Single-cell genomic variation induced by mutational processes in cancer.

How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

Interoperable and scalable data analysis with microservices: applications in metabolomics.

MOTIVATION: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. RESULTS: We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. AVAILABILITY AND IMPLEMENTATION: The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Matrix Effect Compensation in Small-Molecule Profiling for an LC-TOF Platform Using Multicomponent Postcolumn Infusion.

The possible presence of matrix effect is one of the main concerns in liquid chromatography-mass spectrometry (LC-MS)-driven bioanalysis due to its impact on the reliability of the obtained quantitative results. Here we propose an approach to correct for the matrix effect in LC-MS with electrospray ionization using postcolumn infusion of eight internal standards (PCI-IS). We applied this approach to a generic ultraperformance liquid chromatography-time-of-flight (UHPLC-TOF) platform developed for small-molecule profiling with a main focus on drugs. Different urine samples were spiked with 19 drugs with different physicochemical properties and analyzed in order to study matrix effect (in absolute and relative terms). Furthermore, calibration curves for each analyte were constructed and quality control samples at different concentration levels were analyzed to check the applicability of this approach in quantitative analysis. The matrix effect profiles of the PCI-ISs were different: this confirms that the matrix effect is compound-dependent, and therefore the most suitable PCI-IS has to be chosen for each analyte. Chromatograms were reconstructed using analyte and PCI-IS responses, which were used to develop an optimized method which compensates for variation in ionization efficiency. The approach presented here improved the results in terms of matrix effect dramatically. Furthermore, calibration curves of higher quality are obtained, dynamic range is enhanced, and accuracy and precision of QC samples is increased. The use of PCI-ISs is a very promising step toward an analytical platform free of matrix effect, which can make LC-MS analysis even more successful, adding a higher reliability in quantification to its intrinsic high sensitivity and selectivity.

Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer.

Cancer-associated mutations have been documented in normal tissues, but the prevalence and nature of somatic copy number alterations and their role in tumor initiation and evolution is not well understood. Here, using single cell DNA sequencing, we describe the landscape of CNAs in >42,000 breast epithelial cells from women with normal or high risk of developing breast cancer. Accumulation of individual cells with one or two of a specific subset of CNAs (e.g. 1q gain and 16q, 22q, 7q, and 10q loss) is detectable in almost all breast tissues and, in those from BRCA1 or BRCA2 mutations carriers, occurs prior to loss of heterozygosity (LOH) of the wildtype alleles. These CNAs, which are among the most common associated with ductal carcinoma in situ (DCIS) and malignant breast tumors, are enriched almost exclusively in luminal cells not basal myoepithelial cells. Allele-specific analysis of the enriched CNAs reveals that each allele was independently altered, demonstrating convergent evolution of these CNAs in an individual breast. Tissues from BRCA1 or BRCA2 mutation carriers contain a small percentage of cells with extreme aneuploidy, featuring loss of TP53 , LOH of BRCA1 or BRCA2 , and multiple breast cancer-associated CNAs in addition to one or more of the common CNAs in 1q, 10q or 16q. Notably, cells with intermediate levels of CNAs are not detected, arguing against a stepwise gradual accumulation of CNAs. Overall, our findings demonstrate that chromosomal alterations in normal breast epithelium partially mirror those of established cancer genomes and are chromosome- and cell lineage-specific.

MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data.

UNLABELLED: Identification of metabolites using high-resolution multi-stage mass spectrometry (MS(n)) data is a significant challenge demanding access to all sorts of computational infrastructures. MetiTree is a user-friendly, web application dedicated to organize, process, share, visualize and compare MS(n) data. It integrates several features to export and visualize complex MS(n) data, facilitating the exploration and interpretation of metabolomics experiments. A dedicated spectral tree viewer allows the simultaneous presentation of three related types of MS(n) data, namely, the spectral data, the fragmentation tree and the fragmentation reactions. MetiTree stores the data in an internal database to enable searching for similar fragmentation trees and matching against other MS(n) data. As such MetiTree contains much functionality that will make the difficult task of identifying unknown metabolites much easier. AVAILABILITY: MetiTree is accessible at http://www.MetiTree.nl. The source code is available at https://github.com/NetherlandsMetabolomicsCentre/metitree/wiki.

