TMEM41B Is a Pan-flavivirus Host Factor.

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

Single-cell mutation analysis of clonal evolution in myeloid malignancies.

Myeloid malignancies, including acute myeloid leukaemia (AML), arise from the expansion of haematopoietic stem and progenitor cells that acquire somatic mutations. Bulk molecular profiling has suggested that mutations are acquired in a stepwise fashion: mutant genes with high variant allele frequencies appear early in leukaemogenesis, and mutations with lower variant allele frequencies are thought to be acquired later1-3. Although bulk sequencing can provide information about leukaemia biology and prognosis, it cannot distinguish which mutations occur in the same clone(s), accurately measure clonal complexity, or definitively elucidate the order of mutations. To delineate the clonal framework of myeloid malignancies, we performed single-cell mutational profiling on 146 samples from 123 patients. Here we show that AML is dominated by a small number of clones, which frequently harbour co-occurring mutations in epigenetic regulators. Conversely, mutations in signalling genes often occur more than once in distinct subclones, consistent with increasing clonal diversity. We mapped clonal trajectories for each sample and uncovered combinations of mutations that synergized to promote clonal expansion and dominance. Finally, we combined protein expression with mutational analysis to map somatic genotype and clonal architecture with immunophenotype. Our findings provide insights into the pathogenesis of myeloid transformation and how clonal complexity evolves with disease progression.

Molecular predictors of immunophenotypic measurable residual disease clearance in acute myeloid leukemia.

Measurable residual disease (MRD) is a powerful prognostic factor in acute myeloid leukemia (AML). However, pre-treatment molecular predictors of immunophenotypic MRD clearance remain unclear. We analyzed a dataset of 211 patients with pre-treatment next-generation sequencing who received induction chemotherapy and had MRD assessed by serial immunophenotypic monitoring after induction, subsequent therapy, and allogeneic stem cell transplant (allo-SCT). Induction chemotherapy led to MRD- remission, MRD+ remission, and persistent disease in 35%, 27%, and 38% of patients, respectively. With subsequent therapy, 34% of patients with MRD+ and 26% of patients with persistent disease converted to MRD-. Mutations in CEBPA, NRAS, KRAS, and NPM1 predicted high rates of MRD- remission, while mutations in TP53, SF3B1, ASXL1, and RUNX1 and karyotypic abnormalities including inv (3), monosomy 5 or 7 predicted low rates of MRD- remission. Patients with fewer individual clones were more likely to achieve MRD- remission. Among 132 patients who underwent allo-SCT, outcomes were favorable whether patients achieved early MRD- after induction or later MRD- after subsequent therapy prior to allo-SCT. As MRD conversion with chemotherapy prior to allo-SCT is rarely achieved in patients with specific baseline mutational patterns and high clone numbers, upfront inclusion of these patients into clinical trials should be considered.

Outcomes of Esophagogastric Cancer Surgery During Eight Years of Surgical Auditing by the Dutch Upper Gastrointestinal Cancer Audit (DUCA).

OBJECTIVE: To evaluate changes in treatment and outcomes of esophagogastric cancer surgery after introduction of the DUCA. In addition, the presence of risk-averse behavior was assessed. SUMMARY OF BACKGROUND DATA: Clinical auditing is seen as an important quality improvement tool; however, its long-term efficacy remains largely unknown. In addition, critics claim that enhancements result from risk-averse behavior rather than positive effects of auditing. METHODS: DUCA data were used from registration start (1-1-2011) until 31-12-2018. Trends in patient, tumor, hospital and treatment characteristics were univariably assessed. Trends in short-term outcomes were investigated using multilevel multivariable logistic regression. Presence of risk aversion was described by the corrected proportion of patients undergoing surgery, using data from the Netherlands Cancer Registry. To evaluate the impact of centralization on time trends identified, the association between hospital volume and outcomes was investigated. RESULTS: This study included 6172 patients with esophageal and 3,690 with gastric cancer who underwent surgery. Pathological outcomes (lymph node yield, radicality) improved and futile surgery decreased over the years. In-hospital/30-day mortality decreased for esophagectomy (4.2% to 2.5%) and for gastrectomy (7.1% to 4.3%). Reinterventions, (minor) complications and readmissions increased. Risk aversion appeared absent. Between 2011-2018, annual median hospital volumes increased from 38 to 53 for esophagectomy and from 14 to 29 for gastrectomy. Higher hospital volumes were associated with several improved outcomes measures. CONCLUSIONS: During 8 years of auditing, outcomes improved, with no signs of risk-averse behavior. These improvements occurred in parallel with centralization. Feedback on postoperative complications remains the focus of the DUCA.

