Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data

[EN]Increasingly, treatment decisions for cancer patients are being made from next-generation sequencing results generated from formalin-fixed and paraffin-embedded (FFPE) biopsies. However, this material is prone to sequence artefacts that cannot be easily identified. In order to address this issue, we designed a machine learning-based algorithm to identify these artefacts using data from >1600000 variants from 27 paired FFPE and fresh-frozen breast cancer samples. Using these data, we assembled a series of variant features and evaluated the classification performance of five machine learning algorithms. Using leave-one-sample-out cross-validation, we found that XGBoost (extreme gradient boosting)and random forest obtained AUC (area under the receiver operating characteristic curve) values >0.86. Performance was further tested using two independent datasets that resulted in AUC values of 0.96, whereas a comparison with previously published tools resulted in a maximum AUC value of 0.92. The most discriminating features were read pair orientation bias, genomic context and variant allele frequency. In summary, our results show a promising future for the use of these samples in molecular testing. We built the algorithm into an R package called Ideafix (DEAmination FIXing) that is freely available at https://github.com/mmaitenat/ideafix.Departamento de Educaci ́on, Universidades e Investi- gaci ́on of the Basque Government [PRE 2019 2 0211 to M.T.A]; Ikerbasque, Basque Foundation for Science [to C.L.]; Starmer–Smith Memorial Fund [to C.L.]; Ministerio de Econom ́ıa, Industria y Competitividad (MINECO) of the Spanish Central Government [to C.L., PID2019- 104933GB-10 to B.C.]; ISCIII and FEDER Funds [PI12/00663, PIE13/00048, DTS14/00109, PI15/00275 and PI18/01710 to C.L.]; Departamento de Desarrollo Econ ́omico y Competitividad and Departamento de Sanidad of the Basque Government [to C.L.]; Aso- ciaci ́on Espa ̃nola Contra el Cancer (AECC) [to C.L.]; Diputaci ́on Foral de Guipuzcoa (DFG) [to C.L.]; Depar- tamento de Industria of the Basque Government [ELKA- RTEK Programme, project code: KK-2018/00038 to C.L., ELKARTEK Programme, project code: KK-2020/00049 to B.C., IT-1244-19 to B.C.

Digital Orthopaedics: A Glimpse Into the Future in the Midst of a Pandemic.

BackgroundThe response to COVID-19 catalyzed the adoption and integration of digital health tools into the health care delivery model for musculoskeletal patients. The change, suspension, or relaxation of Medicare and federal guidelines enabled the rapid implementation of these technologies. The expansion of payment models for virtual care facilitated its rapid adoption. The authors aim to provide several examples of digital health solutions utilized to manage orthopedic patients during the pandemic and discuss what features of these technologies are likely to continue to provide value to patients and clinicians following its resolution.ConclusionThe widespread adoption of new technologies enabling providers to care for patients remotely has the potential to permanently change the expectations of all stakeholders about the way care is provided in orthopedics. The new era of Digital Orthopaedics will see a gradual and nondisruptive integration of technologies that support the patient's journey through the successful management of their musculoskeletal disease

High prevalence of radiographic outliers and revisions with unicompartmental knee arthroplasty

BACKGROUND: Alignment outcomes and their impact on implant survival following unicompartmental knee arthroplasty (UKA) are unclear. The purpose of this study was to assess the implant survival and radiographic outcomes after UKA as well as the impact of component alignment and overhang on implant survival. METHODS: We performed a retrospective analysis of 253 primary fixed-bearing and mobile-bearing medial UKAs from a single academic center. All UKAs were performed by 2 high-volume fellowship-trained arthroplasty surgeons. UKAs comprised \u3c10% of their knee arthroplasty practices, with an average of 14.2 medial UKAs per surgeon per year. Implant survival was assessed. Femoral coronal (FCA), femoral sagittal (FSA), tibial coronal (TCA), and tibial sagittal (TSA) angles as well as implant overhang were radiographically measured. Outliers were defined for FCA (\u3e±10° deviation from neutral), FSA (\u3e15° of flexion), TCA (\u3e±5° deviation from neutral), and TSA (\u3e±5° deviation from 7°). Far outliers were an additional \u3e±2° of deviation. Outliers for overhang were identified as \u3e3 mm for anterior overhang, \u3e2 mm for posterior overhang, and \u3e2 mm for medial overhang. RESULTS: Among patients with a failed UKA, revision was performed at an average of 3.7 years (range, 0.03 to 8.7 years). The cumulative revision rate was 14.2%. Kaplan-Meier survival analysis demonstrated 5 and 10-year survival rates of 88.0% (95% confidence interval [CI] = 82.0% to 91.0%) and 70.0% (95% CI = 56.0% to 80.0%), respectively. Only 19.0% (48) of the UKAs met target alignment for all 4 alignment measures, and only 72.7% (184) met all 3 targets for overhang. Only 11.9% (30) fell within all alignment and overhang targets. The risk of implant failure was significantly impacted by outliers for FCA (failure rate = 15.4%, p = 0.036), FSA (16.2%, p = 0.028), TCA (17.9%, p = 0.020), and TSA (15.2%, p = 0.034) compared with implants with no alignment or overhang errors (0%); this was also true for far outliers (p \u3c 0.05). Other risk factors for failure were posterior overhang (failure rate = 25.0%, p = 0.006) and medial overhang (38.2%, p \u3c 0.001); anterior overhang was not a significant risk factor (10.0%, p = 0.090). CONCLUSIONS: The proportions of UKA revisions and alignment outliers were greater than expected, even among high-volume arthroplasty surgeons performing an average of 14.2 UKAs per year (just below the high-volume UKA threshold of 15). Alignment and overhang outliers were significant risk factors for implant failure. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence

The impact of surgeon volume and training status on implant alignment in total knee arthroplasty

BACKGROUND: Implant malalignment may predispose patients to prosthetic failure following total knee arthroplasty (TKA). A more thorough understanding of the surgeon-specific factors that contribute to implant malalignment following TKA may uncover actionable strategies for improving implant survival. The purpose of this study was to determine the impact of surgeon volume and training status on malalignment. METHODS: In this retrospective multicenter study, we performed a radiographic analysis of 1,570 primary TKAs performed at 4 private academic and state-funded centers in the U.S. and U.K. Surgeons were categorized as high-volume (≥50 TKAs/year) or low-volume (\u3c50 TKAs/year), and as a trainee (fellow/resident under the supervision of an attending surgeon) or a non-trainee (attending surgeon). On the basis of these designations, 3 groups were defined: high-volume non-trainee, low-volume non-trainee, and trainee. The postoperative medial distal femoral angle (DFA), medial proximal tibial angle (PTA), and posterior tibial slope angle (PSA) were radiographically measured. Outlier measurements were defined as follows: DFA, outside of 5° ± 3° of valgus; PTA, \u3e±3° deviation from the neutral axis; and PSA, \u3c0° or \u3e7° of flexion for cruciate-retaining or \u3c0° or \u3e5° of flexion for posterior-stabilized TKAs. Far outliers were defined as measurements falling \u3e± 2° outside of these ranges. The proportions of outliers were compared between the groups using univariate and multivariate analyses. RESULTS: When comparing the high and low-volume non-trainee groups using univariate analysis, the proportions of knees with outlier measurements for the PTA (5.3% versus 17.4%) and PSA (17.4% versus 28.3%) and the proportion of total outliers (11.8% versus 20.7%) were significantly lower in the high-volume group (all p \u3c 0.001). The proportions of DFA (1.9% versus 6.5%), PTA (1.8% versus 5.7%), PSA (5.5% versus 12.6%), and total far outliers (3.1% versus 8.3%) were also significantly lower in the high-volume non-trainee group (all p \u3c 0.001). Compared with the trainee group, the high-volume non-trainee group had significantly lower proportions of DFA (12.6% versus 21.6%), PTA (5.3% versus 12.0%), PSA (17.4% versus 33.3%), and total outliers (11.8% versus 22.3%) (all p \u3c 0.001) as well as DFA (1.9% versus 3.9%; p = 0.027), PSA (5.5% versus 12.6%; p \u3c 0.001), and total far outliers (3.1% versus 6.4%; p = 0.004). No significant differences were identified when comparing the low-volume non-trainee group and the trainee group, with the exception of PTA outliers (17.4% versus 12.0%; p = 0.041) and PTA far outliers (5.7% versus 2.6%; p = 0.033). Findings from multivariate analysis accounting for the effects of patient age, body mass index, and individual surgeon demonstrated similar results. CONCLUSIONS: Low surgical volume and trainee status were risk factors for outlier and far-outlier malalignment in primary TKA, even when accounting for differences in individual surgeon and patient characteristics. Trainee surgeons performed similarly, and certainly not inferiorly, to low-volume non-trainee surgeons. Even among high-volume non-trainees, the best-performing cohort in our study, the proportion of TKA alignment outliers was still high. LEVEL OF EVIDENCE: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence

Identification of Recurrent Mutations in the microRNA-Binding Sites of B-Cell Lymphoma-Associated Genes in Follicular Lymphoma.

