A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.

A Protocol for the Management of the Inpatient Fracture Neck of Femur is Required.

Falls within a hospital environment are a major cause of morbidity and may even lead to mortality. Pathways for patients suffering a Fractured Neck of Femur (FNOF) in the community are well established following the development of the Blue Book, BOAST guidelines and National Hip Fracture Database (NHFD). However, there is no such agreed pathway for patients suffering FNOF within a hospital environment. Such patients have been demonstrated to have a higher risk of delays in medical optimisation, delays in operative management, and mortality. There is, therefore, a need to create a nationally agreed guideline for the care of the "inpatient FNOF" as this is an important subgroup of patients. This article highlights this issue as well as advising medical staff on how to identify a potential FNOF within a hospital environment in order to ensure prompt management of a vulnerable group of patients.

Acute Fracture Neck of Femur Among Inpatients: Severe Injuries Which Need to be Taken Seriously.

OBJECTIVES: This study assesses fall prevention measures and subsequent incident reporting of falls resulting in an "inpatient fracture neck of femur (FNOF)" within a single NHS Trust, with the aim of identifying potential areas of improvement and changing practice within a Trust. METHODS: Forty patients (mean age, 82.6 years) sustained an injury while being treated in hospital for an unrelated cause between January 2012 and June 2013. Case notes and incident reports were analyzed retrospectively. RESULTS: Thirty-three (82.5%) of 40 patients had at least 1 fall screen on admission, with 27 patients (81.8%) identified as a fall risk. Fifteen patients (37.5%) had at least one fall before sustaining a FNOF. Fifteen falls occurred between midnight-0500 hours and only 4 falls were witnessed. Thirty-nine of 40 falls were reported, but none were rated as "severe" injuries. Twenty-eight (71.8%) of 39 patients had a root cause analysis performed for the injury, but only 10 root cause analyses (25.6%) produced an action plan. Fifty percent of patients died within 1 year of injury. CONCLUSION: Accurate fall risk assessments and adequate patient supervision are essential to minimize risks of falls, as the inpatient FNOF is linked to a higher mortality rate than patients injured in the community. A standardized method of analyzing such incidents and dissemination of the results of investigation are also required to reduce the risk of similar incidents from occurring within the hospital environment.

The treatment of periarticular soft tissue sarcoma following neo-adjuvant radiotherapy: a cohort study.

BACKGROUND: Optimising post-operative joint function is challenging when treating periarticular soft tissue sarcoma (STS). Radiotherapy reduces local recurrence rates but periarticular fibrosis may adversely affect joint function. Neo-adjuvant radiotherapy requires lower doses and smaller treatment volumes and therefore has potential benefits for the management of periarticular STS, but has previously been shown to be associated with an increased risk of post-operative wound complications. This study assesses initial outcome and complications after treatment with neo-adjuvant radiotherapy and surgery for patients with periarticular STS. METHODS: Seventeen patients (mean age 52.5 years) were treated using a standard protocol between January 2009 and June 2012 with three-dimensional conformal neo-adjuvant radiotherapy to a dose of 50 Gy in 25 fractions at a single centre, followed by limb salvage surgery. Patients were assessed weekly for adverse effects during radiotherapy. Surgery was planned for 6 weeks following completion of radiotherapy. Patients remain under follow-up with regular Toronto Extremity Salvage Scores (TESS) performed. RESULTS: No patients had a significant adverse effect during radiotherapy. Three patients (17.6%) suffered a wound complication following surgery, all treated conservatively. Magnetic resonance imaging (MRI) demonstrated a reduction in mean maximal tumour diameter from 7.56 to 5.24 cm (p = 0.017, 11 of 17 patients). Tumour necrosis was measured between 50% and 100% in 10 of 11 resections where accurate assessment was possible. One patient had further surgery due to incomplete margins. No patients required post-operative radiotherapy. No local recurrences have occurred after a mean follow-up of 32 months (range 19 to 59 months). Two patients have developed metastatic disease. Mean TESS scores for upper and lower limb patients were 98.5 and 85.5, respectively, at latest follow-up. CONCLUSIONS: We have demonstrated improved wound complication rates compared to the existing literature on the use of neo-adjuvant radiotherapy. This may relate to modification of the technique and patient selection compared to previous series. Excellent functional outcomes can be obtained with this treatment strategy.

