Advanced complex trait analysis

MOTIVATION

The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance.

RESULTS

We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min.

AVAILABILITY AND IMPLEMENTATION

The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta.

CONTACT

a.gray@ed.ac.uk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enabling HIV self-testing in South Africa

In a South African context, we consider the implications of the United States Food and Drug Administration’s recent approval of the OraQuick HIV self-testing kit. We argue that current law and policy inhibit the roll-out of accurate and well-regulated self-testing kits, and create a loophole for sale in supermarkets, but not pharmacies.

Guideline on the investigation and management of acute transfusion reactions. Prepared by the BCSH Blood Transfusion Task Force

Although acute non-haemolytic febrile or allergic reactions (ATRs) are a common complication of transfusion and often result in little or no morbidity, prompt recognition and management are essential. The serious hazards of transfusion haemovigilance organisation (SHOT) receives 30-40 reports of anaphylactic reactions each year. Other serious complications of transfusion, such as acute haemolysis, bacterial contamination, transfusion-related acute lung injury (TRALI) or transfusion-associated circulatory overload (TACO) may present with similar clinical features to ATR. This guideline describes the approach to a patient developing adverse symptoms and signs related to transfusion, including initial recognition, establishing a likely cause, treatment, investigations, planning future transfusion and reporting within the hospital and to haemovigilance organisations. Key recommendations are that adrenaline should be used as first line treatment of anaphylaxis, and that transfusions should only be carried out where patients can be directly observed and where staff are trained in manging complications of transfusion, particularly anaphylaxis. Management of ATRs is not dependent on classification but should be guided by symptoms and signs. Patients who have experienced an anaphylactic reaction should be discussed with an allergist or immunologist, in keeping with UK resuscitation council guidelines.

Predictors of fracture following suspected injury to the scaphoid

A prospective study was performed to develop a clinical prediction rule that incorporated demographic and clinical factors predictive of a fracture of the scaphoid. Of 260 consecutive patients with a clinically suspected or radiologically confirmed scaphoid fracture, 223 returned for evaluation two weeks after injury and formed the basis of our analysis. Patients were evaluated within 72 hours of injury and at approximately two and six weeks after injury using clinical assessment and standard radiographs. Demographic data and the results of seven specific tests in the clinical examination were recorded. There were 116 (52%) men and their mean age was 33 years (13 to 95; SD 17.9). In 62 patients (28%) a scaphoid fracture was confirmed. A logistic regression model identified male gender (p = 0.002), sports injury (p = 0.004), anatomical snuff box pain on ulnar deviation of the wrist within 72 hours of injury (p < 0.001), and scaphoid tubercle tenderness at two weeks (p < 0.001) as independent predictors of fracture. All patients with no pain at the anatomical snuff box on ulnar deviation of the wrist within 72 hours of injury did not have a fracture (n = 72, 32%). With four independently significant factors positive, the risk of fracture was 91%. Our study has demonstrated that clinical prediction rules have a considerable influence on the probability of a suspected scaphoid fracture. This will help improve the use of supplementary investigations where the diagnosis remains in doubt.

Controlling the topology of Fermi surfaces in metal nanofilms

The properties of metal crystals are governed by the electrons of the highest occupied states at the Fermi level and determined by Fermi surfaces, the Fermi energy contours in momentum space. Topological regulation of the Fermi surface has been an important issue in synthesizing functional materials, which we found to be realized at room temperature in nanometer-thick films. Reducing the thickness of a metal thin film down to its electron wavelength scale induces the quantum size effect and the electronic system changes from three to two-dimensional, transforming the Fermi surface topology. Such an ultrathin film further changes its topology through one-dimensional (1D) structural deformation of the film when it is grown on a 1D substrate. In particular, when the interface has 1D metallic bands, the system is additionally stabilized by forming an electron energy gap by hybridization between 1D states of the film and substrate.

A national analysis of complications following hemiarthroplasty for hip fracture in older patients

BACKGROUND

There is emerging evidence that patients with fractured neck of femur (FNOF) aged >85 years have different demands on a health-care system when compared to younger patients.

AIM

We sought to better quantify this in terms of comorbidity and complication rates.

DESIGN

Retrospective review of national database.

METHODS

Data on all patients who underwent hip hemiarthroplasty for FNOF between January 2005 and December 2008 were extracted from the English hospital episode statistics database.

RESULTS

There were 41 770 patients aged 65-84 years and 35 321 patients aged ≥85 years. The older cohort was less likely to have diabetes, chronic obstructive pulmonary disease and rheumatoid arthritis. However, they exhibited a significantly higher risk of lower respiratory tract infection [odds ratio (OR) = 1.58, 95% confidence interval (CI) 1.50-1.67)], myocardial infarction (OR = 1.67, 1.52-1.83) and acute renal failure (OR = 1.54, 1.40-1.70) within 30 days of surgery with an inpatient mortality risk at 90 days, double that of the younger age group. Length of stay (LoS) was significantly longer in patients >85 years compared to younger patients (median 18 days vs. 15, P < 0.001).