Failure to Cure in Patients Undergoing Surgery for Gastric Cancer: A Nationwide Cohort Study.

BACKGROUND: This study aimed to describe the incidence of failure to cure (a composite outcome measure defined as surgery not meeting its initial aim), and the impact of hospital variation in the administration of neoadjuvant therapy on this outcome measure. METHODS: All patients in the Dutch Upper Gastrointestinal Cancer Audit undergoing curatively intended gastric cancer surgery in 2011-2019 were included. Failure to cure was defined as (1) 'open-close' surgery; (2) irradical surgery (R1/R2); or (3) 30-day/in-hospital mortality. Case-mix-corrected funnel plots, based on multivariable logistic regression analyses, investigated hospital variation. The impact of a hospital's tendency to administer neoadjuvant chemotherapy on the heterogeneity in failure to cure between hospitals was assessed based on median odds ratios and multilevel logistic regression analyses. RESULTS: Some 3862 patients from 28 hospitals were included. Failure to cure was noted in 22.3% (hospital variation: 14.5-34.8%). After case-mix correction, two hospitals had significantly higher-than-expected failure to cure rates, and one hospital had a lower-than-expected rate. The failure to cure rate was significantly higher in hospitals with a low tendency to administer neoadjuvant chemotherapy. Approximately 29% of hospital variation in failure to cure could be attributed to different hospital policies regarding neoadjuvant therapy. CONCLUSIONS: Failure to cure has an incidence of 22% in patients undergoing gastric cancer surgery. Higher failure to cure rates were seen in centers administering less neoadjuvant chemotherapy, which confirms the Dutch guideline recommendation on the administration of neoadjuvant chemotherapy. Failure to cure provides short loop feedback and can be used as a quality indicator in surgical audits.

Controllable Enhancement of p-Wave Superconductivity via Magnetic Coupling to a Conventional Superconductor.

Unconventional superconductors are of high interest due to their rich physics, a topical example being topological edge states associated with p-wave superconductivity. A practical obstacle in studying such systems is the very low critical temperature T_{c} that is required to realize a p-wave superconducting phase in a material. We predict that the T_{c} of an intrinsic p-wave superconductor can be significantly enhanced by coupling to a conventional s-wave or d-wave superconductor with a higher critical temperature via an atomically thin ferromagnetic (F) layer. We show that this T_{c} boost is tunable via the direction of the magnetization in F. Moreover, we show that the enhancement in T_{c} can also be achieved using the Zeeman effect of an external magnetic field. Our findings provide a way to increase T_{c} in p-wave superconductors in a controllable way and make the exotic physics associated with such materials more easily accessible experimentally.

Reporting National Outcomes After Esophagectomy and Gastrectomy According to the Esophageal Complications Consensus Group (ECCG).

