Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 95 tumor genome sequences from breast, head and neck, colorectal, and prostate carcinomas, and from melanoma, multiple myeloma, and chronic lymphocytic leukemia. We discover three genomic factors that are significantly correlated with the distribution of rearrangements: replication time, transcription rate, and GC content. The correlation is complex, and different patterns are observed between tumor types, within tumor types, and even between different types of rearrangements. Mutations in the APC gene correlate with and, hence, potentially contribute to DNA breakage in late-replicating, low %GC, untranscribed regions of the genome. We show that somatic rearrangements display less microhomology than germline rearrangements, and that breakpoint loci are correlated with local hypermutability with a particular enrichment for C ↔ G transversions

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

Detection of somatic point substitutions is a key step in characterizing the cancer genome. Mutations in cancer are rare (0.1–100/Mb) and often occur only in a subset of the sequenced cells, either due to contamination by normal cells or due to tumor heterogeneity. Consequently, mutation calling methods need to be both specific, avoiding false positives, and sensitive to detect clonal and sub-clonal mutations. The decreased sensitivity of existing methods for low allelic fraction mutations highlights the pressing need for improved and systematically evaluated mutation detection methods. Here we present MuTect, a method based on a Bayesian classifier designed to detect somatic mutations with very low allele-fractions, requiring only a few supporting reads, followed by a set of carefully tuned filters that ensure high specificity. We also describe novel benchmarking approaches, which use real sequencing data to evaluate the sensitivity and specificity as a function of sequencing depth, base quality and allelic fraction. Compared with other methods, MuTect has higher sensitivity with similar specificity, especially for mutations with allelic fractions as low as 0.1 and below, making MuTect particularly useful for studying cancer subclones and their evolution in standard exome and genome sequencing data

Triggered Palliative Care for Late-stage Dementia: a Pilot Randomized Trial

Context Persons with late-stage dementia have limited access to palliative care. Objective To test dementia-specific specialty palliative care triggered by hospitalization. Methods This pilot randomized controlled trial enrolled 62 dyads of persons with late-stage dementia and family decision-makers on admission to hospital. Intervention dyads received dementia-specific specialty palliative care consultation plus post-acute transitional care. Control dyads received usual care and educational information. The primary outcome was 60-day hospital or emergency department visits. Secondary patient and family-centered outcomes were patient comfort, family distress, palliative care domains addressed in the treatment plan, and access to hospice or community-based palliative care. Secondary decision-making outcomes were discussion of prognosis, goals of care, completion of Medical Orders for Scope of Treatment (MOST), and treatment decisions. Results Of 137 eligible dyads, 62 (45%) enrolled. The intervention proved feasible, with protocol completion ranging from 77% (family 2-week call) to 93% (initial consultation). Hospital and emergency department visits did not differ (intervention vs control, 0.68 vs 0.53 transfers per 60 days, p=0.415). Intervention patients had more palliative care domains addressed, and were more likely to receive hospice (25% vs 3%, p<0.019). Intervention families were more likely to discuss prognosis (90% vs 3%, p<0.001) and goals of care (90% vs 25%, p<0.001), and to have a MOST at 60-day follow-up (79% vs 30%, p<0.001). More intervention families made decisions to avoid re-hospitalization (13% vs 0%, p=0.033). Conclusion Specialty palliative care consultation for hospitalized patients with for late-stage dementia is feasible and promising to improve decision-making and some treatment outcomes

A Mendelian randomization study of testosterone and cognition in men

Testosterone replacement for older men is increasingly common, with some observations suggesting a protective effect on cognitive function. We examined the association of endogenous testosterone with cognitive function among older men in a Mendelian randomization study using a separate-sample instrumental variable (SSIV) analysis estimator to minimize confounding and reverse causality. A genetic score predicting testosterone was developed in 289 young Chinese men from Hong Kong, based on selected testosterone-related single nucleotide polymorphisms (rs10046, rs1008805 and rs1256031). The association of genetically predicted testosterone with delayed 10-word recall score and Mini-Mental State Examination (MMSE) score was assessed at baseline and follow-up using generalized estimating equation among 4,212 older Chinese men from the Guangzhou Biobank Cohort Study. Predicted testosterone was not associated with delayed 10-word recall score (−0.02 per nmol/L testosterone, 95% confidence interval (CI) −0.06–0.02) or MMSE score (0.06, 95% CI −0.002–0.12). These estimates were similar after additional adjustment for age, education, smoking, use of alcohol, body mass index and the Framingham score. Our findings do not corroborate observed protective effects of testosterone on cognitive function among older men

