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Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

ABSTRACT: Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles, there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RNA-seq over microarrays, we assessed differences in transcript expression in anterior cruciate ligament (ACL) tissues based on time-from-injury. ACL remnants were collected from patients with an ACL tear at the time of ACL reconstruction. RNA prepared from torn ACL remnants was subjected to Agilent microarrays (N?=?24) and RNA-seq (N?=?8). The correlation of biological replicates in RNA-seq and microarrays data was similar (0.98 vs. 0.97), demonstrating that each platform has high internal reproducibility. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarrays values were moderate. The cross-platform concordance for differentially expressed transcripts or enriched pathways was linearly correlated (r?=?0.64). RNA-Seq was superior in detecting low abundance transcripts and differentiating biologically critical isoforms. Additional independent validation of transcript expression was undertaken using microfluidic PCR for selected genes. PCR data showed 100% concordance (in expression pattern) with RNA-seq and microarrays data. These findings demonstrate that RNA-seq has advantages over microarrays for transcriptome profiling of ligament tissues when available and affordable. Furthermore, these findings are likely transferable to other musculoskeletal tissues where tissue collection is challenging and cells are in low abundance. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:484-497, 2018.

SUBMITTER: Rai MF

PROVIDER: S-EPMC5787041 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

Rai Muhammad Farooq MF Tycksen Eric D ED Sandell Linda J LJ Brophy Robert H RH

Journal of orthopaedic research : official publication of the Orthopaedic Research Society 20170829 1

Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles, there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RN ...[more]

PMID: 28749036

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Project description:BackgroundAn anterior cruciate ligament (ACL) tear is a common knee injury, particularly among young and active individuals. Little is known, however, about the societal impacts of ACL tears, which could be large given the typical patient age and increased lifetime risk of knee osteoarthritis. This study evaluates the cost-effectiveness of ACL reconstruction compared with structured rehabilitation only.MethodsA cost-utility analysis of ACL reconstruction compared with structured rehabilitation only was conducted with use of a Markov decision model over two time horizons: the short to intermediate term (six years), on the basis of Level-I evidence derived from the KANON Study and the Multicenter Orthopaedic Outcomes Network (MOON) database; and the lifetime, on the basis of a comprehensive literature review. Utilities were assessed with use of the SF-6D. Costs (in 2012 U.S. dollars) were estimated from the societal perspective and included the effects of the ACL tear on work status, earnings, and disability. Effectiveness was expressed as quality-adjusted life years (QALYs) gained.ResultsIn the short to intermediate term, ACL reconstruction was both less costly (a cost reduction of $4503) and more effective (a QALY gain of 0.18) compared with rehabilitation. In the long term, the mean lifetime cost to society for a typical patient undergoing ACL reconstruction was $38,121 compared with $88,538 for rehabilitation. ACL reconstruction resulted in a mean incremental cost savings of $50,417 while providing an incremental QALY gain of 0.72 compared with rehabilitation. Effectiveness gains were driven by the higher probability of an unstable knee and associated lower utility in the rehabilitation group. Results were most sensitive to the rate of knee instability after initial rehabilitation.ConclusionsACL reconstruction is the preferred cost-effective treatment strategy for ACL tears and yields reduced societal costs relative to rehabilitation once indirect cost factors, such as work status and earnings, are considered. The cost of an ACL tear over the lifetime of a patient is substantial, and resources should be directed to developing innovations for injury prevention and for altering the natural history of an ACL injury.

Project description:PurposeTo evaluate the incidence of complete lateral meniscal posterior root tears (LMPRTs) repaired at revision as compared with primary anterior cruciate ligament (ACL) reconstruction (PACLR) and to determine whether other demographic or surgical characteristics were associated with LMPRTs needing repair.MethodsA chart review was performed to identify the PACLR and revision ACL reconstruction (RACLR) cohorts. Demographic and surgical characteristics were recorded. Cases with concurrent lateral meniscal posterior root repair were identified. Cases were classified as acute (<5 months) or chronic (>5 months) based on the time from reported injury to surgery. Tunnel malposition in revision cases was recorded if either tunnel or both tunnels were malpositioned on radiographs and magnetic resonance imaging.ResultsData from 167 cases, 140 PACLR and 27 RACLR cases, were included. The cohorts had similar demographic characteristics including age, sex, and lateral meniscal injury. The overall incidence of lateral meniscal root repair in ACL reconstruction patients was 12.6% (21 of 167 patients). The incidence of LMPRT repair was 7.1% (10 of 140 patients) in the PACLR cohort versus 40.7% (11 of 27 patients) in the RACLR cohort. The revision cohort was significantly more likely to have a chronic injury (66.7% [18 of 27 patients] vs 31.4% [44 of 140 patients]). The most significant predictor of concurrent lateral meniscal posterior root repair was RACLR versus PACLR for both univariate and multivariate logistic regression analyses (χ2 = 20.603; P < .0001; odds ratio, 13.887; 95% confidence interval, 1.531-125.993). Analysis of tunnel positions for the revision group revealed that PACLR tunnel malposition was a significant predictor of LMPRTs (χ2 = 4.91, P = .027).ConclusionsComplete LMPRTs warranting repair are encountered with a significantly greater frequency at RACLR as compared with PACLR. The overall incidence of LMPRT repair at RACLR is high. In this cohort, LMPRT repair in RACLR cases was associated with tunnel malposition of the PACLR.Level of evidenceLevel III, retrospective cohort study.