OBJECTIVE: This nation-wide population-based study aimed to report postoperative morbidity and mortality after esophagectomy and gastrectomy in the Netherlands according to the definitions of the Esophagectomy Complications Consensus Group (ECCG). BACKGROUND: To standardize international outcome reporting in esophageal surgery, the ECCG developed a standardized outcomes set. METHODS: For this national cohort study, all patients undergoing esophagectomy or gastrectomy for cancer between 2016 and 2017 were selected from the Dutch Upper gastrointestinal Cancer Audit. In a random sample of hospitals, data completeness and accuracy were validated by reabstraction of the data. The investigated outcomes in the present study were postoperative complications, major complications (Clavien-Dindo grade ≥III), and 30-day mortality, according to definitions of the ECCG. RESULTS: A total of 2545 patients from 22 hospitals were included. The completeness of the Dutch Upper gastrointestinal Cancer Audit was estimated at 99.8%. Data accuracy on different items was 94% to 100%. After esophagectomy, 1046 of 1617 patients (65%) had a postoperative complication including 468 patients (29%) with a major complication. Most common complications were pneumonia (21%), esophago-enteric leak from anastomosis, staple line or localized conduit necrosis (19%), and atrial dysrhythmia (15%). The 30-day mortality was 1.7%. After gastrectomy, 397 of 928 patients (42%) had a postoperative complication including 180 patients (19%) with a major complication. Most common complications were pneumonia (12%), esophago-enteric leak from anastomosis, staple line or localized conduit necrosis (9%), and acute delirium (5%). The 30-day mortality was 4.4%. CONCLUSIONS: Reporting complications according to the ECCG platform is feasible in the Netherlands and facilitates international benchmarking.

A National Cohort Study Evaluating the Association Between Short-term Outcomes and Long-term Survival After Esophageal and Gastric Cancer Surgery.

OBJECTIVE: The aim of this study was to investigate the association between short-term outcome indicators and long-term survival after esophagogastric resections. SUMMARY BACKGROUND DATA: Short-term outcome indicators are often used to compare performance between care providers. Some short-term outcome indicators concern the direct quality of care, that is, complications, others are used because they are expected to be associated with long-term outcomes. METHOD: For this national cohort study, all patients who underwent esophagectomy or gastrectomy for cancer with curative intent between 2011 and 2016 and were registered in the Dutch Upper gastrointestinal Cancer Audit were included. Primary outcome was conditional survival (under the condition of surviving the first postoperative 30 days and hospital admission). Cox regression modeling was used to study the independent association between "textbook outcome" with survival. "Textbook outcome," a composite quality indicator, was defined as a pathological complete resection with at least 15 retrieved lymph nodes, an uneventful postoperative course, and no hospital readmission. RESULTS: In total, 4414 and 2943 patients with esophageal or gastric cancer, respectively, were included. The 1-, 2-, and 3-year overall survival rates were 76%, 62%, and 54%, and 71%, 56%, and 49% for esophageal and gastric cancer, respectively. Textbook outcome was achieved in 33% and 35% of patients respectively. "Textbook outcome" was independently associated with longer conditional survival [hazard ratio: 0.75 (95% confidence interval, 0.68-0.84) and 0.69 (0.60-0.79), respectively]. CONCLUSION: This study showed that the short-term outcome indicator textbook outcome is associated with long-term overall survival and therefore may accentuate the importance of using these indicators in clinical audits.

Needs and perceptions regarding healthy eating among people at risk of food insecurity: a qualitative analysis.

BACKGROUND: Healthy eating behaviour is an essential determinant of overall health. This behaviour is generally poor among people at risk of experiencing food insecurity, which may be caused by many factors including perceived higher costs of healthy foods, financial stress, inadequate nutritional knowledge, and inadequate skills required for healthy food preparation. Few studies have examined how these factors influence eating behaviour among people at risk of experiencing food insecurity. We therefore aimed to gain a better understanding of the needs and perceptions regarding healthy eating in this target group. METHODS: We conducted a qualitative exploration grounded in data using inductive analyses with 10 participants at risk of experiencing food insecurity. The analysis using an inductive approach identified four core factors influencing eating behaviour: Health related topics; Social and cultural influences; Influences by the physical environment; and Financial influences. RESULTS: Overall, participants showed adequate nutrition knowledge. However, eating behaviour was strongly influenced by both social factors (e.g. child food preferences and cultural food habits), and physical environmental factors (e.g. temptations in the local food environment). Perceived barriers for healthy eating behaviour included poor mental health, financial stress, and high food prices. Participants had a generally conscious attitude towards their financial situation, reflected in their strategies to cope with a limited budget. Food insecurity was mostly mentioned in reference to the past or to others and not to participants' own current experiences. Participants were familiar with several existing resources to reduce food-related financial strain (e.g. debt assistance) and generally had a positive attitude towards these resources. An exception was the Food Bank, of which the food parcel content was not well appreciated. Proposed interventions to reduce food-related financial strain included distributing free meals, facilitating social contacts, increasing healthy food supply in the neighbourhood, and lowering prices of healthy foods. CONCLUSION: The insights from this study increase understanding of factors influencing eating behaviour of people at risk of food insecurity. Therefore, this study could inform future development of potential interventions aiming at helping people at risk of experiencing food insecurity to improve healthy eating, thereby decreasing the risk of diet-related diseases.