CONCLUSION

Patients aged ≥85 years admitted for FNOF were found to have a lower incidence of major chronic disease but exhibited a greater incidence of acute events following hemiarthroplasty and their LoS was increased. Targeted medical interventions that focus upon this susceptible patient group may help reduce morbidity and improve survival.

The effectiveness and cost of single and multi-factorial cardiovascular risk factor modification to guideline targets in type 2 diabetes

AIMS

Cardiovascular disease is the main cause of morbidity and mortality in type 2 diabetes (T2DM), at huge cost to the NHS. We investigated the potential effect on population cardiovascular risk and associated costs of single and multi-factorial intervention, to target levels, in individuals with T2DM.

METHODS

Baseline population means and proportions for cardiovascular risk factors were calculated for 159 patients with T2DM from 3 general practices. Predicted 10year cardiovascular risk, and associated costs were calculated using the LIP2687 risk calculator, based on Framingham and UKPDS equations. Systolic blood pressure, HbA(1C), total cholesterol and HDL-cholesterol were altered to NICE and SIGN target levels and the model run again. The difference in outcomes was observed.

RESULTS

45%, 76% and 38% of patients met NICE targets for cholesterol, systolic blood pressure and HbA1c, respectively. As expected, comparing the two guidelines, fewer patients met the 'stricter' targets (P=0.0001). Treatment-to-target produced no significant difference in cardiovascular risk or costs, although greater reductions in outcomes were seen with multi-factorial intervention.

CONCLUSION

This small study suggests that intervention in only those patients with the highest cardiovascular risk brings little reduction in population cardiovascular risk and associated health costs. Multi-factorial intervention in all patients with T2DM, regardless of baseline values, is likely to bring greater reductions. This raises the question as to whether the current emphasis on treatment to target should be modified to encourage multi-factorial intervention in all patients with T2DM, even those with baseline values below target levels.

NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments

SUMMARY

Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings.

AVAILABILITY

Downloable and web-based versions of NASP are freely available at http://web.cbio.uct.ac.za/~yves/nasp_portal.php

CONTACT

yves@cbio.uct.ac.za

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Ewing's Sarcoma of the Head and Neck: A Retrospective Analysis of 24 Cases

Introduction and purpose. Primary Ewing's sarcoma arising from the bones of the head and neck region is extremely rare representing only 1– 4% of all Ewing's sarcoma cases. Previous reports suggest a better prognosis for that particular anatomic site. The purpose of this study was to analyze the clinico-epidemiologic characteristics of that rare clinical presentation, as well as its patterns of failure and prognosis following treatment.

Materials and methods. This study included a retrospective review of the medical records of patients with the diagnosis of Ewing's sarcoma of the head and neck region treated at King Faisal Specialist Hospital and Research Center between 1975 and 1996.

Results. Out of a total number of 24 cases analyzed, there were 17 males and 7 females with a ratio of 2.4:1. The median age at diagnosis was 16.5 years. A painful swelling was the most common clinical presentation.The maxilla was the most common site of presentation (9/24 cases). There were 3/24 cases who presented with metastatic disease at diagnosis.The majority of patients (16/24 cases) had a tumor size >10 cm. Most patients were treated with systemic chemotherapy plus localized irradiation following an initial biopsy.With a mean follow up of 3.4 years, the 5-year actual overall survival (OS) for the whole group was 53%, while the 5-year actuarial disease-free survival (DFS) was 30%. These figures were higher than those repor ted from our institution for young patients (≤ 14 years treated for Ewing' s sarcoma in other anatomic locations (30% v 15%). The response to chemotherapy was the only prognostic factor that affected both the OS and DFS.

Conclusion. The prognosis of Ewing's sarcoma of the head and neck region is slightly better than that of other anatomic sites.The response to systemic chemotherapy is one of the most important prognostic factors affecting both DFS and OS of Ewing's sarcoma of the head and neck. Multimodality therapy consisting of an initial biopsy, aggressive combination chemotherapy and localized radiotherapy is the treatment of choice for Ewing's sarcoma of the head and neck region and may result in long-term survival.

MAVARIC - a comparison of automation-assisted and manual cervical screening: a randomised controlled trial

OBJECTIVES

The principal objective was to compare automation-assisted reading of cervical cytology with manual reading using the histological end point of cervical intraepithelial neoplasia grade II (CIN2) or worse (CIN2+). Secondary objectives included (i) an assessment of the slide ranking facility of the Becton Dickinson (BD) FocalPoint™ Slide Profiler (Becton Dickinson, Franklin Lakes, NJ, USA), especially 'No Further Review', (ii) a comparison of the two approved automated systems, the ThinPrep® Imaging System (Hologic, Bedford, MA, USA) and the BD FocalPoint Guided Screener Imaging System, and (iii) automated versus manual in terms of productivity and cost-effectiveness.

DESIGN

A 1 : 2 randomised allocation of slides to either manual reading or automation-assisted paired with manual reading. Cytoscreeners were blinded to whether samples would be read only manually or manually paired with automated. Slide reading procedures followed real-life laboratory protocol to produce a final result and, for paired readings, the worse result determined the management. Costs per event were estimated and combined with productivity to produce a cost per slide, per woman and per CIN2+ and cervical intraepithelial neoplasia grade III (CIN3) or worse (CIN3+) lesion detected. Cost-effectiveness was estimated using cost per CIN2+ detected. Lifetime cost-effectiveness in terms of life-years and quality-adjusted life-years was estimated using a mathematical model.

SETTING

Liquid-based cytology samples were obtained in primary care, and a small number of abnormal samples were obtained from local colposcopy clinics, from different women, in order to enrich the proportion of abnormals. All of the samples were read in a single large service laboratory. Liquid residues used for human papillomavirus (HPV) triage were tested (with Hybrid Capture 2, Qiagen, Crawley, UK) in a specialist virology laboratory in Edinburgh, UK. Histopathology was read by a specialist gynaecological pathology team blinded to HPV results and type of reading.

PARTICIPANTS

Samples were obtained from women aged 25-64 years undergoing primary cervical screening in Greater Manchester, UK, with small proportions from women outside this age range and from women undergoing colposcopy.

INTERVENTIONS

The principal intervention was automation-assisted reading of cervical cytology slides which was paired with a manual reading of the same slide. Low-grade cytological abnormalities (borderline and mild dyskaryosis) were triaged with HPV testing to direct colposcopy referral. Women with high-grade cytology were referred for colposcopy and those with negative cytology were returned to recall.

MAIN OUTCOME MEASURES

The principal outcome measure was the sensitivity of automation-assisted reading relative to manual for the detection of CIN2+. A secondary outcome measure was cost-effectiveness of each type of reading to detect CIN2+. The study was powered to detect a relative sensitivity difference equivalent to an absolute difference of 5%.

RESULTS

The principal finding was that automated reading was 8% less sensitive relative to manual, 6.3% in absolute terms. 'No further review' was very reliable and, if restricted to routine screening samples, < 1% of CIN2+ would have been missed. Automated and manual were very similar in terms of cost-effectiveness despite a 60%-80% increase in productivity for automation-assisted reading.

CONCLUSIONS

The significantly reduced sensitivity of automated reading, combined with uncertainty over cost-effectiveness, suggests no justification at present to recommend its introduction. The reliability of 'no further review' warrants further consideration as a means of saving staff time.

TRIAL REGISTRATION

Current Controlled Trials ISRCTN66377374.

FUNDING

This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 15, No. 3. See the HTA programme website for further project information.

Integration of e-learning resources into a medical school curriculum

BACKGROUND

E-learning has the potential to make important contributions to medical education, but there has been limited study of a blended approach in which the digital resources are introduced alongside traditional teaching methods such as lectures.

METHODS

We describe the successful embedding of an e-learning resource into 3 of the 5 weeks of cardiovascular system teaching for 164 first-year medical students by providing scheduled slots in the timetables. A questionnaire completed by the students at the end of the 5 weeks had a response rate of 66%. Students varied in how they made use of the resource, some systematically working through it and others browsing and studying sections felt to be personally most relevant.

RESULTS

Almost all (96%) rated the e-learning resources as probably or definitely of value: they particularly valued interactive activities, animations, video demonstrations, video clips of experts and self-assessment exercises. Graduate students had a significantly more favourable assessment of the e-learning resources than their undergraduate colleagues, while female students felt the value in supporting existing learning opportunities more strongly than male students.

CONCLUSIONS

It should not be assumed that all students will choose to use an e-learning resource in the same way and instructional design should enable alternative approaches. The sequence in which the e-learning resource is used in relation to the other learning opportunities, such as lectures and PBL group discussions, may be important and merits further consideration. The experiences reported in this study provide encouragement and pointers for others engaged in the integration of e-learning in their curriculum.

Identifying the psychosocial correlates of condom use by female sex workers in Hong Kong

This study examined factors affecting condom use by Hong Kong female sex workers when they have sex with their clients and steady partners. Our respondents consisted of 109 active female sex workers, mainly streetwalkers or sex workers who worked in villas. During a 30-minute interview, respondents were interviewed individually and were asked questions regarding their condom use practice. These questions were designed to measure various factors affecting their condom use practice, including attitudes toward condom use, normative pressure, perceived behavioural control, perceived AIDS risks, past condom use behaviour, and future condom use intentions with respect to the two types of partners. Multiple regression analyses reveal that perceived behavioural control is the most important factor associated with these respondents' future condom use across the two types of partners. Perceived AIDS risk is the additional predictor for condom use with clients, while normative pressure is the additional predictor for condom use with steady partners. Past condom use behaviour also provided significant additional prediction for both types of partners, implying the habitual nature of condom use among our respondents. These results have significant implications for designing intervention programmes targeting at increasing condom use by female sex workers in Hong Kong.