Follicular lymphoma (FL) is a common indolent B-cell lymphoma that can transform into the more aggressive transformed FL (tFL). However, the molecular process driving this transformation is uncertain. In this work, we aimed to identify microRNA (miRNA)-binding sites recurrently mutated in follicular lymphoma patients, as well as in transformed FL patients. Using whole-genome sequencing data from FL tumors, we discovered 544 mutations located in bioinformatically predicted microRNA-binding sites. We then studied these specific regions using targeted sequencing in a cohort of 55 FL patients, found 16 recurrent mutations, and identified a further 69 variants. After filtering for QC, we identified 21 genes with mutated miRNA-binding sites that were also enriched for B-cell-associated genes by Gene Ontology. Over 40% of mutations identified in these genes were present exclusively in tFL patients. We validated the predicted miRNA-binding sites of five of the genes by luciferase assay and demonstrated that the identified mutations in BCL2 and EZH2 genes impaired the binding efficiency of miR-5008 and miR-144 and regulated the endogenous levels of messenger RNA (mRNA)

MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited - Copyright @ 2011 Chi et al.Background: MicroRNAs are small RNA species that regulate gene expression post-transcriptionally and are aberrantly expressed in many cancers including hematological malignancies. However, the role of microRNAs in the pathogenesis of multiple myeloma (MM) is only poorly understood. We therefore used microarray analysis to elucidate the complete miRNome (miRBase version 13.0) of purified tumor (CD138+) cells from 33 patients with MM, 5 patients with monoclonal gammopathy of undetermined significance (MGUS) and 9 controls. Results: Unsupervised cluster analysis revealed that MM and MGUS samples have a distinct microRNA expression profile from control CD138+ cells. The majority of microRNAs aberrantly expressed in MM (109/129) were up-regulated. A comparison of these microRNAs with those aberrantly expressed in other B-cell and T-cell malignancies revealed a surprising degree of similarity (~40%) suggesting the existence of a common lymphoma microRNA signature. We identified 39 microRNAs associated with the pre-malignant condition MGUS. Twenty-three (59%) of these were also aberrantly expressed in MM suggesting common microRNA expression events in MM progression. MM is characterized by multiple chromosomal abnormalities of varying prognostic significance. We identified specific microRNA signatures associated with the most common IgH translocations (t(4;14) and t(11;14)) and del(13q). Expression levels of these microRNAs were distinct between the genetic subtypes (by cluster analysis) and correctly predicted these abnormalities in > 85% of cases using the support vector machine algorithm. Additionally, we identified microRNAs associated with light chain only myeloma, as well as IgG and IgA-type MM. Finally, we identified 32 microRNAs associated with event-free survival (EFS) in MM, ten of which were significant by univariate (logrank) survival analysis. Conclusions: In summary, this work has identified aberrantly expressed microRNAs associated with the diagnosis, pathogenesis and prognosis of MM, data which will prove an invaluable resource for understanding the role of microRNAs in this devastating disease.This work was funded by grants from Leukaemia and Lymphoma Research (JC, EB, X-HC, DT, JB and JSW) and the Julian Starmer-Smith Memorial Fund (CHL). The authors acknowledge financial support from the Department of Health via the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre award to Oxford Radcliffe NHS Trust

A holistic approach to understanding the desorption of phosphorus in soils

The mobility and resupply of inorganic phosphorus (P) from the solid phase were studied in 32 soils from the UK. The combined use of diffusive gradients in thin films (DGT), diffusive equilibration in thin films (DET) and the “DGT-induced fluxes in sediments” model (DIFS) were adapted to explore the basic principles of solid-to-solution P desorption kinetics in previously unattainable detail. On average across soil types, the response time (Tc) was 3.6 h, the desorption rate constant (k–1) was 0.0046 h–1, and the desorption rate was 4.71 nmol l–1 s–1. While the relative DGT-induced inorganic P flux responses in the first hour is mainly a function of soil water retention and % Corg, at longer times it is a function of the P resupply from the soil solid phase. Desorption rates and resupply from solid phase were fundamentally influenced by P status as reflected by their high correlation with P concentration in FeO strips, Olsen, NaOH–EDTA and water extracts. Soil pH and particle size distribution showed no significant correlation with the evaluated mobility and resupply parameters. The DGT and DET techniques, along with the DIFS model, were considered accurate and practical tools for studying parameters related to soil P desorption kinetics