Design and Testing of a New Diatom-Based Index for Heavy Metal Pollution.

The Tinto and Odiel river basins (SW Spain) are known worldwide for their unique water characteristics. Such uniqueness is a consequence of their flow through the Iberian Pyrite Belt (an area rich in metal sulphides) and the mining activities in the basins. A process of sulphide oxidation occurs in this region, which acidifies the water and increases the amount of heavy metals in it. As a result, the rivers suffer the so-called "acid mine drainage" (AMD). Traditional biotic diatom-based indexes (IPS, IBD, EPI-D, etc.) do not take into account the pollution caused by AMD. The purpose of this paper is to develop a new diatom-based index which can serve as a useful and quick monitoring tool. Such tool must reflect the level of AMD while being user friendly. We present the development and validation of the ICM (Índice de Contaminación por Metales or Metal Pollution Index). ICM demonstrated to meet successfully the above criteria and, therefore, can assess water quality in the Tinto and Odiel Rivers. In addition, ICM was applied with satisfactory results in the Guadiamar River (SW Spain), which was subjected to AMD too. Thus, we propose to make use of it in any other basin with the same type of pollution.

For Debate: Personalized Health Care: As Exemplified by Home Sodium Measurements in a Child with Central Diabetes Insipidus and Impaired Thirst Perception.

BACKGROUND: We describe a 6-year old boy with central diabetes insipidus (CDI) caused by destruction of the pituitary gland due to treatment of an optical pathway glioma. He has been treated with chemotherapy and has had several debulking operations over the past years and consequently developed central hypocortisolism, hypothyroidism and CDI. The treatment of CDI was gravely complicated by an impaired thirst perception and compulsive drinking behavior. He was frequently seen at the ER or admitted due to dysregulation of fluid balance. METHODS: In order to provide better self-reliance, home point of care testing (POCT) sodium measurement was introduced. RESULTS: Realizing POCT sodium measurement resulted in a significant decrease of ER visits and clinical admissions due to dysregulation of fluid balance. CONCLUSION: This case is an example of personalized health care and has led to better self-reliance and quality of life.

Textbook Outcome: A Composite Measure for Quality of Elective Aneurysm Surgery.

OBJECTIVE: To investigate a new composite quality measurement, which comprises a desirable outcome for elective aneurysm surgery, called "Textbook Outcome" (TO). BACKGROUND: Single-quality indicators in vascular surgery are often not distinctive and insufficiently reflect the quality of care. METHODS: All patients undergoing elective abdominal aortic aneurysm repair, registered in the Dutch Surgical Aneurysm Audit between 2014 and 2015 were included. TO was defined as the percentage of patients who had abdominal aortic aneurysm-repair without intraoperative complications, postoperative surgical complications, reinterventions, prolonged hospital stay [endovascular aneurysm repair (EVAR) ≤4 d, open surgical repair (OSR) ≤10 d], readmissions, and postoperative mortality (≤30 d after surgery/at discharge). Case-mix adjusted TO rates were used to compare hospitals and to compare individual hospital results for different procedures. RESULTS: Five thousand one hundred seventy patients were included, of whom 4039 were treated with EVAR and 1131 with OSR. TO was achieved in 71% of EVAR and 53% of OSR. Important obstacles for achieving TO were a prolonged hospital stay, postoperative complications, and readmissions. Adjusted TO rates varied from 38% to 89% (EVAR) and from 0% to 97% (OSR) between individual hospitals. Hospitals with a high TO for OSR also had a high TO for EVAR; however, a high TO for EVAR did not implicate a high TO for OSR. CONCLUSIONS: TO generates additional information to evaluate the overall quality of the care of elective aneurysm surgery, which subsequently can be used by hospitals to improve the quality of their care.

