42 research outputs found

    Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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    Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

    High Variability of the Definition of Recurrent Glenohumeral Instability: An Analysis of the Current Literature by a Systematic Review

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    Purpose: To determine the definitions for recurrence used in the literature, assess the consensus in using these definitions, and determine the impact of these definitions on recurrence rates. Methods: A literature search was performed in PubMed and EMBASE including studies from 2000 to 2020 reporting on recurrence rates after anterior arthroscopic shoulder instability surgery. Dislocation, apprehension, subluxation and recurrence rates were compared. Results: Ninety-one studies were included. In 68% of the eligible studies, recurrence rates are not well defined. Thirty (33%) studies did not report on dislocations, 45 (49%) did not report on subluxations, and 58 (64%) did not report on apprehension. Seventeen different definitions for recurrence of instability, 4 definitions of dislocations, and 8 definitions of subluxation were used. Conclusion: Recurrence rates are poorly specified and likely underreported in the literature, hampering comparison with results of other studies. This highlights the need for a consensus on definition of recurrence across shoulder instability studies. We recommend not using the definition recurrence of instability anymore. We endorse defining dislocations as a radiographically confirmed dislocation or a dislocation that is manually reduced, subluxations as the feeling of a dislocation that can be (spontaneously) reduced without the need for a radiographically confirmed dislocation, and a positive apprehension sign as fear of imminent dislocation when placing the arm in abduction and external rotation during physical examination. Reporting on the events resulting in a dislocation or subluxation aids in making an estimation of the severity of instability. Level of Evidence: Level IV, systematic review

    Total Elbow Arthroplasty: A Systematic Review

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    Most total elbow arthroplasty (TEA) designs aim to replicate anatomy and provide stability in the treatment of the degenerative elbow joint. Given the promising results that have been reported following the use of TEA for the treatment of complex fractures, the indications for this procedure are growing. The objective of the present study was to review the most recent literature on the results of the most commonly performed TEAs. A comprehensive literature search was conducted. All relevant studies were reviewed according to a set of predefined inclusion and exclusion criteria. After the initial assessment, 2 authors extracted data from the included articles. Groups were created on the basis of the design of TEA implant, the type of implant (linked or unlinked), and the indication for treatment. Outcome parameters were survival rate, pain, range of motion, complications, and specific elbow outcome scores. Seventy-three articles involving a total of 9,379 TEAs were included. The level of evidence was primarily Level IV. Nineteen specific designs of TEA implants were described, including the Souter-Strathclyde (n = 2,387), Coonrad-Morrey (n = 1,586), Kudo (n = 560), and GSB III (n = 498). The most common indication for TEA was rheumatoid arthritis (70%). The weighted mean survival rate for the linked and unlinked prostheses was 85.5% at 7.8 years and 74% at 12.3 years, respectively. For the Coonrad-Morrey, Souter-Strathclyde, and GSB III, the weighted mean survival rate was 87.2% at 7.2 years, 70.6% at 14.2 years, and 81.7% at 9.5 years, respectively. The range of motion after TEA was good overall, with a mean flexion angle of 129° and a mean extension lag angle of 30°. The complication rates ranged from 11% to 38%, with clinical loosening being the most frequently reported complication (7%). The results of TEA are respectable overall. It appears that there are small differences between designs. However, despite the fairly good functional results and elbow scores, the survival and complication rates are still not as favorable as those following arthroplasties in other joints. Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidenc

    Recurrence in traumatic anterior shoulder dislocations increases the prevalence of Hill–Sachs and Bankart lesions: a systematic review and meta-analysis

