Anatomical evaluation of the transpubic screw corridor based on a 3D statistical model of the pelvic ring

Retrograde transpubic screw fixation is a common procedure for the treatment of anterior pelvic ring fractures. With its sparing surgical approach and significant pain relief after screw fixations allowing early mobilisation, it has gained importance especially in the treatment of insufficiency fractures in elderly patients. However, positioning of transpubic screw osteosynthesis is not always possible due to narrowness and curvature of the screw corridor. The aim of the present study was to evaluate availability and length of the screw corridor using a 3D statistical model of the pelvic ring consisting out of 150 uninjured pelves. Virtual bore probes with a diameter of 7.5 mm were analysed as to accessibility, length and grey value distribution in Hounsfield Unit (HU). A transpubic corridor with a diameter of ≥ 7.5 mm was available in 185 of 300 investigated superior pubic rami with mean screw length of 131.7 mm. Accessibility of the screw corridor was higher in males than in females. However, screw length showed no systematic differences between the sexes or ethnicities. Analysis of the grey value distribution demonstrated the strongest bone to be located at the lateral ilium and the supraacetabular region

Electronic self-reporting of adverse events for patients undergoing cancer treatment: the eRAPID research programme including two RCTs

Abstract Background Cancer is treated using multiple modalities (e.g. surgery, radiotherapy and systemic therapies) and is frequently associated with adverse events that affect treatment delivery and quality of life. Regular adverse event reporting could improve care and safety through timely detection and management. Information technology provides a feasible monitoring model, but applied research is needed. This research programme developed and evaluated an electronic system, called eRAPID, for cancer patients to remotely self-report adverse events. Objectives The objectives were to address the following research questions: is it feasible to collect adverse event data from patients’ homes and in clinics during cancer treatment? Can eRAPID be implemented in different hospitals and treatment settings? Will oncology health-care professionals review eRAPID reports for decision-making? When added to usual care, will the eRAPID intervention (i.e. self-reporting with tailored advice) lead to clinical benefits (e.g. better adverse event control, improved patient safety and experiences)? Will eRAPID be cost-effective? Design Five mixed-methods work packages were conducted, incorporating co-design with patients and health-care professionals: work package 1 – development and implementation of the electronic platform across hospital centres; work package 2 – development of patient-reported adverse event items and advice (systematic and scoping reviews, patient interviews, Delphi exercise); work package 3 – mapping health-care professionals and care pathways; work package 4 – feasibility pilot studies to assess patient and clinician acceptability; and work package 5 – a single-centre randomised controlled trial of systemic treatment with a full health economic assessment. Setting The setting was three UK cancer centres (in Leeds, Manchester and Bristol). Participants The intervention was developed and evaluated with patients and clinicians. The systemic randomised controlled trial included 508 participants who were starting treatment for breast, colorectal or gynaecological cancer and 55 health-care professionals. The radiotherapy feasibility pilot recruited 167 patients undergoing treatment for pelvic cancers. The surgical feasibility pilot included 40 gastrointestinal cancer patients. Intervention eRAPID is an online system that allows patients to complete adverse event/symptom reports from home or hospital. The system provides immediate severity-graded advice based on clinical algorithms to guide self-management or hospital contact. Adverse event data are transferred to electronic patient records for review by clinical teams. Patients complete an online symptom report every week and whenever they experience symptoms. Main outcome measures In systemic treatment, the primary outcome was Functional Assessment of Cancer Therapy – General, Physical Well-Being score assessed at 6, 12 and 18 weeks (primary end point). Secondary outcomes included cost-effectiveness assessed through the comparison of health-care costs and quality-adjusted life-years. Patient self-efficacy was measured (using the Self-Efficacy for Managing Chronic Diseases 6-item Scale). The radiotherapy pilot studied feasibility (recruitment and attrition rates) and selection of outcome measures. The surgical pilot examined symptom report completeness, system actions, barriers to using eRAPID and technical performance. Results eRAPID was successfully developed and introduced across the treatments and centres. The systemic randomised controlled trial found no statistically significant effect of eRAPID on the primary end point at 18 weeks. There