Correction: Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups.

Chronic lymphocytic leukaemia (CLL) consists of two biologically and clinically distinct subtypes defined by the abundance of somatic hypermutation (SHM) affecting the Ig variable heavy-chain locus (IgHV). The molecular mechanisms underlying these subtypes are incompletely understood. Here, we present a comprehensive whole-genome sequencing analysis of somatically acquired genetic events from 46 CLL patients, including a systematic comparison of coding and non-coding single-nucleotide variants, copy number variants and structural variants, regions of kataegis and mutation signatures between IgHVmut and IgHVunmut subtypes. We demonstrate that one-quarter of non-coding mutations in regions of kataegis outside the Ig loci are located in genes relevant to CLL. We show that non-coding mutations in ATM may negatively impact on ATM expression and find non-coding and regulatory region mutations in TCL1A, and in IgHVunmut CLL in IKZF3, SAMHD1,PAX5 and BIRC3. Finally, we show that IgHVunmut CLL is dominated by coding mutations in driver genes and an aging signature, whereas IgHVmut CLL has a high incidence of promoter and enhancer mutations caused by aberrant activation-induced cytidine deaminase activity. Taken together, our data support the hypothesis that differences in clinical outcome and biological characteristics between the two subgroups might reflect differences in mutation distribution, incidence and distinct underlying mutagenic mechanisms.

Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups.

This corrects the article DOI: 10.1038/leu.2017.177.

Targeted deep sequencing reveals clinically relevant subclonal IgHV rearrangements in chronic lymphocytic leukemia.

The immunoglobulin heavy-chain variable region gene (IgHV) mutational status is considered the gold standard of prognostication in chronic lymphocytic leukemia (CLL) and is currently determined by Sanger sequencing that allows the analysis of the major clone. Using next-generation sequencing (NGS), we sequenced the IgHV gene from two independent cohorts: (A) 270 consecutive patient samples obtained at diagnosis and (B) 227 patients from the UK ARCTIC-AdMIRe clinical trials. Using complementary DNA from purified CD19+CD5+ cells, we demonstrate the presence of multiple rearrangements in independent experiments and showed that 24.4% of CLL patients express multiple productive clonally unrelated IgHV rearrangements. On the basis of IgHV-NGS subclonal profiles, we defined five different categories: patients with (a) multiple hypermutated (M) clones, (b) 1 M clone, (c) a mix of M-unmutated (UM) clones, (d) 1 UM clone and (e) multiple UM clones. In population A, IgHV-NGS classification stratified patients into five different subgroups with median treatment-free survival (TFS) of >280(a), 131(b), 94(c), 29(d), 15(e) months (P<0.0001) and a median OS of >397(a), 292(b), 196(c), 137(d) and 100(e) months (P<0.0001). In population B, the poor prognosis of multiple UM patients was confirmed with a median TFS of 2 months (P=0.0038). In conclusion, IgHV-NGS highlighted one quarter of CLL patients with multiple productive IgHV subclones and improves disease stratification and raises important questions concerning the pre-leukemic cellular origin of CLL.

Heavy-flavour and quarkonium production in the LHC era: from proton-proton to heavy-ion collisions.

This report reviews the study of open heavy-flavour and quarkonium production in high-energy hadronic collisions, as tools to investigate fundamental aspects of Quantum Chromodynamics, from the proton and nucleus structure at high energy to deconfinement and the properties of the Quark-Gluon Plasma. Emphasis is given to the lessons learnt from LHC Run 1 results, which are reviewed in a global picture with the results from SPS and RHIC at lower energies, as well as to the questions to be addressed in the future. The report covers heavy flavour and quarkonium production in proton-proton, proton-nucleus and nucleus-nucleus collisions. This includes discussion of the effects of hot and cold strongly interacting matter, quarkonium photoproduction in nucleus-nucleus collisions and perspectives on the study of heavy flavour and quarkonium with upgrades of existing experiments and new experiments. The report results from the activity of the SaporeGravis network of the I3 Hadron Physics programme of the European Union 7[Formula: see text] Framework Programme.

Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia.

Histone methyltransferases (HMTs) are important epigenetic regulators of gene transcription and are disrupted at the genomic level in a spectrum of human tumours including haematological malignancies. Using high-resolution single nucleotide polymorphism (SNP) arrays, we identified recurrent deletions of the SETD2 locus in 3% (8/261) of chronic lymphocytic leukaemia (CLL) patients. Further validation in two independent cohorts showed that SETD2 deletions were associated with loss of TP53, genomic complexity and chromothripsis. With next-generation sequencing we detected mutations of SETD2 in an additional 3.8% of patients (23/602). In most cases, SETD2 deletions or mutations were often observed as a clonal event and always as a mono-allelic lesion, leading to reduced mRNA expression in SETD2-disrupted cases. Patients with SETD2 abnormalities and wild-type TP53 and ATM from five clinical trials employing chemotherapy or chemo-immunotherapy had reduced progression-free and overall survival compared with cases wild type for all three genes. Consistent with its postulated role as a tumour suppressor, our data highlight SETD2 aberration as a recurrent, early loss-of-function event in CLL pathobiology linked to aggressive disease.

Healthy worker survivor analysis in an occupational cohort study of Dutch agricultural workers.

OBJECTIVES: High microbial exposures in farmers and agricultural workers are associated with less atopy. Although it has been speculated that healthy worker survival could be an explanation, this has not been studied so far. Therefore, we investigated the presence of healthy worker survival in a five-year follow-up study of an occupational cohort of Dutch farmers and agricultural industry (company) workers. METHODS: We compared baseline demographic characteristics, respiratory health, atopy and endotoxin exposure of 259 workers followed up with 124 workers lost to follow-up. Additionally, baseline health status of 31 participants who had changed to lower exposure jobs at follow-up was compared to those with similar or higher exposure jobs at follow-up. RESULTS: In general, no major healthy worker survival effect was found. Nonetheless, small differences were observed between subjects included in follow-up and those lost to follow-up. Those lost to follow-up were older, had a lower peak expiratory flow, and were less often raised on a farm. Company workers lost to follow-up with a farm childhood had more often self-reported allergy, but this was not observed for subjects with atopic sensitization or other respiratory symptoms. No differences were found for any of the studied characteristics in participants with lower exposure at follow-up compared to participants with similar or higher exposure at follow-up. CONCLUSIONS: No major healthy worker survival is present in this organic dust exposed cohort. Differences between participants lost to follow-up and participants included in follow-up with regard to health characteristics are small and unlikely to explain the previously reported inverse associations between endotoxin exposure and atopy.

Shifted T-cell polarisation after agricultural dust exposure in mice and men.

RATIONALE: A low prevalence of asthma and atopy has been shown in farmers and agricultural workers. However, in these workers, a higher prevalence of respiratory symptoms has been reported, in which T helper 1 (Th1) and/or Th17 responses may play a role. AIM: We investigated the effect of exposure to dust extracts (DEs) from different farms on airway inflammation and T-cell polarisation in a mouse model and assessed T-cell polarisation in agricultural workers from the same farms. METHODS: DEs were prepared from settled dust collected at cattle and pig farms and bulb and onion industries. Mice were exposed to phosphate-buffered saline (PBS), DEs, house dust mite (HDM) or HDM+DE via nasal instillation, four times per week during 5 weeks. Hyperresponsiveness, airway inflammation, IgE levels and T-cell polarisation were assessed. Th-cell and T cytotoxic (Tc)-cell subsets were investigated in peripheral blood samples from 33 agricultural workers and 9 non-exposed controls. RESULTS: DEs induced interleukin(IL)-17, IL-1ß and IL-6 in mouse lung homogenates. DE-exposed mice had more mixed inflammatory infiltrates in the lungs, and more neutrophils compared with PBS-exposed mice. DEs protected against the HDM-induced Th2 response and methacholine hyperresponsiveness. Interestingly, occupationally exposed humans had higher frequencies of Th cells spontaneously expressing IL-17 and interferon γ compared with controls. CONCLUSION: Chronic exposure to different types of farm dust induces a Th/Tc-17 inflammatory response in mice and agricultural workers. This may contribute to the low prevalence of Th2-related diseases but may constitute a risk for other chronic respiratory diseases.

