Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue

Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB but low clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure

Individualised and complex experiences of integrative cancer support care: combining qualitative and quantitative data

Objectives: The widespread use of complementary therapies alongside biomedical treatment by people with cancer is not supported by evidence from clinical trials. We aimed to use combined qualitative and quantitative data to describe and measure individualised experiences and outcomes. Materials and methods In three integrative cancer support centres (two breast cancer only) in the UK, consecutive patients completed the individualised outcome questionnaire Measure Yourself Concerns and Wellbeing (MYCaW) before and after treatment. MYCaW collects quantitative data (seven-point scales) and written qualitative data and the qualitative data were analysed using published categories. Results: Seven hundred eighty-two participants, 92% female, mean age 51 years, nominated a wide range of concerns. Psychological and emotional concerns predominated. At follow-up, the mean change (improvement) in scores (n = 588) were: concern 1, 2.06 (95% CI 1.92–2.20); concern 2, 1.74 (95% CI 1.60–1.90); and well-being, 0.64 (95% CI 0.52–0.75). The most common responses to ‘what has been the most important aspect for you?’ were ‘receiving complementary therapies on an individual or group basis’ (26.2%); ‘support and understanding received from therapists’ (17.1%) and ‘time spent with other patients at the centres’ (16.1%). Positive (61.5%) and negative (38.5%) descriptions of ‘other things affecting your health’ correlated with larger and smaller improvement in concerns and well-being, respectively. Conclusions: In a multicentre evaluation, the MYCaW questionnaire provides rich data about patient experience, changes over time and perceptions of what was important to each individual with cancer within that experience. It is unlikely that meaningful evaluations of this complex intervention could be carried out by quantitative methods alone

Rif1 S-acylation mediates DNA double-strand break repair at the inner nuclear membrane

Rif1 is involved in telomere homeostasis, DNA replication timing, and DNA double-strand break (DSB) repair pathway choice from yeast to human. The molecular mechanisms that enable Rif1 to fulfill its diverse roles remain to be determined. Here, we demonstrate that Rif1 is S-acylated within its conserved N-terminal domain at cysteine residues C466 and C473 by the DHHC family palmitoyl acyltransferase Pfa4. Rif1 S-acylation facilitates the accumulation of Rif1 at DSBs, the attenuation of DNA end-resection, and DSB repair by non-homologous end-joining (NHEJ). These findings identify S-acylation as a posttranslational modification regulating DNA repair. S-acylated Rif1 mounts a localized DNA-damage response proximal to the inner nuclear membrane, revealing a mechanism of compartmentalized DSB repair pathway choice by sequestration of a fatty acylated repair factor at the inner nuclear membrane

Schizophrenia and psychotic symptoms in families of two American Indian tribes

Abstract Background The risk of schizophrenia is thought to be higher in population isolates that have recently been exposed to major and accelerated cultural change, accompanied by ensuing socio-environmental stressors/triggers, than in dominant, mainstream societies. We investigated the prevalence and phenomenology of schizophrenia in 329 females and 253 males of a Southwestern American Indian tribe, and in 194 females and 137 males of a Plains American Indian tribe. These tribal groups were evaluated as part of a broader program of gene-environment investigations of alcoholism and other psychiatric disorders. Methods Semi-structured psychiatric interviews were conducted to allow diagnoses utilizing standardized psychiatric diagnostic criteria, and to limit cultural biases. Study participants were recruited from the community on the basis of membership in pedigrees, and not by convenience. After independent raters evaluated the interviews blindly, DSM-III-R diagnoses were assigned by a consensus of experts well-versed in the local cultures. Results Five of the 582 Southwestern American Indian respondents (prevalence = 8.6 per 1000), and one of the 331 interviewed Plains American Indians (prevalence = 3.02 per 1000) had a lifetime diagnosis of schizophrenia. The lifetime prevalence rates of schizophrenia within these two distinct American Indian tribal groups is consistent with lifetime expectancy rates reported for the general United States population and most isolate and homogeneous populations for which prevalence rates of schizophrenia are available. While we were unable to factor in the potential modifying effect that mortality rates of schizophrenia-suffering tribal members may have had on the overall tribal rates, the incidence of schizophrenia among the living was well within the normative range. Conclusion The occurrence of schizophrenia among members of these two tribal population groups is consistent with prevalence rates reported for population isolates and in the general population. Vulnerabilities to early onset alcohol and drug use disorders do not lend convincing support to a diathesis-stressor model with these stressors, commonly reported with these tribes. Nearly one-fifth of the respondents reported experiencing psychotic-like symptoms, reaffirming the need to examine sociocultural factors actively before making positive diagnoses of psychosis or schizophrenia.</p

Advantages of a cohort study on cardiac arrest conducted by nurses

AbstractOBJECTIVEIdentifying factors associated to survival after cardiac arrest.METHODAn experience report of a cohort study conducted in a university hospital, with a consecutive sample comprised of 285 patients. Data were collected for a year by trained nurses. The training strategy was conducted through an expository dialogue lecture. Collection monitoring was carried out by nurses via telephone calls, visits to the emergency room and by medical record searches. The neurological status of survivors was evaluated at discharge, after six months and one year.RESULTSOf the 285 patients, 16 survived until hospital discharge, and 13 remained alive after one year, making possible to identify factors associated with survival. There were no losses in the process.CONCLUSIONCohort studies help identify risks and disease outcomes. Considering cardiac arrest, they can subsidize public policies, encourage future studies and training programs for CPR, thereby improving the prognosis of patients

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal.

Clear-cell renal cell carcinoma (ccRCC) exhibits a broad range of metastatic phenotypes that have not been systematically studied to date. Here, we analyzed 575 primary and 335 metastatic biopsies across 100 patients with metastatic ccRCC, including two cases sampledat post-mortem. Metastatic competence was afforded by chromosome complexity, and we identify 9p loss as a highly selected event driving metastasis and ccRCC-related mortality (p = 0.0014). Distinct patterns of metastatic dissemination were observed, including rapid progression to multiple tissue sites seeded by primary tumors of monoclonal structure. By contrast, we observed attenuated progression in cases characterized by high primary tumor heterogeneity, with metastatic competence acquired gradually and initial progression to solitary metastasis. Finally, we observed early divergence of primitive ancestral clones and protracted latency of up to two decades as a feature of pancreatic metastases

Social exclusion of older persons: a scoping review and conceptual framework

As a concept, social exclusion has considerable potential to explain and respond to disadvantage in later life. However, in the context of ageing populations, the construct remains ambiguous. A disjointed evidence-base, spread across disparate disciplines, compounds the challenge of developing a coherent understanding of exclusion in older age. This article addresses this research deficit by presenting the findings of a two-stage scoping review encompassing seven separate reviews of the international literature pertaining to old-age social exclusion. Stage one involved a review of conceptual frameworks on old-age exclusion, identifying conceptual understandings and key domains of later-life exclusion. Stage two involved scoping reviews on each domain (six in all). Stage one identified six conceptual frameworks on old-age exclusion and six common domains across these frameworks: neighbourhood and community; services, amenities and mobility; social relations; material and financial resources; socio-cultural aspects; and civic participation. International literature concentrated on the first four domains, but indicated a general lack of research knowledge and of theoretical development. Drawing on all seven scoping reviews and a knowledge synthesis, the article presents a new definition and conceptual framework relating to old-age exclusion