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    Purpose: The extent of shoulder instability and the indication for surgery may be determined by the prevalence or size of associated lesions. However, a varying prevalence is reported and the actual values are therefore unclear. In addition, it is unclear whether these lesions are present after the first dislocation and whether or not these lesions increase in size after recurrence. The aim of this systematic review was (1) to determine the prevalence of lesions associated with traumatic anterior shoulder dislocations, (2) to determine if the prevalence is higher following recurrent dislocations compared to first-time dislocations and (3) to determine if the prevalence is higher following complete dislocations compared to subluxations. Methods: PubMed, EMBASE, Cochrane and Web of Science were searched. Studies examining shoulders after traumatic anterior dislocations during arthroscopy or with MRI/MRA or CT published after 1999 were included. A total of 22 studies (1920 shoulders) were included. Results: The proportion of Hill–Sachs and Bankart lesions was higher in recurrent dislocations (85%; 66%) compared to first-time dislocations (71%; 59%) and this was statistically significant (P < 0.01; P = 0.05). No significant difference between recurrent and first-time dislocations was observed for SLAP lesions, rotator-cuff tears, bony Bankart lesions, HAGL lesions and ALPSA lesions. The proportion of Hill–Sachs lesions was significantly higher in complete dislocations (82%) compared to subluxations (54%; P < 0.01). Conclusion: Higher proportions of Hill–Sachs and Bankart were observed in recurrent dislocations compared to first-time dislocations. No difference was observed for bony Bankart, HAGL, SLAP, rotator-cuff tear and ALPSA. Especially when a Hill–Sachs or Bankart is present after first-time dislocation, early surgical stabilization may need to be considered as other lesions may not be expected after recurrence and to limit lesion growth. However, results should be interpreted with caution due to substantial heterogeneity and large variance. Level of evidence: IV

    Greater Tuberosity Fractures: Does Fracture Assessment and Treatment Recommendation Vary Based on Imaging Modality?

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    For greater tuberosity fractures, 5-mm displacement is a commonly used threshold for recommending surgery; however, it is unclear if displacement can be assessed with this degree of precision and reliability using plain radiographs. It also is unclear if CT images provide additional information that might change decision making. We asked: (1) Does interobserver agreement for assessment of the amount and direction of fracture-fragment displacement vary based on imaging modality (radiographs only; 2-dimensional [2-D] CT images and radiographs; and 3-dimensional [3-D] and 2-D CT images and radiographs)? (2) Does the likelihood of recommending surgery vary based on imaging modality? (3) Does the level of confidence regarding the decision for treatment vary based on imaging modality? We invited 791 orthopaedic surgeons to complete a survey on greater tuberosity fractures. One hundred eighty (23%) responded and were randomized on a 1:1:1 basis in one of the three imaging modality groups and evaluated the same set of 22 fractures. We described age, sex, mechanism of injury, days between injury and imaging, and that patients had no comorbidities or signs of neurovascular damage for every case. One hundred sixty-four of the 180 respondents completed the study and there was an imbalance in noncompletion between the three groups (two of 67 [3.0%] in the radiograph only group; nine of 57 [16%] in the 2-D CT and radiograph group; and five of 56 [8.9%] in the 3-D CT, 2-D CT, and radiograph group; p = 0.043 by Fisher's exact test). Participants assessed amount (in millimeters) and direction (posterosuperior/posteroinferior/anterosuperior/anteroinferior/no displacement) of displacement; recommended treatment (surgical or nonoperative); and indicated their level of confidence regarding the recommended treatment on a scale from 0 to 10 for every case. Overall recommendation for treatment was expressed as a surgery score per surgeon by dividing the amount of cases they would operate on by the total number of cases (n = 22) and presented as a percentage. Confidence regarding the decision for treatment was calculated by averaging the confidence score per surgeon, ranging from 0 to 10. We compared interobserver agreement using kappa for categorical variables and intraclass correlation (ICC) for continuous variables. We used multivariable linear regression to assess difference in surgery score and confidence level between imaging groups, controlling for surgeon characteristics. Interobserver agreement for assessment of amount (radiographs: ICC, 0.55, 2-D CT + radiographs ICC, 0.53, 3-D CT + 2-D CT + radiographs ICC, 0.57; p values on all comparisons >0.7) and direction (radiographs: kappa, 0.30, 2-D CT + radiographs kappa, 0.43, 3-D CT + 2-D CT + radiographs kappa, 0.40; p values for all comparisons >0.096) of displacement did not vary by imaging modality. 2-D CT and radiographs (β regression coefficient [β], 3.1; p = 0.253) and 3-D CT, 2-D CT and radiographs (β, 1.6; p = 0.561) did not result in a difference in recommendation for surgery compared with radiographs alone. 2-D CT and radiographs (β, 0.40; p = 0.021) and 3-D CT, 2-D CT and radiographs (β, 0.44; p = 0.011) were associated with slightly higher levels of confidence compared with radiographs alone. Imaging modality, with the numbers evaluated, does not influence interobserver agreement of greater tuberosity fracture assessment, nor did it influence the recommendation for surgical treatment. However, surgeons did feel slightly more confident about their treatment recommendation when assessing CT images with radiographs compared with radiographs alone. Our results therefore suggest no additional value of CT scans for assessment of greater tuberosity fractures when displacement seems to be minimal on plain radiographs. CT scans could be helpful in borderline cases, or in case other fractures can be expected (eg, an occult surgical neck fracture). Level III, diagnostic stud

