Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor.

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.

Wound Bed Preparation 2024: Delphi Consensus on Foot Ulcer Management in Resource-Limited Settings.

GENERAL PURPOSE: To review a practical and scientifically sound application of the wound bed preparation model for communities without ideal resources. TARGET AUDIENCE: This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and registered nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant will:1. Summarize issues related to wound assessment.2. Identify a class of drugs for the treatment of type II diabetes mellitus that has been shown to improve glycemia, nephroprotection, and cardiovascular outcomes.3. Synthesize strategies for wound management, including treatment in resource-limited settings.4. Specify the target time for edge advancement in chronic, healable wounds.

Chronic wound management in low-resource settings deserves special attention. Rural or underresourced settings (ie, those with limited basic needs/healthcare supplies and inconsistent availability of interprofessional team members) may not have the capacity to apply or duplicate best practices from urban or abundantly-resourced settings. The authors linked world expertise to develop a practical and scientifically sound application of the wound bed preparation model for communities without ideal resources. A group of 41 wound experts from 15 countries reached a consensus on wound bed preparation in resource-limited settings. Each statement of 10 key concepts (32 substatements) reached more than 88% consensus. The consensus statements and rationales can guide clinical practice and research for practitioners in low-resource settings. These concepts should prompt ongoing innovation to improve patient outcomes and healthcare system efficiency for all persons with foot ulcers, especially persons with diabetes.

Wound Bed Preparation 2021.

GENERAL PURPOSE: To present the 2021 update of the Wound Bed Preparation paradigm. TARGET AUDIENCE: This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant will: 1. Apply wound assessment strategies. 2. Identify patient concerns about wound care. 3. Select management options for healable, nonhealable, and maintenance wounds.

Wound Bed Preparation is a paradigm to optimize chronic wound treatment. This holistic approach examines the treatment of the cause and patient-centered concerns to determine if a wound is healable, a maintenance wound, or nonhealable (palliative). For healable wounds (with adequate blood supply and a cause that can be corrected), moisture balance is indicated along with active debridement and control of local infection or abnormal inflammation. In maintenance and nonhealable wounds, the emphasis changes to patient comfort, relieving pain, controlling odor, preventing infection by decreasing bacteria on the wound surface, conservative debridement of slough, and moisture management including exudate control. In this fourth revision, the authors have reformulated the model into 10 statements. This article will focus on the literature in the last 5 years or new interpretations of older literature. This process is designed to facilitate knowledge translation in the clinical setting and improve patient outcomes at a lower cost to the healthcare system.

Diabetic foot ulcers: Part I. Pathophysiology and prevention.

Diabetes mellitus is a serious, life-long condition that is the sixth leading cause of death in North America. Dermatologists frequently encounter patients with diabetes mellitus. Up to 25% of patients with diabetes mellitus will develop diabetic foot ulcers. Foot ulcer patients have an increased risk of amputation and increased mortality rate. The high-risk diabetic foot can be identified with a simplified screening, and subsequent foot ulcers can be prevented. Early recognition of the high-risk foot and timely treatment will save legs and improve patients' quality of life. Peripheral arterial disease, neuropathy, deformity, previous amputation, and infection are the main factors contributing to the development of diabetic foot ulcers. Early recognition of the high-risk foot is imperative to decrease the rates of mortality and morbidity. An interprofessional approach (ie, physicians, nurses, and foot care specialists) is often needed to support patients' needs.

Diabetic foot ulcers: Part II. Management.

The management of diabetic foot ulcers can be optimized by using an interdisciplinary team approach addressing the correctable risk factors (ie, poor vascular supply, infection control and treatment, and plantar pressure redistribution) along with optimizing local wound care. Dermatologists can initiate diabetic foot care. The first step is recognizing that a loss of skin integrity (ie, a callus, blister, or ulcer) considerably increases the risk of preventable amputations. A holistic approach to wound assessment is required. Early detection and effective management of these ulcers can reduce complications, including preventable amputations and possible mortality.

The diploid genome sequence of an Asian individual.