Harmonization of Serum Thyroid-Stimulating Hormone Measurements Paves the Way for the Adoption of a More Uniform Reference Interval.

BACKGROUND: The IFCC Committee for Standardization of Thyroid Function Tests developed a global harmonization approach for thyroid-stimulating hormone measurements. It is based on a multiassay method comparison study with clinical serum samples and target setting with a robust factor analysis method. Here we describe the Phase IV method comparison and reference interval (RI) studies conducted with the objective to recalibrate the participating assays and demonstrate the proof-of-concept. METHODS: Fourteen manufacturers measured the harmonization and RI panel; 4 of them quantified the harmonization and first follow-up panel in parallel. All recalibrated their assays to the statistically inferred targets. For validation, we used desirable specifications from the biological variation for the bias and total error (TE). The RI measurements were done with the assays' current calibrators, but data were also reported after transformation to the new calibration status. We estimated the pre- and postrecalibration RIs with a nonparametric bootstrap procedure. RESULTS: After recalibration, 14 of 15 assays met the bias specification with 95% confidence; 8 assays complied with the TE specification. The CV of the assay means for the harmonization panel was reduced from 9.5% to 4.2%. The RI study showed improved uniformity after recalibration: the ranges (i.e., maximum differences) exhibited by the assay-specific 2.5th, 50th, and 97.5th percentile estimates were reduced from 0.27, 0.89, and 2.13 mIU/L to 0.12, 0.29, and 0.77 mIU/L. CONCLUSIONS: We showed that harmonization increased the agreement of results from the participating immunoassays, and may allow them to adopt a more uniform RI in the future.

Standardization of Free Thyroxine Measurements Allows the Adoption of a More Uniform Reference Interval.

BACKGROUND: The IFCC Committee for Standardization of Thyroid Function Tests intended to standardize free thyroxine (FT4) immunoassays. We developed a Système International d'Unités traceable conventional reference measurement procedure (RMP) based on equilibrium dialysis and mass spectrometry. We describe here the latest studies intended to recalibrate against the RMP and supply a proof of concept, which should allow continued standardization efforts. METHODS: We used the RMP to target the standardization and reference interval (RI) panels, which were also measured by 13 manufacturers. We validated the suitability of the recalibrated results to meet specifications for bias (3.3%) and total error (8.0%) determined from biological variation. However, because these specifications were stringent, we expanded them to 10% and 13%, respectively. The results for the RI panel were reported as if the assays were recalibrated. We estimated all but 1 RI using parametric statistical procedures and hypothesized that the RI determined by the RMP was suitable for use by the recalibrated assays. RESULTS: Twelve of 13 recalibrated assays had a bias, meeting the 10% specification with 95% confidence; for 7 assays, this applied even for the 3.3% specification. Only 1 assay met the 13% total error specification. Recalibration reduced the CV of the assay means for the standardization panel from 13% to 5%. The proof-of-concept study confirmed our hypothesis regarding the RI but within constraints. CONCLUSIONS: Recalibration to the RMP significantly reduced the FT4 immunoassays' bias, so that the RI determined by the RMP was suitable for common use within a margin of 12.5%.

The influence of a composite hospital volume on outcomes for gastric cancer surgery: A Dutch population-based study.