The Optimal Treatment for Partial Thickness Burns: A Cost-Utility Analysis of Skin Allograft vs. Topical Silver Dressings.

INTRODUCTION: Partial thickness burns not undergoing surgical excision are treated with topical silver products including silver sulfadiazine (SSD) and Mepilex Ag. Skin allograft is a more costly alternative that acts as definitive wound coverage until autogenous epithelialization. Economic constraints and the movement toward value-based care demand cost and outcome justification prior to adopting more costly products. METHODS: A cost-utility analysis was performed comparing skin allograft to SSD and Mepilex Ag using decision tree analysis. The base case modeled a superficial partial thickness 20% total body surface area burn. Utilities were derived from expert opinion on the basis of personal experience. Costs were derived from 2019 Medicare payments. Quality adjusted life years were calculated using rollback method assuming standard life expectancies in the United States. Probabilistic sensitivity analysis was performed to asses model robustness. RESULTS: The incremental costs of skin allograft to Mepilex Ag and SSD were $907.71 and $1257.86, respectively. The incremental quality adjusted life year (QALY) gains from allograft over Mepilex Ag and SSD were 0.011 and 0.016. This yielded an incremental cost-utility ratio for allograft vs. Mepilex Ag of $84,189.29/QALY compared with an incremental cost-utility ratio of $79,684.63/QALY for allograft vs. SSD. Assuming willingness-to-pay thresholds of $100,000/QALY, probabilistic sensitivity analysis demonstrated that allograft was cost effective to Mepilex Ag in 62.1% of scenarios, and cost effective to SSD in 64.9% of simulations. CONCLUSION: Skin allograft showed greater QALYs compared with topical silver dressings at a higher cost. Depending on willingness-to-pay thresholds, skin allograft may be a considered a cost-effective treatment of partial-thickness burns.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

Donor-site preferences in women during autologous skin grafting.

BACKGROUND: Autologous split-thickness skin grafting has been proven to provide the best cosmetic and functional outcome after cutaneous burn injuries and thus is the standard of care. Clinical observations have shown that female burn patients frequently have greater difficulty choosing a donor site than do male burn patients. However, there is a lack of data characterizing donor-site preferences among women with burns. METHODS: The purpose of this study was to examine donor-site preferences among women using an online survey that included 356 responders between January 4, 2012, and April 4, 2012. RESULTS: This study found that there was a preference for posterior donor sites, with lower back, left buttock, and left posterior thigh being the most preferred sites. The least preferred locations were the right anterior upper arm, any aspect of the forearms, and the chest. Those surveyed and reporting a higher education level or concerns with scarring were least likely to choose anterior locations. Age, concern for color changes, and prior surgery or grafting had no statistically significant effect on donor-site preference. CONCLUSION: Given these strong preferences among female patients, posterior donor sites should be considered and discussed as compared with the current standard of using lateral or anterior thigh donor sites.

Cost-effectiveness comparison between topical silver sulfadiazine and enclosed silver dressing for partial-thickness burn treatment.

The standard treatment of partial-thickness burns includes topical silver products such as silver sulfadiazine (SSD) cream and enclosed dressings including silver-impregnated foam (Mepilex Ag; Molnlycke Health Care, Gothenburg, Sweden) and silver-laden sheets (Aquacel Ag; ConvaTec, Skillman, NJ). The current state of health care is limited by resources, with an emphasis on evidence-based outcomes and cost-effective treatments. This study includes a decision analysis with an incremental cost-utility ratio comparing enclosed silver dressings with SSD in partial-thickness burn patients with TBSA less than 20%. A comprehensive literature review was conducted to identify clinically relevant health states in partial-thickness burn patients. These health states include successful healing, infection, and noninfected delayed healing requiring either surgery or conservative management. The probabilities of these health states were combined with Medicare CPT reimbursement codes (cost) and patient-derived utilities to fit into the decision model. Utilities were obtained using a visual analog scale during patient interviews. Expected cost and quality-adjusted life years (QALYs) were calculated using the roll-back method. The incremental cost-utility ratio for enclosed silver dressing relative to SSD was $40,167.99/QALY. One-way sensitivity analysis of complication rates confirmed robustness of the model. Assuming a maximum willingness to pay $50,000/QALY, the complication rate for SSD must be 22% or higher for enclosed silver dressing to be cost effective. By varying complication rates for SSD and enclosed silver dressings, the two-way sensitivity analysis demonstrated the cost effectiveness of using enclosed silver dressing at the majority of complication rates for both treatment modalities. Enclosed silver dressings are a cost-effective means of treating partial thickness burns.