Modeling problem-oriented clinical notes.

OBJECTIVES: To develop a model as a starting-point for developing a problem-oriented clinical notes application as a generic component of an Electronic Health Record (EHR). METHODS: We used the generic conceptualization of Weed's problem-oriented medical record (POMR) to link progress notes to problems, and the Subjective, Objective, Assessment, Plan (SOAP) headings to classify elements of these notes. Health Level 7 (HL7) Version 3 and Unified Modeling Language (UML) were used for modeling. We looked especially at the role of Conditions and Concerns, and how to model these to document clinical reasoning. RESULTS: We developed a generic HL7-based model for progress notes. In this model the specific clinical note has a condition as its reason. An assertion can be made about a condition. Any condition, observation or procedure can be a concern that has to be tracked. Utmost important is the relationship between constituting parts of a progress note and specially between progress notes by linking a progress note to conditions that are part of an earlier progress note. From this model a comprehensive hierarchical condition tree can be built. Several views, such as chronological, SOAP and condition-oriented, are possible. The clinical notes application is used in daily clinical practice. The model meets explicit design criteria and clinical needs. CONCLUSIONS: With the comprehensive HL7 standard it is possible to model and map progress notes using SOAP headings and POMR methodology. We have developed a generic, flexible and applicable paradigm by using acts for each assessment that refer to a condition (1), by separating conditions from concerns (2), and by an extensive use of the working list act (3).

IVF patients show three types of online behaviour.

BACKGROUND: The internet introduces new ways to deal with stress. However, it is unclear how its resources are used in everyday life. Using a web-based personal health record (PHR), we observed the patient's online behaviour and linked this to distress, theories on dealing with stress and demographics. METHODS: Between 2004 and 2007, all viewed web-pages were logged and categorized into 14 content types. Behavioural styles were elicited using factor analysis. These behavioural styles were subsequently correlated to data on demographics, coping mechanisms and distress from the female partner of the first 53 patient couples that used the PHR. RESULTS: One thousand and fifty patient couples viewed 588 887 web pages during their first treatment cycle. Factor analysis elicited three online behavioural styles explaining 66.9% of all variance in usage of the website: an 'individual information style', a 'generic information style' and a 'communication style'. The 'individual information style' correlated negatively to having paid employment (Spearman = -0.364, P = 0.007) and emotional coping mechanisms (Spearman = -0.305, P = 0.028). The 'communication style' correlated positively to having paid employment (Spearman = 0.318, P = 0.021) and anxiety (Spearman = 0.381, P = 0.005). CONCLUSIONS: IVF patients show three types of online behaviour. Only limited correlations exist between these styles and demographics, coping mechanisms or distress. When planning a website or portal for IVF patients, content should be adopted accordingly.

Estimating morbidity rates from electronic medical records in general practice. Evaluation of a grouping system.

OBJECTIVES: In this study, we evaluated the internal validity of EPICON, an application for grouping ICPC-coded diagnoses from electronic medical records into episodes of care. These episodes are used to estimate morbidity rates in general practice. METHODS: Morbidity rates based on EPICON were compared to a gold standard; i.e. the rates from the second Dutch National Survey of General Practice. We calculated the deviation from the gold standard for 677 prevalence and 681 incidence rates, based on the full dataset. Additionally, we examined the effect of case-based reasoning within EPICON using a comparison to a simple, not case-based method (EPI-0). Finally, we used a split sample procedure to evaluate the performance of EPICON. RESULTS: Morbidity rates that are based on EPICON deviate only slightly from the gold standard and show no systematic bias. The effect of case-based reasoning within EPICON is evident. The addition of case-based reasoning to the grouping system reduced both systematic and random error. Although the morbidity rates that are based on the split sample procedure show no systematic bias, they do deviate more from the gold standard than morbidity rates for the full dataset. CONCLUSIONS: Results from this study indicate that the internal validity of EPICON is adequate. Assuming that the standard is gold, EPICON provides valid outcomes for this study population. EPICON seems useful for registries in general practice for the purpose of estimating morbidity rates.