was a significant effect at 6 weeks (adjusted difference least square means 1.08, 95% confidence interval 0.12 to 2.05; p = 0.028) and 12 weeks (adjusted difference least square means 1.01, 95% confidence interval 0.05 to 1.98; p = 0.0395). No between-arm differences were found for admissions or calls/visits to acute oncology or chemotherapy delivery. Health economic analyses over 18 weeks indicated no statistically significant difference between the cost of the eRAPID information technology system and the cost of usual care (£12.28, 95% confidence interval –£1240.91 to £1167.69; p > 0.05). Mean differences were small, with eRAPID having a 55% probability of being cost-effective at the National Institute for Health and Care Excellence-recommended cost-effectiveness threshold of £20,000 per quality-adjusted life-year gained. Patient self-efficacy was greater in the intervention arm (0.48, 95% confidence interval 0.13 to 0.83; p = 0.0073). Qualitative interviews indicated that many participants found eRAPID useful for support and guidance. Patient adherence to adverse-event symptom reporting was good (median compliance 72.2%). In the radiotherapy pilot, high levels of consent (73.2%) and low attrition rates (10%) were observed. Patient quality-of-life outcomes indicated a potential intervention benefit in chemoradiotherapy arms. In the surgical pilot, 40 out of 91 approached patients (44%) consented. Symptom report completion rates were high. Across the studies, clinician intervention engagement was varied. Both patient and staff feedback on the value of eRAPID was positive. Limitations The randomised controlled trial methodology led to small numbers of patients simultaneously using the intervention, thus reducing overall clinician exposure to and engagement with eRAPID. Furthermore, staff saw patients across both arms, introducing a contamination bias and potentially reducing the intervention effect. The health economic results were limited by numbers of missing data (e.g. for use of resources and EuroQol-5 Dimensions). Conclusions This research provides evidence that online symptom monitoring with inbuilt patient advice is acceptable to patients and clinical teams. Evidence of patient benefit was found, particularly during the early phases of treatment and in relation to self-efficacy. The findings will help improve the intervention and guide future trial designs. Future work Definitive trials in radiotherapy and surgical settings are suggested. Future research during systemic treatments could study self-report online interventions to replace elements of traditional follow-up care in the curative setting. Further research during modern targeted treatments (e.g. immunotherapy and small-molecule oral therapy) and in metastatic disease is recommended. Trial registration The systemic randomised controlled trial is registered as ISRCTN88520246. The radiotherapy trial is registered as ClinicalTrials.gov NCT02747264. Funding This project was funded by the National Institute for Health Research (NIHR) Programme Grants for Applied Research programme and will be published in full in Programme Grants for Applied Research; Vol. 10, No. 1. See the NIHR Journals Library website for further project information

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Phenotypic Characterization of <i>EIF2AK4</i> Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 ( BMPR2 ) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene ( EIF2AK4 ) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. Methods: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource–Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of &lt;1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. Results: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (K co ; 33% [interquartile range, 30%–35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23–38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. Conclusions: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low K co and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation. </jats:sec

Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes.

Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.JW is supported by a Cancer Research UK Cambridge Cancer Centre Clinical Research Training Fellowship. Funding for the NIHR BioResource – Rare diseases project was provided by the National Institute for Health Research (NIHR, grant number RG65966). ERM acknowledges support from the European Research Council (Advanced Researcher Award), NIHR (Senior Investigator Award and Cambridge NIHR Biomedical Research Centre), Cancer Research UK Cambridge Cancer Centre and Medical Research Council Infrastructure Award. The University of Cambridge has received salary support in respect of EM from the NHS in the East of England through the Clinical Academic Reserve. The views expressed are those of the authors and not necessarily those of the NHS or Department of Health. DGE is an NIHR Senior Investigator and is supported by the all Manchester NIHR Biomedical Research Centre

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead