SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0443-x) contains supplementary material, which is available to authorized users.     

When a Duck Initiates Movement,Do Others Follow? Testing Preference in Groups

Choice tests have been widely used to assess animal preferences. In the case of group‐living species, these tests are commonly presented to animals in groups, because isolation can have strong effects on behaviour and motivation. However, assessing preference at the group level could be misleading if strong control of movement, through influential individuals, and group cohesion were present. The needs of majority of the population might not be properly represented by the test results. The current study investigated whether or not groups of ducks (four ducklings per group) have individuals that consistently initiate movement and considered the implications for group cohesion, synchronisation and a measure of preference during a choice test. In all groups included in the analyses, there were ducks that initiated more movements than the rest, and this trend was stronger when leading towards areas providing resources such as pools. Also, more ducks preferentially followed the first initiator (birds initiating most movements within a group) into the bathing area. Group cohesion was higher in groups that frequently had the same individual initiating movement. The number of followers following the ducks that initiated most movements was associated with the measure of preference (time spent at preferred area, as a proportion of total time spent at any area) but the number of movements initiated by these individuals was not. These results highlight the need to consider the effects of initiators and group‐cohesive forces when conducting choice tests in groups of animals.     

Gene expression profiles during short‐term heat stress in the red sea coral Stylophora pistillata

During the past several decades, corals worldwide have been affected by severe bleaching events leading to wide‐spread coral mortality triggered by global warming. The symbiotic Red Sea coral Stylophora pistillata from the Gulf of Eilat is considered an opportunistic ‘r’ strategist. It can thrive in relatively unstable environments and is considered a stress‐tolerant species. Here, we used a S. pistillata custom microarray to examine gene expression patterns and cellular pathways during short‐term (13‐day) heat stress. The results allowed us to identify a two‐step reaction to heat stress, which intensified significantly as the temperature was raised to a 32 °C threshold, beyond which, coping strategies failed at 34 °C. We identified potential ‘early warning genes’ and ‘severe heat‐related genes’. Our findings suggest that during short‐term heat stress, S. pistillata may divert cellular energy into mechanisms such as the ER‐unfolded protein response (UPR) and ER‐associated degradation (ERAD) at the expense of growth and biomineralization processes in an effort to survive and subsequently recover from the stress. We suggest a mechanistic theory for the heat stress responses that may explain the success of some species which can thrive under a wider range of temperatures relative to others.     

The Treatment Cascade for Chronic Hepatitis C Virus Infection in the United States: A Systematic Review and Meta-Analysis

Background

Identifying gaps in care for people with chronic hepatitis C virus (HCV) infection is important to clinicians, public health officials, and federal agencies. The objective of this study was to systematically review the literature to provide estimates of the proportion of chronic HCV-infected persons in the United States (U.S.) completing each step along a proposed HCV treatment cascade: (1) infected with chronic HCV; (2) diagnosed and aware of their infection; (3) with access to outpatient care; (4) HCV RNA confirmed; (5) liver fibrosis staged by biopsy; (6) prescribed HCV treatment; and (7) achieved sustained virologic response (SVR).

Methods

We searched MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews for articles published between January 2003 and July 2013. Two reviewers independently identified articles addressing each step in the cascade. Studies were excluded if they focused on specific populations, did not present original data, involved only a single site, were conducted outside of the U.S., or only included data collected prior to 2000.

Results

9,581 articles were identified, 117 were retrieved for full text review, and 10 were included. Overall, 3.5 million people were estimated to have chronic HCV in the U.S. Fifty percent (95% CI 43–57%) were diagnosed and aware of their infection, 43% (CI 40–47%) had access to outpatient care, 27% (CI 27–28%) had HCV RNA confirmed, 17% (CI 16–17%) underwent liver fibrosis staging, 16% (CI 15–16%) were prescribed treatment, and 9% (CI 9–10%) achieved SVR.

Conclusions

Continued efforts are needed to improve HCV care in the U.S. The proposed HCV treatment cascade provides a framework for evaluating the delivery of HCV care over time and within subgroups, and will be useful in monitoring the impact of new screening efforts and advances in antiviral therapy.     

HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

Adolescent idiopathic scoliosis: natural history and long term treatment effects

Objective

To quantify and compare the forces exerted by scoliosis patients in fiberglass braces during exercises usually prescribed in departments where casts are made. The exercises are intended to increase corrective forces, activate muscles, stimulate ventilation and help the patient psychologically.

Setting

Outpatient care.

Patients

17 consecutive adolescent patients wearing fiberglass brace for idiopathic scoliosis.

Interventions

Exercises (kyphotization, rotation, "escape from the pad") in different positions (sitting, supine, on all fours).

Main outcome measure

Pressure detected by the F-Socket System between the rib hump and the pad of the brace.

Results

In static and dynamic conditions, the position adopted did not alter the total pressure exerted by the brace, although the part of the sensor stimulated did vary. Kyphotization and rotation exercises produced a significant increase of pressure (+ 58.9% and +29.8%, respectively); however, the "escape from the pad" exercise, despite its name, did not produce any significant variation of pressure.

Conclusion

Exercises in the brace allow adjunctive forces to be applied on soft tissues and through them, presumably on the spine. Different exercises can be chosen to obtain different actions. Physical exercises and sporting activities are useful in mechanical terms, although other important actions should not be overlooked.     

Adolescent idiopathic scoliosis: natural history and long term treatment effects

ABSTRACT : Adolescent idiopathic scoliosis is a lifetime, probably systemic condition of unknown cause, resulting in a spinal curve or curves of ten degrees or more in about 2.5% of most populations. However, in only about 0.25% does the curve progress to the point that treatment is warranted.Untreated, adolescent idiopathic scoliosis does not increase mortality rate, even though on rare occasions it can progress to the >100 degrees range and cause premature death. The rate of shortness of breath is not increased, although patients with 50 degrees curves at maturity or 80 degrees curves during adulthood are at increased risk of developing shortness of breath. Compared to non-scoliotic controls, most patients with untreated adolescent idiopathic scoliosis function at or near normal levels. They do have increased pain prevalence and may or may not have increased pain severity. Self-image is often decreased. Mental health is usually not affected. Social function, including marriage and childbearing may be affected, but only at the threshold of relatively larger curves.Non-operative treatment consists of bracing for curves of 25 degrees to 35 degrees or 40 degrees in patients with one to two years or more of growth remaining. Curve progression of >/= 6 degrees is 20 to 40% more likely with observation than with bracing. Operative treatment consists of instrumentation and arthrodesis to realign and stabilize the most affected portion of the spine. Lasting curve improvement of approximately 40% is usually achieved.In the most completely studied series to date, at 20 to 28 years follow-up both braced and operated patients had similar, significant, and clinically meaningful reduced function and increased pain compared to non-scoliotic controls. However, their function and pain scores were much closer to normal than patient groups with other, more serious conditions.Risks associated with treatment include temporary decrease in self-image in braced patients. Operated patients face the usual risks of major surgery, a 6 to 29% chance of requiring re-operation, and the remote possibility of developing a pain management problem.Knowledge of adolescent idiopathic scoliosis natural history and long-term treatment effects is and will always remain somewhat incomplete. However, enough is know to provide patients and parents the information needed to make informed decisions about management options.