BACKGROUND: Volume-outcome associations for complex surgical procedures have motivated centralization of care worldwide. The aim of this study was to investigate the association between overall hospital experience with complex upper gastrointestinal (GI) cancer resections and outcomes after gastric cancer surgery. METHODS: Data on all patients (n = 4837) who underwent a resection for non metastatic invasive gastric cancer between 2005 and 2014 were obtained from the Netherlands Cancer Registry (NCR). Annual hospital volume categories were based on the combined volume of gastrectomies, esophagectomies, and pancreatectomies (composite hospital volume). Volume-outcome analyses were performed for lymph node yield, 30-day mortality, and overall survival. RESULTS: The proportion of gastric cancer resections performed in hospitals with an annual composite hospital volume of ≥40 upper GI cancer resections increased from 6% in 2005 to 80% in 2014. A higher composite hospital volume was univariably associated with a higher lymph node yield, lower 30-day mortality, and increased overall survival. Statistical significance was lost after adjusting for case mix. But, sub group analysis including only elderly patients (≥75 years) showed a significant association between composite hospital volume and 30-day mortality. CONCLUSION: In the Netherlands, an increasing proportion of gastric cancer resections is performed in hospitals with a high composite hospital volume of gastric, esophageal, and pancreatic cancer resections. Special attention is warranted to referral of elderly patients, as these patients might specifically benefit from this centralization.

Surgical treatment of childhood hepatoblastoma in the Netherlands (1990-2013).

BACKGROUND: Achievement of complete surgical resection plays a key role in the successful treatment of children with hepatoblastoma. The aim of this study is to assess the surgical outcomes after partial liver resections for hepatoblastoma, focusing on postoperative complications, resection margins, 30-day mortality, and long-term survival. METHOD: Chart reviews were carried out on all patients treated for hepatoblastoma in the Netherlands between 1990 and 2013. RESULTS: A total of 103 patients were included, of whom 94 underwent surgery. Partial hepatectomy was performed in 76 patients and 18 patients received a liver transplant as a primary procedure. In 42 of 73 (58 %) patients, one or more complications were reported. In 3 patients, information regarding complications was not available. Hemorrhage necessitating blood transfusion occurred in 33 (45 %) patients and 9 (12 %) patients developed biliary complications, of whom 8 needed one or more additional surgical interventions. Overall, 5-year disease-specific survival was 82, 92 % in the group of patients who underwent partial hepatectomy, and 77 % in the group of patients who underwent liver transplantation. CONCLUSIONS: Partial hepatectomy after chemotherapy in children with hepatoblastoma offers good chances of survival. This type of major surgery is associated with a high rate of surgical complications (58 %), which is not detrimental to survival.

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase.

Iron-dependent halogenases employ cis-halo-Fe(IV)-oxo (haloferryl) complexes to functionalize unactivated aliphatic carbon centers, a capability elusive to synthetic chemists. Halogenation requires (i) coordination of a halide anion (Cl(-) or Br(-)) to the enzyme's Fe(II) cofactor, (ii) coupled activation of O2 and decarboxylation of α-ketoglutarate to generate the haloferryl intermediate, (iii) abstraction of hydrogen (H•) from the substrate by the ferryl and (iv) transfer of the cis halogen as Cl• or Br• to the substrate radical. This enzymatic solution to an unsolved chemical challenge is potentially generalizable to installation of other functional groups, provided that the corresponding anions can support the four requisite steps. We show here that the wild-type halogenase SyrB2 can indeed direct aliphatic nitration and azidation reactions by the same chemical logic. The discovery and enhancement by mutagenesis of these previously unknown reaction types suggest unrecognized or untapped versatility in ferryl-mediated enzymatic C-H bond activation.

The Empower project - a new way of assessing and monitoring test comparability and stability.