Project description:BackgroundBridge-enhanced anterior cruciate ligament repair (BEAR) has noninferior patient-reported outcomes when compared with autograft anterior cruciate ligament reconstruction (ACLR) at 2 years. However, the comparison of BEAR and autograft ACLR at earlier time points-including important outcomes such as resolution of knee pain and symptoms, recovery of strength, and return to sport-has not yet been reported.HypothesisIt was hypothesized that the BEAR group would have higher outcomes on the International Knee Documentation Committee and Knee injury and Osteoarthritis Outcome Score, as well as improved muscle strength, in the early postoperative period.Study designRandomized controlled trial; Level of evidence, 1.MethodsA total of 100 patients aged 13 to 35 years with complete midsubstance anterior cruciate ligament injuries were randomized to receive a suture repair augmented with an extracellular matrix implant (n = 65) or an autograft ACLR (n = 35). Outcomes were assessed at time points up to 2 years postoperatively. Mixed-model repeated-measures analyses were used to compare BEAR and ACLR outcomes. Patients were unblinded after their 2-year visit.ResultsRepeated-measures testing revealed a significant effect of group on the International Knee Documentation Committee Subjective Score (P = .015), most pronounced at 6 months after surgery (BEAR = 86 points vs ACLR = 78 points; P = .001). There was a significant effect of group on the Knee injury and Osteoarthritis Outcome Score-Symptoms subscale scores (P = .010), largely attributed to the higher BEAR scores at the 1-year postoperative time point (88 vs 82; P = .009). The effect of group on hamstring strength was significant in the repeated-measures analysis (P < .001), as well as at all postoperative time points (P < .001 for all comparisons). At 1 year after surgery, approximately 88% of the patients in the BEAR group and 76% of the ACLR group had been cleared for return to sport (P = .261).ConclusionPatients undergoing the BEAR procedure had earlier resolution of symptoms and increased satisfaction about their knee function, as well as improved resolution of hamstring muscle strength throughout the 2-year follow-up period.RegistrationNCT02664545 (ClinicalTrials.gov identifier).

Project description:ObjectivesPartial ACL tears are increasingly recognized in young active patients. They can evolve into complete tears. Controversy exists regarding the need to spare intact ACL bundle as it has its advantages considering biomechanical strength, blood supply and proprioception. The current study determined the challenges in partial ACL tear management and assessed the functional outcomes.MethodsTwenty consecutive patients with partial ACL tears were studied. Inclusion criteria were: age 16-45yrs and patients operated for partial ACL tear. Exclusion criteria were: combined ACL-PCL injuries, associated collateral injuries, complete ACL tear, chondral defect or bony malalignment and patients with radiographic signs of arthritis. 'Partial' tear was defined as continuous fibers from native tibial ACL footprint to native femoral ACL footprint in arthroscopy. Clinical and radiological assessment was done to evaluate anteromedial(AM) or posterolateral(PL) bundle tears. We used the term "ACL-augmentation" without disturbing the intact bundle or preserving the intact fibers as much as possible. Functional scoring was done using Lysholm score. Standard post-operative protocols were followed. Statistical analysis was done using SPSS software.ResultsMean age of patients was 31.2 years. Physically active age group (<30yrs) included 62.5% patients. Males were 87.5%. Pain and instability were the presenting complaints in 75% and 70% respectively. Average duration of presentation since injury was 4.2 months. Sports activities were the most common mode of injury (45%) followed by road traffic accidents (37.5%). Anterior drawer test was positive in 40%, pivot shift in 35% and Lachman test was positive in 65%. On arthroscopy, 65% had AM bundle tears and 35% had PL bundle tears. The intact bundle was found lax in 13% cases. Associated meniscal tear was present in 28% patients. Stiff knee was the most common post-operative complaint. Preoperative Lysholm knee score of 74.5 improved to 87.7 at 12months (p < 0.001). Around 97.5% of the patients reported outcomes as good and fair.ConclusionThe treatment strategy needs to be individualized. The ACL augmentation needs more systematic and accurate placement of portals while sparing the intact ACL fibers. For AM bundle, tibial tunnel entry point is about 1-2 cm medial to tibial tuberosity. For PL bundle, it is about 3-4 cm medial to tibial tuberosity to protect the AM bundle. Long term studies with greater number of subjects are required.

Dataset Information

Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

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Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

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