Discovery and saturation analysis of cancer genes across 21 tumor types

Summary While a few cancer genes are mutated in a high proportion of tumors of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalog of cancer genes, we analyzed somatic point mutations in exome sequence from 4,742 tumor-normal pairs across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumor types. Our analysis also identified 33 genes not previously known to be significantly mutated, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes, mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5000 samples per tumor type, depending on background mutation rate. The results help guide the next stage of cancer genomics

Paradox as invitation to act in problematic change situations

It has been argued that organizational life typically contains paradoxical situations such as efforts to manage change which nonetheless seem to reinforce inertia. Four logical options for coping with paradox have been explicated, three of which seek resolution and one of which ‘keeps the paradox open’. The purpose of this article is to explore the potential for managerial action where the paradox is held open through the use of theory on ‘serious playfulness’. Our argument is that paradoxes, as intrinsic features in organizational life, cannot always be resolved through cognitive processes. What may be possible, however, is that such paradoxes are transformed, or ‘moved on’ through action and as a result the overall change effort need not be stalled by the existence of embedded paradoxes

Relationship between moderate-to-vigorous physical activity, abdominal fat and immunometabolic markers in postmenopausal women

AbstractObjectsTo assess the burden of levels of physical activity, non-esterified fatty acids (NEFA), triacylglycerol and abdominal fat on the immunometabolic profile of postmenopausal women.Study designForty-nine postmenopausal women [mean age 59.43 (standard deviation 5.61) years] who did not undertake regular physical exercise participated in this study. Body composition was assessed using dual-energy X-ray absorptiometry, and levels of NEFA, tumour necrosis factor-α, adiponectin, insulin and triacylglycerol were assessed using fasting blood samples. The level of physical activity was assessed using an accelerometer (Actigraph GTX3x), and reported as counts/min, time spent undertaking sedentary activities and time spent undertaking moderate-to-vigorous physical activity (MVPA). The following conditions were considered to be risk factors: (i) sedentary lifestyle (<150min of MVPA per week); (ii) high level (above median) of abdominal fat; and (iii) hypertriacylglycerolaemia (<150mg/dl of triacylglycerol).ResultsIn comparison with active women, sedentary women had higher levels of body fat (%) (p=0.041) and NEFA (p=0.064). Women with higher levels of abdominal fat had impaired insulin resistance (HOMA-IR) (p=0.016) and spent more time undertaking sedentary activities (p=0.043). Moreover, the women with two risk factors or more had high levels of NEFA and HOMA-IR (p<0.05), as well as an eight-fold higher risk of a high level of NEFA, independent of age (p<0.05). No significant relationship was found between levels of physical activity, abdominal fat, tumour necrosis factor-α and adiponectin (p>0.05).ConclusionPostmenopausal women with a combination of hypertriacylglycerolaemia, a high level of abdominal fat and a sedentary lifestyle are more likely to have metabolic disturbances

Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1,2 and will help facilitate the development of new approaches for disease gene discovery3. Large-scale surveys of human genetic variation have reported signatures of recent explosive population growth4-6, notable for an excess of rare genetic variants, qualitatively suggesting that many mutations arose recently. To more quantitatively assess the distribution of mutation ages, we resequenced 15,336 genes in 6,515 individuals of European (n=4,298) and African (n=2,217) American ancestry and inferred the age of 1,146,401 autosomal single nucleotide variants (SNVs). We estimate that ~73% of all protein-coding SNVs and ~86% of SNVs predicted to be deleterious arose in the past 5,000-10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs compared to other genes. Furthermore, European Americans had an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans, consistent with weaker purifying selection due to the out-of-Africa dispersal. Our results better delimit the historical details of human protein-coding variation, illustrate the profound effect recent human history has had on the burden of deleterious SNVs segregating in contemporary populations, and provides important practical information that can be used to prioritize variants in disease gene discovery