Impact of a spirometry expert system on general practitioners' decision making.

The present study assessed the impact of computerised spirometry interpretation expert support on the diagnostic achievements of general practitioners (GPs), and on GPs' decision making in diagnosing chronic respiratory disease. A cluster-randomised controlled trial was performed in 78 GPs who each completed 10 standardised paper case descriptions. Intervention consisted of support for GPs' spirometry interpretation either by an expert system (expert support group) or by sham information (control group). Agreement of GPs' diagnoses was compared with an expert panel judgement, which served as the primary outcome. Secondary outcomes were: additional diagnostic test rates; width of differential diagnosis; certainty of diagnosis; estimated severity of disease; referral rate; and medication or nonmedication changes. Effects were expressed as odds ratios (ORs) with 95% confidence intervals (CIs). There were no differences between the expert support and control groups in the agreement between GPs and expert panel diagnosis of chronic obstructive pulmonary disease (OR (95% CI) 1.08 (0.70-1.66)), asthma (1.13 (0.70-1.80)), and absence of respiratory disease (1.32 (0.61-2.86)). A higher rate of additional diagnostic tests was observed in the expert support group (2.5 (1.17-5.35)). Computerised spirometry expert support had no detectable benefit on general practitioners' diagnostic achievements and the decision-making process when diagnosing chronic respiratory disease.

[Clinical knowledge cannot only be acquired in practice]. / Klinische kennis kan niet alleen in de praktijk verkregen worden.

Methodological training is necessary in order to cope with the ever-growing volume of knowledge by clinical experience. This training involves ways of reasoning and collecting relevant evidence. This type of instruction should be given in concurrence with the first exercises in clinical reasoning. Such instruction should focus on acquisition of the ability to clearly substantiate decisions made during medical practice.

Patient-centred care: using online personal medical records in IVF practice.

BACKGROUND: Generic patient-accessible medical records have shown promise in enhancing patient-centred care for patients with chronic diseases. We sought to design, implement and evaluate a patient-accessible medical record specifically for patients undergoing a course of assisted reproduction (IVF or ICSI). METHODS: The personal medical record (PMR) database was developed using three formative evaluation steps, and its user-experience was evaluated through a cross-sectional study. Fifty-four patient-couples receiving an IVF or ICSI treatment in our hospital were granted access to the PMR. Main outcomes concern the usage of the PMR, the perceived usefulness of its functions and user attitudes towards privacy and financial issues. RESULTS: The PMR consists of 15 major functions that can be classified into personal information, general information and communication functions. Fifty-three patient-couples accessed the website and 51 couples filled out the evaluation questionnaire. They rated most functions as useful and preferred personalized to general functions. The results also show that some functions require further development. Patients using the PMR have little concerns regarding privacy, and 76% are willing to pay for such a service in the future. CONCLUSIONS: The patients in this study frequently and intensively used the Internet-accessible PMR. This suggests that the PMR offers very useful functions from an IVF/ICSI patient's perspective.

EGOOZ: specifying the components of electronic patient record-related education.

OBJECTIVE: To determine whether educators consider electronic patient record (EPR)-related education necessary and if so, what subjects have to be taught more extensively in the future. METHODS: A list of possibly relevant subjects was determined from the literature. A questionnaire was designed which contained those subjects and the respondents were asked to indicate, for each subject, its competency level and required competency level in current teaching. Since the response rate was low a second questionnaire was developed to have the results of the analysis of the first questionnaire validated by a larger group of educators. RESULTS: In total 45 learning goals were identified from the literature. The questionnaire was sent to representatives of several disciplines: basic medical education, medical specializations, pharmacy, dentistry and nursing. The analysis of the first questionnaire resulted in nine subjects that needed more attention in the future. Because of the low response the needs could not be specified for the individual disciplines. This insight was obtained from a second questionnaire. The response to this questionnaire was high. From the analysis of the second questionnaire differences between views of educators involved in the training of GPs and educators involved in the training of other specializations were observed. CONCLUSION: Educators find EPR-related education important. There are different opinions about the phase in which EPR-related education should be given.