The usefulness of patient-reported measures for clinical practice.

BACKGROUND: The authors assessed the diagnostic potential of commonly used patient-reported measures, namely, the Boston Carpal Tunnel Questionnaire (function and symptom severity), QuickDASH (a shortened version of the Disabilities of the Arm, Shoulder and Hand questionnaire), and the Short Form-8. METHODS: Measure scores were extracted retrospectively from the records of 262 patients (397 hands) and compared using analysis of variance to determine statistical differences among diagnoses assigned by the same surgeon at the time of visit. Patients were grouped into one of two diagnostic groups: those with Dupuytren disease and those with carpal tunnel, osteoarthritis, and tenosynovitis conditions. Logistic regression analysis was performed, and a receiver operating characteristic curve was used in data analysis. RESULTS: Analysis of variance showed statistical differences among the five diagnoses for each patient-reported measure. Results showed that Dupuytren disease was significantly different from the other diagnoses. Carpal tunnel, osteoarthritis, and tenosynovitis conditions were statistically associated with higher Boston Carpal Tunnel Questionnaire function and symptom severity and QuickDASH scores compared with Dupuytren disease. Lower physical and mental summary Short Form-8 scores were associated with the carpal tunnel, osteoarthritis, and tenosynovitis conditions. QuickDASH scores of 25 or higher and Boston Carpal Tunnel Questionnaire symptom severity scores and function scores of 2.5 or higher and of 2 or higher, respectively, are the best patient-reported measure threshold values for distinguishing between the two diagnostic groups. CONCLUSIONS: The QuickDASH and Boston Carpal Tunnel Questionnaire patient-reported measures have diagnostic potential. Establishing threshold values for predicting a diagnostic group may prove to be a useful tool for referring providers. CLINICAL QUESTION/LEVEL OF EVIDENCE: Diagnostic, IV.

Comparing five alternative methods of breast reconstruction surgery: a cost-effectiveness analysis.

BACKGROUND: The purpose of this study was to assess the cost-effectiveness of five standardized procedures for breast reconstruction to delineate the best reconstructive approach in postmastectomy patients in the settings of nonirradiated and irradiated chest walls. METHODS: A decision tree was used to model five breast reconstruction procedures from the provider perspective to evaluate cost-effectiveness. Procedures included autologous flaps with pedicled tissue, autologous flaps with free tissue, latissimus dorsi flaps with breast implants, expanders with implant exchange, and immediate implant placement. All methods were compared with a "do-nothing" alternative. Data for model parameters were collected through a systematic review, and patient health utilities were calculated from an ad hoc survey of reconstructive surgeons. Results were measured in cost (2011 U.S. dollars) per quality-adjusted life-year. Univariate sensitivity analyses and Bayesian multivariate probabilistic sensitivity analysis were conducted. RESULTS: Pedicled autologous tissue and free autologous tissue reconstruction were cost-effective compared with the do-nothing alternative. Pedicled autologous tissue was the slightly more cost-effective of the two. The other procedures were not found to be cost-effective. The results were robust to a number of sensitivity analyses, although the margin between pedicled and free autologous tissue reconstruction is small and affected by some parameter values. CONCLUSIONS: Autologous pedicled tissue was slightly more cost-effective than free tissue reconstruction in irradiated and nonirradiated patients. Implant-based techniques were not cost-effective. This is in agreement with the growing trend at academic institutions to encourage autologous tissue reconstruction because of its natural recreation of the breast contour, suppleness, and resiliency in the setting of irradiated recipient beds.