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

Wound bed preparation 2014 update: management of critical colonization with a gentian violet and methylene blue absorbent antibacterial dressing and elevated levels of matrix metalloproteases with an ovine collagen extracellular matrix dressing.

Wound bed preparation (WBP) is a paradigm for holistic patient care that includes treatment of the cause along with patient-centered concerns before optimizing the components of local wound care (debridement, infection/inflammation, moisture balance, and, when required, the edge effect). This review incorporates a methylene blue and gentian violet bound foam dressing for critical colonization and an ovine collagen extracellular matrix dressing for reduction of elevated levels of matrix metalloproteases into the WBP paradigm.

Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay.

We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.

HER3, p95HER2, and HER2 protein expression levels define multiple subtypes of HER2-positive metastatic breast cancer.

Trastuzumab is effective in the treatment of HER2/neu over-expressing breast cancer, but not all patients benefit from it. In vitro data suggest a role for HER3 in the initiation of signaling activity involving the AKT­mTOR pathway leading to trastuzumab insensitivity. We sought to investigate the potential of HER3 alone and in the context of p95HER2 (p95), a trastuzumab resistance marker, as biomarkers of trastuzumab escape. Using the VeraTag® assay platform, we developed a dual antibody proximity-based assay for the precise quantitation of HER3 total protein (H3T) from formalin-fixed paraffin-embedded (FFPE) breast tumors. We then measured H3T in 89 patients with metastatic breast cancer treated with trastuzumab-based therapy, and correlated the results with progression-free survival and overall survival using Kaplan­Meier and decision tree analyses that also included HER2 total (H2T) and p95 expression levels. Within the sub-population of patients that over-expressed HER2, high levels of HER3 and/or p95 protein expression were significantly associated with poor clinical outcomes on trastuzumab-based therapy. Based on quantitative H3T, p95, and H2T measurements, multiple subtypes of HER2-positive breast cancer were identified that differ in their outcome following trastuzumab therapy. These data suggest that HER3 and p95 are informative biomarkers of clinical outcomes on trastuzumab therapy, and that multiple subtypes of HER2-positive breast cancer may be defined by quantitative measurements of H3T, p95, and H2T.

Single borrowers versus coborrowers in the pandemic: Mortgage forbearance take-up and performance.

Early in the COVID-19 pandemic, policymakers initiated a forbearance program-that allowed borrowers to pause their mortgage payments-to prevent a large-scale foreclosure crisis. Using detailed loan-level performance data, we study forbearance take-up and subsequent performance among two distinct group of mortgage borrowers: single borrowers versus coborrowers. We provide stylized facts that compared to coborrowers, single borrowers have lower incomes, lower credit scores, higher loan-to-value ratios and higher debt-to-income ratios and are hence more financially vulnerable. We find that single borrowers are more apt to elect forbearance, all else constant. We further find that forbearance had a stronger positive effect on helping single borrowers avoid or recover and exit delinquency than coborrowers.

Identification of a Novel NRG1 Fusion with Targeted Therapeutic Implications in Locally Advanced Pediatric Cholangiocarcinoma: A Case Report.

Locally advanced cholangiocarcinoma has a poor prognosis, with long-term survival only for patients where complete surgical resection is achieved. Median overall survival with chemotherapy alone is less than 1 year. Novel strategies combining conventional chemotherapy and radiotherapy followed by targeted agents can lead to durable treatment responses and are applicable to cholangiocarcinoma management. Pediatric cholangiocarcinoma is exceedingly rare, with an estimate of 15-22 cases reported in the last 40 years. As such, no standard therapeutic regimen exists. We present a case of a 16-year-old previously healthy patient with unresectable cholangiocarcinoma whose tumor genetic sequencing revealed a novel, actionable neuregulin-1 (NRG1) gene translocation. The patient underwent standard systemic chemotherapy with gemcitabine and cisplatin followed by hypofractionated proton radiation therapy for local control. The patient then started an oral pan-ERBB (erythroblastic B receptor tyrosine kinases including ErbB1/EGFR, ErbB2/HER2, ErbB3/HER3, ErbB4/HER4) family inhibitor as a maintenance medication, remaining with stable disease and excellent quality of life for over 2 years. This case highlights a novel NRG1 fusion in a rare clinical entity that provided an opportunity to utilize a multimodal therapeutic strategy in the pediatric setting.

Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay.

We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.

A consensus approach to wound care in epidermolysis bullosa.

BACKGROUND: Wound care is the cornerstone of treatment for patients with epidermolysis bullosa (EB); however, there are currently no guidelines to help practitioners care for these patients. OBJECTIVES: The objective of this study was to generate a list of recommendations that will enable practitioners to better care for patients with EB. METHODS: An expert panel generated a list of recommendations based on the best evidence available. The recommendations were translated into a survey, and sent to other EB experts to generate consensus using an online-based modified Delphi method. The list was refined and grouped into themes and specific recommendations. RESULTS: There were 15 respondents (45% response rate), with significant experience in the EB field (>10 years [67%]). Respondents included physicians (67%), nurses (17%), and allied health professionals (7%). There was more than 85% agreement for all the proposed items. These were further refined and grouped into 5 main themes (assessment and management of factors that impair healing, patient-centered concerns, local wound care, development of an individualized care plan, and organizational support) and 17 specific recommendations. LIMITATIONS: There is a paucity of scientific evidence with most recommendations based on expert opinion. CONCLUSIONS: These recommendations will provide practitioners with a framework for caring for these patients. Additional scientific research including effectiveness studies for everyday practice and expert consensus, may further refine these recommendations.

A global perspective of Wound Care©.

Chronic wounds, particularly foot ulcers in persons with diabetes, have become a global pandemic in the developing and developed world. The authors propose a longitudinal interactive education program (knowledge, skills, and attitudes) linked to interprofessional centers of excellence to reduce the incidence of foot ulcers and unnecessary lower-limb amputations. This model is generalizable to other skin and wound conditions.

Screening for the high-risk diabetic foot: a 60-second tool (2012).

People with diabetes mellitus will develop lower-limb complications, such as neuropathy, peripheral vascular disease, foot ulcers, and lower-leg amputations. Resources to control elevated hemoglobin A1c and blood pressure, along with the standardized approach using the 60-second tool (2012), can detect the high-risk diabetic foot and help prevent complications.

A Decade of GigaScience: Women in Science: Past, Present, and Future.

Over the last decade, women have made decisive advances in increasing equality in science, technology, engineering, and medicine (STEM), but they still do not rival that of men. Many mechanisms to reduce gender discrimination have been addressed; however, little to nothing has been done to tackle the differences in the amount of time women spend on responsibilities at home. This has never been more apparent than during the COVID-19 pandemic. After a decade of advances promoting women, the last two years have seen these advances halted, and the long-term implications for women in STEM will be substantial. Moving forward, career advancement and funding mechanisms need to be adjusted to not just help women catch up, but to become a permanent support mechanism for women in the workplace. The higher amount of responsibilities at home and lack of support for women is not reserved for times of international upheaval: it has just become more apparent.

A Decade of GigaScience: Milestones in Open Science.

Open Science has gained momentum over the past decade, and embracing that, GigaScience, from its launch a decade ago has aimed at pushing scientific publishing beyond just making articles open access toward making the entire research process open and available as an embedded part of the publishing process. Before the journal's launch in July 2012, the editors aimed to make publishing more than a narrative presentation of work already done into a fully open process. Major milestones include creating our own data repository, embracing FAIR principles, promoting and integrating preprints, and working with other platforms to contribute to a 21st century publishing infrastructure. Almost 10 years after GigaScience's launch, UNESCO published its Open Science Recommendations. With these in mind, looking back, we are happy to have contributed in various ways to UNESCO's aim to "foster a culture of Open Science and aligning incentives for Open Science" from the very beginning, and, more, to use those recommendations to guide our path into the future: to truly embrace the full spectrum of information, tools, and access to Open Science for all participants in scientific endeavours.

Quantitative assays for the measurement of HER1-HER2 heterodimerization and phosphorylation in cell lines and breast tumors: applications for diagnostics and targeted drug mechanism of action.