BACKGROUND: Manufacturers and laboratories might benefit from using a modern integrated tool for quality management/assurance. The tool should not be confounded by commutability issues and focus on the intrinsic analytical quality and comparability of assays as performed in routine laboratories. In addition, it should enable monitoring of long-term stability of performance, with the possibility to quasi "real-time" remedial action. Therefore, we developed the "Empower" project. METHODS: The project comprises four pillars: (i) master comparisons with panels of frozen single-donation samples, (ii) monitoring of patient percentiles and (iii) internal quality control data, and (iv) conceptual and statistical education about analytical quality. In the pillars described here (i and ii), state-of-the-art as well as biologically derived specifications are used. RESULTS: In the 2014 master comparisons survey, 125 laboratories forming 8 peer groups participated. It showed not only good intrinsic analytical quality of assays but also assay biases/non-comparability. Although laboratory performance was mostly satisfactory, sometimes huge between-laboratory differences were observed. In patient percentile monitoring, currently, 100 laboratories participate with 182 devices. Particularly, laboratories with a high daily throughput and low patient population variation show a stable moving median in time with good between-instrument concordance. Shifts/drifts due to lot changes are sometimes revealed. There is evidence that outpatient medians mirror the calibration set-points shown in the master comparisons. CONCLUSIONS: The Empower project gives manufacturers and laboratories a realistic view on assay quality/comparability as well as stability of performance and/or the reasons for increased variation. Therefore, it is a modern tool for quality management/assurance toward improved patient care.

Self-sampling for analysis of respiratory viruses in a large-scale epidemiological study in Sweden.

Viral diagnosis of respiratory tract infections has so far required sampling by health professionals,hampering large-scale epidemiological studies of virus-specific disease outcomes. As part of a population-based, prospective study of work-related risk factors for transmission of viral infections (SWEDE-I), we developed a scheme for self-sampling with nasal swabs. Random selection from the gainfully employed population of a medium-sized town in central Sweden resulted in a study cohort of 2,237 men and women aged 25 to 63 years. From September 2011 through May 2012, the cohort reported all instances of respiratory tract infection or gastroenteritis and participants concomitantly sent self-sampled nasal swabs for analysis using regular mail. Diagnosis of 14 viruses was performed. A total of 1,843 samples were received. The week-wise average delay between disease on set and arrival of the specimens at the laboratory varied between four and six days, and the corresponding median delay was between 3.5 and six days. In line with previous community-based studies, picorna- and coronaviruses dominated in specimens obtained from the self-sampling scheme. The results of self-sampling were contrasted to those from contemporaneous routine clinical sampling, on the same age group, in the adjacent Stockholm county. Although higher proportions of positive samples for respiratory syncytial virus and influenza were observed in the clinical sampling scheme, estimations of seasonality for influenza A and picornaviruses derived from both schemes were similar. Our findings show that nasal self-sampling is feasible in large-scale surveillance of respiratory infections and opens new prospects for population based,virologically verified research on virus spread,burden of disease, and effects of environmental factors or interventions.

Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity.

Acute myeloid leukemia (AML) has a poor prognosis and a heterogeneous mutation landscape. Although common mutations are well-studied, little research has characterized how the sequence of mutations relates to clinical features. Using published, single-cell DNA sequencing data from three institutions, we compared clonal evolution patterns in AML to patient characteristics, disease phenotype, and outcomes. Mutation trees, which represent the order of select mutations, were created for 207 patients from targeted panel sequencing data using 1 639 162 cells, 823 mutations, and 275 samples. In 224 distinct orderings of mutated genes, mutations related to DNA methylation typically preceded those related to cell signaling, but signaling-first cases did occur, and had higher peripheral cell counts, increased signaling mutation homozygosity, and younger patient age. Serial sample analysis suggested that NPM1 and DNA methylation mutations provide an advantage to signaling mutations in AML. Interestingly, WT1 mutation evolution shared features with signaling mutations, such as WT1-early being proliferative and occurring in younger individuals, trends that remained in multivariable regression. Some mutation orderings had a worse prognosis, but this was mediated by unfavorable mutations, not mutation order. These findings add a dimension to the mutation landscape of AML, identifying uncommon patterns of leukemogenesis and shedding light on heterogeneous phenotypes.