A comparison of acellular dermal matrix to autologous dermal flaps in single-stage, implant-based immediate breast reconstruction: a cost-effectiveness analysis.

BACKGROUND: The use of acellular dermal matrix has allowed for single-stage immediate breast reconstruction after mastectomy at a significantly decreased cost compared with two-stage expander/implant reconstruction. The use of a pedicled autologous dermal flap in the same fashion as acellular dermal matrix in women with larger, ptotic breasts has also allowed for single-stage immediate breast reconstruction with similarly low complication rates and without the added procedural cost of using acellular dermal matrix. There have been no prior studies evaluating whether the added procedural cost for acellular dermal matrix is cost-effective relative to using an autologous dermal flap in single-stage immediate breast reconstruction following mastectomy. METHODS: A comprehensive literature review was conducted to identify published complication rates for single-stage, implant-based immediate breast reconstruction using either acellular dermal matrix or an autologous dermal flap. The probabilities of the most common complications were combined with Medicare Current Procedural Terminology reimbursement codes and expert utility estimates to fit into a decision model to evaluate the cost-effectiveness of acellular dermal matrix. RESULTS: : The decision model revealed a baseline cost difference of $261.72 and a 0.001 increase in the quality-adjusted life years when using acellular dermal matrix, yielding an incremental cost-utility ratio of $261,720 per quality-adjusted life year. Sensitivity analysis showed that acellular dermal matrix was not cost-effective when the complication rate for autologous dermal flaps was below 20 percent. CONCLUSIONS: The authors' study demonstrates that acellular dermal matrix is not a cost-effective technology in patients who can have an autologous dermal flap in single-stage immediate breast reconstruction.

A comparison of free autologous breast reconstruction with and without the use of laser-assisted indocyanine green angiography: a cost-effectiveness analysis.

BACKGROUND: Laser-assisted indocyanine green angiography is a U.S. Food and Drug Administration-approved technology used to assess tissue viability and perfusion. Its use in plastic and reconstructive surgery to assess flap perfusion in autologous breast reconstruction is relatively new. There have been no previous studies evaluating the cost-effectiveness of this new technology compared with the current practice of clinical judgment in evaluating tissue perfusion and viability in free autologous breast reconstruction in patients who have undergone mastectomy. METHODS: A comprehensive literature review was performed to identify the complication rate of the most common complications with and without laser-assisted indocyanine green angiography in free autologous breast reconstruction after mastectomy. These probabilities were combined with Medicare Current Procedural Terminology provider reimbursement codes (cost) and utility estimates for common complications from a survey of 10 plastic surgeons to fit into a decision model to evaluate the cost-effectiveness of laser-assisted indocyanine green angiography. RESULTS: The decision model revealed a baseline cost difference of $773.66 and a 0.22 difference in the quality-adjusted life-years, yielding an incremental cost-utility ratio of $3516.64 per quality-adjusted life year favoring laser-assisted indocyanine green angiography. Sensitivity analysis showed that using laser-assisted indocyanine green angiography was more cost-effective when the complication rate without using laser-assisted indocyanine green angiography (clinical judgment alone) was 4 percent or higher. CONCLUSIONS: The authors' study demonstrates that laser-assisted indocyanine green angiography is a cost-effective technology under the most stringent acceptable thresholds when used in immediate free autologous breast reconstruction.

A review of lasers and light sources in the treatment of acne vulgaris.

There are various treatment modalities for acne vulgaris including topical and oral therapy as well as microdermabrasion and chemical peels. Recently, there has been an emergence of novel laser and light sources as a means for treating acne vulgaris. This article will review the advances of laser and light sources in the treatment of acne vulgaris.

An assessment of traditional and novel therapies for cellulite.

There are numerous treatments for cellulite including topical, surgical, laser and other therapies. Many of these treatments are expensive. Part of the difficulty in treating cellulite arises from our incomplete understanding of this phenomenon. As noted previously in this journal, there is no consensus as to the etiology of cellulite. This article will focus on both traditional and novel treatments for cellulite and assess their efficacy based on the scientific literature.