    Bony reconstruction after failed labral repair is associated with higher recurrence rates compared to primary bony reconstruction: a systematic review and meta-analysis of 1319 shoulders in studies with a minimum of 2-year follow-up

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    Background: There is uncertainty with regard to the optimal revision procedure after failed labral repair for anterior shoulder instability. An overview of outcomes of these procedures with quantitative analysis is not available in literature. The aim of this review is (1) to compare recurrence rates after revision labral repair (RLR) and revision bony reconstruction (RBR), both following failed labral repair. In addition, (2) recurrence rates after RBR following failed labral repair and primary bony reconstruction (PBR) are compared to determine if a previous failed labral repair influences the outcomes of the bony reconstruction. Methods: Randomized controlled trials and cohort studies with a minimum follow-up of 2 years and reporting recurrence rates of (1) RBR following failed labral repair and PBR and/or (2) RLR following failed labral repair and RBR following failed labral repair were identified by searching PubMed, Embase/Ovid, Cochrane Database of Systematic Reviews/Wiley, Cochrane Central Register of Controlled Trials/Wiley, and Web of Science/Clarivate Analytics. Results: Thirteen studies met the inclusion criteria and comprised 1319 shoulders. Meta-analyses showed that RBR has a significantly higher recurrence rate than PBR (risk ratio [RR] 0.51, P < .008) but found no significant difference in the recurrence rates for RLR and RBR (RR 1.40, P < .49). Also, no significant differences were found between PBR and RBR in return to sport (RR 1.07, P < .41), revision surgery (RR 0.8, P < .44), and complications (RR 0.84, P < .53). Lastly, no significant differences between RLR and RBR for revision surgery (RR 3.33, P < .19) were found. Conclusion: The findings of this meta-analyses show that (1) RBR does not demonstrate a significant difference in recurrence rates compared with RLR and that (2) RBR has a significantly higher recurrence rate than PBR

    The Popeye sign: a doctor's and not a patient's problem

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    Background: The Popeye sign is a frequently reported finding following long head of the biceps (LHB) surgery and may be more often detected by doctors than by patients. This study investigates agreement between patients and doctors regarding the presence of a Popeye sign following LHB surgery. Method: This interobserver study investigates agreement between patients and consulting physicians with regard to assessment of a Popeye sign in patients following LHB surgery. Furthermore, this was compared with assessments by non–consulting physicians (observers) using digital photographs of the operated arm, taken both preoperatively and postoperatively. Data about gender, age, and body mass index (BMI) were collected to investigate their role in doctor's reporting of a Popeye sign. Patient's dissatisfaction with a Popeye sign in the operated arm was evaluated as well. Results: Ninety-seven patients (mean age 61 ± 6.0 years, 62% male) underwent LHB surgery. A Popeye sign was reported by 2 patients (2%) as opposed to 32 cases (40%) by consulting physicians, of which only 1 case was in agreement. Krippendorff's alpha (Kalpha) for agreement between observers for preoperative photographs was 0.074 (95% CI −0.277, 0.382) and 0.495 (95% CI 0.317, 0.659) for postoperative cases. Kalpha between observers and consulting physicians for pre- and postoperative cases were 0.033 (95% CI −970, 0.642) and 0.499 (95% CI 0.265, 0.699), respectively. Phi coefficient analysis showed a moderate, statistically significant correlation between male sex and Popeye sign identification. Rank-biserial calculation revealed negligible correlation between BMI and age with regard to detecting a Popeye sign by both consulting physicians and observers. Dissatisfaction about swelling in the upper arm was reported in 1 case, though in a location that did not correspond to the location of a Popeye sign. Conclusion: The Popeye sign is more often identified by doctors than by patients after undergoing LHB surgery. BMI and age are not related to the detection of a Popeye sign, but sex is moderately correlated. Together with the low percentage of dissatisfaction of patients with this swelling, this signifies that a Popeye sign seems to be a doctor's rather than a patient's problem