Measurement of branching fractions and charge asymmetries in B+/--->rho+/-pi0 and B+/--->rho0pi+/- decays, and search for B0-->rho0pi0.

We present measurements of branching fractions and charge asymmetries in B-meson decays to rho(+)pi(0), rho(0)pi(+), and rho(0)pi(0). The data sample comprises 89x10(6) Upsilon(4S)-->BBmacr; decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We find the charge-averaged branching fractions B(B+-->rho(+)pi(0))=[10.9+/-1.9(stat)+/-1.9(syst)]x10(-6) and B(B+-->rho(0)pi(+))=(9.5+/-1.1+/-0.9)x10(-6), and we set a 90% confidence-level upper limit B(B0-->rho(0)pi(0))<2.9x10(-6). We measure the charge asymmetries ACP(pi(0))(rho(+))=0.24+/-0.16+/-0.06 and ACP(pi(+))(rho(0))=-0.19+/-0.11+/-0.02.

Measurement of time-dependent CP asymmetries in B0-->D(*)+/-pi-/+ decays and constraints on sin(2beta+gamma).

We present a measurement of CP-violating asymmetries in fully reconstructed B0-->D(*)+/-pi-/+ decays in approximately 88 x 10(6) upsilon(4S)-->BBmacr; decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at SLAC. From a time-dependent maximum-likelihood fit we obtain the following for the CP-violating parameters: a=-0.022+/-0.038 (stat)+/-0.020 (syst), a*=-0.068+/-0.038 (stat)+/-0.020 (syst), c(lep)=+0.025+/-0.068 (stat)+/-0.033 (syst), and c*(lep)=+0.031+/-0.070 (stat)+/-0.033 (syst). Using other measurements and theoretical assumptions we interpret the results in terms of the angles of the Cabibbo-Kobayashi-Maskawa unitarity triangle, and find |sin((2beta+gamma)|>0.69 at 68% confidence level. We exclude the hypothesis of no CP violation [sin(2beta+gamma)=0] at 83% confidence level.

Measurement of time-dependent CP asymmetries and constraints on sin(2beta+gamma) with partial reconstruction of B0-->D*-/+pi+/- decays.

We present a measurement of time-dependent CP-violating asymmetries in decays of neutral B mesons to the final states D(*-/+)pi(+/-), using approximately 82x10(6) BBmacr; events recorded by the BABAR experiment at the PEP-II e(+)e(-) storage ring. Events containing these decays are selected with a partial reconstruction technique, in which only the high-momentum pi(+/-) from the B decay and the low-momentum pi(-/+) from the D(*-/+) decay are used. We measure the amplitude of the asymmetry to be -0.063+/-0.024(stat)+/-0.014(syst) and compute bounds on |sin((2beta+gamma)|.

Measurements of branching fractions and CP-violating asymmetries in B meson decays to charmless two-body states containing a K(0).

We present measurements of branching fractions and CP-violating asymmetries in decays of B mesons to two-body final states containing a K0. The results are based on a data sample of approximately 88 x 10(6) Upsilon(4S)-->BB decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We measure B(B+-->K(0)pi(+))=(22.3+/-1.7+/-1.1)x10(-6), B(B0-->K(0)pi(0)=(11.4+/-1.7+/-0.8)x10(-6), B(B+-->K(0)K+)<2.5 x 10(-6), and B(B0-->K(0)K(0)<1.8 x 10(-6), where the first uncertainty is statistical and the second is systematic, and the upper limits are at the 90% confidence level. In addition, the following CP-violating asymmetries have been measured: A(CP)(B+-->K(0)pi(+))=-0.05+/-0.08+/-0.01 and A(CP)(B0-->K(0)pi(0)=0.03+/-0.36+/-0.11.