounts of working with uncertainty as part of the management of patient and institutional expectations. We consider their appeals to the importance of modest inquiry and framing of the uncertainties of genomic medicine as normal and at times welcome as they sought to configure professional autonomy and jurisdictions and cultivate an experimental ethos amongst their patients. We argue that these types of uncertainty work [Star, S. L. 1985. "Scientific Work and Uncertainty." Social Studies of Science 15 (3): 391-427] are a key feature of managing expectations at the intersections of genomic research and clinical care.

Enrolling Genomics Research Participants through a Clinical Setting: the Impact of Existing Clinical Relationships on Informed Consent and Expectations for Return of Research Results

Genetic counselors working in a clinical setting may find themselves recruiting, enrolling, and returning results for genomic research, and existing clinical relationships with study participants may impact these research interactions. We present a qualitative study using semi-structured interviews of participants enrolled in a genome sequencing/exome sequencing (GS/ES) study at the same institution where they receive clinical care. Interviews were coded for motivations to participate and expectations of this research. The interviews revealed common motivations for participation, including altruism and hope for benefit for themselves, family members, and/or others with their condition. Additionally, themes emerged related to unintentional influence based on trust of the clinical provider that recruited them to the study. Participant trust in the enrolling provider at times appeared to extend to the study team to decide which research results to return and to do so in an appropriate format. Participants also based expectations for research results return on previous clinical genetic testing experiences, which may or may not be realistic depending on study design. It is imperative that genetic counselors enrolling patients into research studies be aware of the potential influence of their clinical relationship on potential subjects, be transparent about their role on the study team, and help set expectations about the study process, including results return.

"Possibly positive or certainly uncertain?": participants' responses to uncertain diagnostic results from exome sequencing

Purpose

Clinical genome sequencing (GS) produces uncertain diagnostic results, raising concerns about how to communicate the inherent complexities in ways that reduce potential misunderstandings and harms. This study investigates clinicians’ communications and patient/participant responses to uncertain diagnostic results arising from a clinical exome sequencing research study, contributing empirical data to the debate surrounding disclosure of uncertain genomic information.

Methods

We investigated the communication and impact of uncertain diagnostic results using ethnographic observations of result disclosures with 21 adults and 11 parents of child patients, followed by 2 semi-structured interviews with these same participants.

Results

Participants understood their uncertain results in ways that were congruent with clinical geneticists’ communications. They followed recommendations for further consultation, although family testing to resolve uncertainty was not always done. Participants were prepared for learning an uncertain result and grasped the key concept that it should not be used to guide health care or other decisions. They did not express regret for having learned the uncertain result; most regarded it as potentially valuable in the future.

Conclusion

This study suggests that uncertain diagnostic results from GS can be relayed to patients in ways they can understand and consistent with providers’ interpretations, without causing undue harm.

Market-driven production of biospecimens and the role of NHS hospital-led biobanks

Biobanks are vital for biospecimen production in research, despite the regulatory, recruitment and commercial difficulties they face. We conducted interviews with clinicians, researchers, volunteers who recruit biobank participants, regulators and NHS managers about the integration of a biobank into an NHS hospital. We show that medical waste collected for biomedical research acquires its socio-ethical and economic value from the level of integration (both technologically and organisationally) of the biobank into the NHS hospital. There is extensive investment in a range of intellectual and commercial relationships and labour among stakeholders involved in the production of biospecimens. It is not only the boundaries of research, clinical care and commercialisation of biospecimens that blur but also those of volunteerism and citizenship. Hospital-led biobanks provide an opportunity to study the intertwining of biomedical innovation and healthcare.

The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing

Genomic sequencing technology is moving rapidly from the research setting into clinical medicine but significant technological and interpretive challenges remain. Exome sequencing (ES) in its recent clinical application provides a genetic diagnosis in about 25 per cent of cases (Berg 2014). While this diagnostic yield is substantial, it also indicates that in a majority of cases, patients are receiving negative results (i.e. no explanatory genetic variant found) from this technology. There are a number of uncertainties regarding the meaning of a negative result in the current context of ES. A negative result may be due to current technological limitations that hinder detection of disease-causing variants or to gaps in the knowledge base that prohibit accurate interpretation of their pathogenicity; or it may indicate that there is not a genetic etiology for the disorder. In this paper we examine the uncertainties and nuances of the negative result from genome sequencing and how both clinicians and patients make meaning of it as revealed in ethnographic observations of the clinic session where results are returned, and in interviews with patients. We find that clinicians and patients construct the meaning of a negative result in ways that are uncertain, contingent, and multivalent; but invested with optimism, promise, and potentiality.