    Follow-up radiographs in isolated Greater Tuberosity fractures lead to a change in treatment recommendation; an online survey study

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    Introduction: It is common practice to obtain follow-up radiographs of non-operatively treated isolated greater tuberosity (GT) fractures 1 to 2 weeks after trauma. However, the majority of non-operatively treated GT fractures remain stable and do not require reconsideration of the initial treatment decision. Radiological follow-up therefore might be unnecessary. Our primary objective was to study whether radiological folow-up changes the initial treatment recommendation, hypothesizing no change. Materials and methods: Radiographs of 25 patients diagnosed with an isolated GT fracture were selected from our hospital database and presented on a web-based platform. Sixty-eight trauma- and orthopedic surgeons evaluated these radiographs. First the radiographs directly post-trauma and then, in random order, the radiographs 5-14 days post-trauma alongside the first radiographs. Each observer evaluated each set of radiographs once. The observers answered which treatment they would recommend (non-operative/operative), and how certain they were about their advice (absolutely certain, certain, some doubt, very uncertain). Recommendation-consistency and inter-observer agreement are presented as percentages and intra class correlation coefficients (ICC). Results: Overall, 84% (95% CI 82.1–85.8) of treatment recommendations was unchanged after evaluation of the second radiograph. Agreement within each observer ranged from 60 to 98%. The mean proportion of patients about whom the observers were (absolutely) certain of their recommendation increased from 70% at the first evaluation to 83% at the second evaluation (12.8; 95% CI 9.8–15.9). Furthermore, the ICC between the surgeons improved from 0.37 (95% CI 0.26–0.54) for the first evaluation to 0.60 (95% CI 0.47–0.74) for the second. Conclusion: In 16% of the patients the treatment recommendation for an isolated GT fracture changed after the evaluation of radiographs 1 to 2 weeks post-trauma. In addition, surgeons were more certain about their recommendation and there was less inter-observer variation. Radiological follow-up of a non-operatively treated isolated GT fracture therefore seems justifiable. Level of evidence: III, diagnostic study

    The Popeye sign: a doctor's and not a patient's problem

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    Background: The Popeye sign is a frequently reported finding following long head of the biceps (LHB) surgery and may be more often detected by doctors than by patients. This study investigates agreement between patients and doctors regarding the presence of a Popeye sign following LHB surgery. Method: This interobserver study investigates agreement between patients and consulting physicians with regard to assessment of a Popeye sign in patients following LHB surgery. Furthermore, this was compared with assessments by non–consulting physicians (observers) using digital photographs of the operated arm, taken both preoperatively and postoperatively. Data about gender, age, and body mass index (BMI) were collected to investigate their role in doctor's reporting of a Popeye sign. Patient's dissatisfaction with a Popeye sign in the operated arm was evaluated as well. Results: Ninety-seven patients (mean age 61 ± 6.0 years, 62% male) underwent LHB surgery. A Popeye sign was reported by 2 patients (2%) as opposed to 32 cases (40%) by consulting physicians, of which only 1 case was in agreement. Krippendorff's alpha (Kalpha) for agreement between observers for preoperative photographs was 0.074 (95% CI −0.277, 0.382) and 0.495 (95% CI 0.317, 0.659) for postoperative cases. Kalpha between observers and consulting physicians for pre- and postoperative cases were 0.033 (95% CI −970, 0.642) and 0.499 (95% CI 0.265, 0.699), respectively. Phi coefficient analysis showed a moderate, statistically significant correlation between male sex and Popeye sign identification. Rank-biserial calculation revealed negligible correlation between BMI and age with regard to detecting a Popeye sign by both consulting physicians and observers. Dissatisfaction about swelling in the upper arm was reported in 1 case, though in a location that did not correspond to the location of a Popeye sign. Conclusion: The Popeye sign is more often identified by doctors than by patients after undergoing LHB surgery. BMI and age are not related to the detection of a Popeye sign, but sex is moderately correlated. Together with the low percentage of dissatisfaction of patients with this swelling, this signifies that a Popeye sign seems to be a doctor's rather than a patient's problem
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