The inpatient fracture neck of femur: an important subgroup of patients.

Fractured neck of femur (FNOF) is an increasing problem for the National Health Service (NHS) with 61,508 recorded on the National Hip Fracture Database (NHFD) in 2012­2013 and treatment of such patients is estimated to cost the NHS £1.5 billion per year. Inpatients falling in hospital and sustain a FNOF have rarely been studied as a separate group of patients to assess standards of patient care, time to operative management, and patient mortality. Of 694 patients sustaining an acute FNOF at a single trust between January 2012 and June 2013, 40 patients (5.8%) sustained an inpatient FNOF. 19 patients (47.5%) were male and 15 patients (37.5%) had an ASA grade of 4 or 5, compared to 153 patients (23.4%) and 127 patients (19.4%) respectively of "community" FNOF. 39 of 40 patients received operative management. Patients with an "inpatient" FNOF were less likely to be admitted to an orthopaedic ward within 4 h (30%) and receive operative management within 48 h (65%) according to "Blue Book" standards. Results according to best practice tariff (BPT) were also significantly reduced for the "inpatient" FNOF group, with 23 patients (57.5%) receiving operative management within 36 h and only 19 patients (47.5%) achieving BPT compared to 76.5% and 72.5% respectively for "community" FNOF patients. Mortality among inpatients reached 40% at 120 days and 50% at 1 year, significantly higher than community FNOF patients after multivariate analysis. Patients sustaining an "inpatient" FNOF are more likely to have significant medical co-morbidity and require aggressive medical and surgical management, especially due to their increased risk of mortality post-operatively. Such injuries have direct and indirect financial implications to a health care trust, which can be minimised by prompt management of these patients. This study highlights the need for a standardised protocol of management of this important subgroup of patients and for further work on falls prevention strategies within the National Health Service.

Liposarcoma of the great toe: a case report.

Soft tissue sarcomas are rare malignancies, of which liposarcomas are the most common. Pleomorphic liposarcoma accounts for 5% of liposarcoma diagnoses and most commonly presents in the thigh. A 57-year-old female presented with a 5-year history of a persistent, painless swelling of the left great toe that had been previously diagnosed and treated as an in-grown toenail. After magnetic resonance imaging and core biopsy, a grade 2 pleomorphic liposarcoma was diagnosed. Treatment consisted of neoadjuvant radiotherapy and amputation of the great toe and proximal half of the first metatarsal with primary closure. The patient had no evidence of local recurrence or metastatic disease after 1 year of follow-up and, with the use of a prosthesis, had a good functional outcome. This is the first documented presentation of a high-grade pleomorphic liposarcoma of the great toe to our knowledge. Although soft tissue sarcomas are rare, a high index of suspicion is required by clinicians when presented with a soft tissue mass to promptly diagnose and treat these potentially fatal lesions.

Contact allergy to topical medicaments becomes more common with advancing age: an age-stratified study.

Eczema is common in the elderly people who often use topical medicaments. Previous studies in the elderly people have noted allergic positive patch tests in between 43% and 64% of those tested. We set out to assess whether medicament contact allergies are more common in elderly patients. We undertook a retrospective age-stratified study of all patients patch tested at the Royal Hallamshire Hospital, Sheffield, between January 1994 and July 2005. We confirmed that contact allergy to topical medicaments is more common in those aged more than 70 years compared with the younger age groups. There was no sex difference. The commonest problematic allergen types found in medicaments were fragrances and preservatives. The most frequent individual allergens were fragrance mix, Myroxylon pereirae, lanolins, local anaesthetic agents, neomycin and gentamicin, and tixocortol pivolate. The pattern of medicament contact allergens was similar to that of the younger age groups except that multiple allergic positives were more frequent and sensitivities to local anaesthetics and Myroxylon pereirae were proportionally more common. Elderly patients were more likely to have multiple contact allergies than the younger ones. Care needs to be taken when prescribing topical medicaments to elderly patients with eczema, especially for preparations that contain perfumes, lanolins, and local anaesthetics.