INTRODUCTION: Ligand-bound and phosphorylated ErbB/HER heterodimers are potent signaling forms of this receptor family, and quantitative measurements of these active receptors may be predictive of patient response to targeted therapies. Using VeraTag technology, we developed and characterized quantitative assays measuring epidermal growth factor (EGF)-dependent increases in activated HER receptors in tumor cell line lysates and formalin-fixed, paraffin-embedded (FFPE) tumor sections. We demonstrated the ability of the assays to quantitatively measure changes in activated HER1 and HER2 receptor levels in cell lines following treatment with 2C4, erlotinib, and lapatinib. We utilized these assays to determine the prevalence and distribution of activated HER1, HER2, and HER1-HER2 heterodimers in 43 HER2-positive breast tumors. METHODS: Assays for activated HER1 and HER2 receptors in FFPE and cell lysate formats were developed using VeraTag technology, which requires the proximity of an antibody pair for light-dependent release of a fluorescently labeled tag, followed by capillary electrophoresis-based quantitation. RESULTS: Ligand-dependent and independent HER1-HER2 heterodimer levels measured by lysate and FFPE VeraTag assays trended with HER1 and HER2 expression levels in tumor cell lines, which was confirmed by co-immunoprecipitation. The formation of EGF-dependent HER1-HER2 heterodimers were inhibited by the HER2-targeted monoclonal antibody 2C4 and stabilized by the HER1 tyrosine kinase inhibitor (TKI) erlotinib. EGF-dependent HER1 and HER2 phosphorylation was inhibited by lapatinib and erlotinib. Further, we observed that dominant receptor signaling patterns may switch between HER1-HER1 and HER1-HER2, depending on drug mechanism of action and relative levels of HER receptors. In FFPE breast tumors that expressed both HER1 and HER2, HER1-HER2 heterodimers were detected in 25 to 50% of tumors, depending on detection method. The levels of activated phospho-HER1-HER2 heterodimers correlated with HER1 or HER2 levels in an analysis of 43 HER2-positive breast tumors. CONCLUSIONS: VeraTag lysate assays can be used as a tool for understanding the mechanism of action of targeted HER-family inhibitors in the preclinical setting, while VeraTag FFPE assays of activated HER receptors combined with total HER2 measurements (HERmark) in tumor samples may provide a more accurate prediction of clinical response to both HER1 and HER2 targeted therapies.

Early prevention of pressure ulcers among elderly patients admitted through emergency departments: a cost-effectiveness analysis.

STUDY OBJECTIVE: Every year, approximately 6.2 million hospital admissions through emergency departments (ED) involve elderly patients who are at risk of developing pressure ulcers. We evaluated the cost-effectiveness of pressure-redistribution foam mattresses on ED stretchers and beds for early prevention of pressure ulcers in elderly admitted ED patients. METHODS: Using a Markov model, we evaluated the incremental effectiveness (quality-adjusted life-days) and incremental cost (hospital and home care costs) between early prevention and current practice (with standard hospital mattresses) from a health care payer perspective during a 1-year time horizon. RESULTS: The projected incidence of ED-acquired pressure ulcers was 1.90% with current practice and 1.48% with early prevention, corresponding to a number needed to treat of 238 patients. The average upgrading cost from standard to pressure-redistribution mattresses was $0.30 per patient. Compared with current practice, early prevention was more effective, with 0.0015 quality-adjusted life-days gained, and less costly, with a mean cost saving of $32 per patient. If decisionmakers are willing to pay $50,000 per quality-adjusted life-year gained, early prevention was cost-effective even for short ED stay (ie, 1 hour), low hospital-acquired pressure ulcer risk (1% prevalence), and high unit price of pressure-redistribution mattresses ($3,775). Taking input uncertainty into account, early prevention was 81% likely to be cost-effective. Expected value-of-information estimates supported additional randomized controlled trials of pressure-redistribution mattresses to eliminate the remaining decision uncertainty. CONCLUSION: The economic evidence supports early prevention with pressure-redistribution foam mattresses in the ED. Early prevention is likely to improve health for elderly patients and save hospital costs.