The Heterogeneity of Pediatric Knee Infections: A Retrospective Analysis.

BACKGROUND: Musculoskeletal infection is a major cause of morbidity in the pediatric population. Despite the canonical teaching that an irritable joint and signs of infection likely represent an infected joint space, recent evidence in the pediatric hip has demonstrated that alternative diagnoses are equally or more likely and that combinations of pathologies are common. The knee is the second most commonly infected joint in children, yet there remains a paucity of available data regarding the epidemiology and workup of the infected pediatric knee. The authors hypothesize that there is heterogeneity of pathologies, including combinations of pathologies, that presents as a potentially infected knee in a child. The authors aim to show the utility of magnetic resonance imaging and epidemiologic and laboratory markers in the workup of these patients. METHODS: A retrospective review of all consults made to the pediatric orthopaedic surgery team at a single tertiary care center from September 2009 through December 2015 regarding a concern for potential knee infection was performed. Excluded from the study were patients with penetrating trauma, postoperative infection, open fracture, no C-reactive protein (CRP) within 24 hours of admission, sickle cell disease, an immunocompromised state, or chronic osteomyelitis. RESULTS: A total of 120 patients were analyzed in this study. There was marked variability in pathologies. Patients with isolated osteomyelitis or osteomyelitis+septic arthritis were older, had an increased admission CRP, were more likely to be infected with Staphylococcus aureus, required an increased duration of antibiotics, and had an increased incidence of musculoskeletal complications than patients with isolated septic arthritis. CONCLUSIONS: When considering a child with an irritable knee, a heterogeneity of potential underlying pathologies and combinations of pathologies are possible. Importantly, the age of the patient and CRP can guide a clinician when considering further workup. Older patients with a higher admission CRP value warrant an immediate magnetic resonance imaging, as they are likely to have osteomyelitis, which was associated with worse outcomes when compared with patients with isolated septic arthritis. LEVEL OF EVIDENCE: Level III-retrospective research study.

Assessing Diagnostic Arthroscopy Performance in the Operating Room Using the Arthroscopic Surgery Skill Evaluation Tool (ASSET).

PURPOSE: To determine the validity and reliability of using the Arthroscopic Surgery Skill Evaluation Tool (ASSET) to assess arthroscopic skill in the operating room. METHODS: Eight orthopaedic residents, 1 sports medicine fellow, and 3 sports medicine faculty members recorded the diagnostic portion of 3 shoulder and 3 knee procedures in the operating room. Two blinded raters used the ASSET to assess each recorded procedure video. Criterion for a passing score on a procedure was attaining a 3 or greater in all 8 domains assessed. RESULTS: In total 70 videos (36 shoulder, 34 knee) were evaluated by each rater. The attending/fellow group was assigned significantly higher mean ASSET scores compared with resident groups for both procedures (P = .01). The attending/fellow group also had the highest passing percentage (95.8%). Raters were in agreement for total ASSET scores assigned to both diagnostic arthroscopy of the shoulder (intraclass correlation coefficient [ICC] = 0.84) and knee (ICC = 0.81). Agreement on individual ASSET domains was moderate (ICC = 0.61 to 0.80) for all domains except safety and difficulty of procedure. Raters concurred on the pass-fail evaluation in 62 of 70 (88.6%) of procedures evaluated. CONCLUSIONS: Using the ASSET to assess surgical skills in the operating room is feasible, reliable, and valid. CLINICAL RELEVANCE: When combined with previously published results using the ASSET, the ASSET may provide a validated and reliable method for evaluating arthroscopic surgical skills in the surgical simulation lab and operating room.

Droplet Digital™ PCR quantitation of HER2 expression in FFPE breast cancer samples.

UNLABELLED: The human epidermal growth factor receptor 2 (HER2, also known as erbB2) gene is involved in signal transduction for cell growth and differentiation. It is a cell surface receptor tyrosine kinase and a proto-oncogene. Overexpression of HER2 is of clinical relevance in breast cancer due to its prognostic value correlating elevated expression with worsening clinical outcome. At the same time, HER2 assessment is also of importance because successful anti-tumor treatment with Herceptin® is strongly correlated with HER2 overexpression in the tumor (approximately 30% of all breast tumors overexpress HER2). In a comprehensive national study, Wolff et al. [1] state that "Approximately 20% of current HER2 testing may be inaccurate" which underscores the importance of developing more accurate methods to determine HER2 status. Droplet Digital™ PCR (ddPCR™) has the potential to improve upon HER2 measurements due to its ability to quantitate DNA and RNA targets with high precision and accuracy. Here we present a study which investigates whether ddPCR can be used to assess HER2 transcript levels in formalin-fixed paraffin embedded (FFPE) human breast tumors and whether these ddPCR measurements agree with prior assessments of these same samples by pathologists using immunohistochemistry (IHC) and in some cases fluorescence in situ hybridization (FISH). We also determined the copy number of HER2 in these samples as compared to the CEP17 reference gene. RESULTS: Clinical FFPE samples were successfully studied using ddPCR and compared to results from standard FISH and IHC methodology. The results demonstrate that ddPCR can rank order the samples in complete agreement with the current standard methods and that ddPCR has the added benefit of providing quantitative results, rather than relying on the expert skill of a seasoned pathologist for determination.

Walking time to nearest public automated external defibrillator for out-of-hospital cardiac arrest in a major U.S. city.

Background: How frequently out-of-hospital cardiac arrest (OHCA) occurs within a reasonable walking distance to the nearest public automated external defibrillator (AED) has not been well studied. Methods: As Kansas City, Missouri has a comprehensive city-wide public AED registry, we identified adults with an OHCA in Kansas City during 2019-2022 in the Cardiac Arrest Registry to Enhance Survival. Using AED location data from the registry, we computed walking times between OHCAs and the nearest registered AED using the Haversine formula, a mapping algorithm to calculate walking distance in miles from one location to another. Results were stratified by OHCA location (home vs. public) and by whether the patient received bystander cardiopulmonary resuscitation (CPR). Results: Of 1,522 OHCAs, 1,291 (84.8%) occurred at home and 231 (15.2%) in public. Among at-home OHCAs, 634 (49.1%) received bystander CPR and no patients had an AED applied even as 297 (23.0%) were within a 4-minute walk to the closest public AED. Among OHCAs in public, 108 (46.8%) were within a 4-minute walk to the closest public AED. For public OHCAs within a 4-minute walk, bystanders applied an AED in 13 (12.0%) of these cases and in 24.5% (13/53) of those who received bystander CPR. Conclusion: In one U.S. city with a publicly available AED registry, there were no instances in which a bystander accessed a public AED for an OHCA at home. For OHCAs in public, nearly half occurred within a 4-minute walk to the closest AED but bystander use of an AED was low.

In-hospital post-operative fever after posterior spinal fusion for neuromuscular scoliosis in non-ambulatory cerebral palsy patients: is there value for clinical workup for an isolated fever?

PURPOSE: Children with neuromuscular scoliosis (NMS) resultant to cerebral palsy (CP) are at a heightened risk for complications following surgical treatment. These children have a reported 22-64% rate of post-operative fever development, and additional fever workup has been shown to have limited clinical utility. However, this has yet to be investigated in the setting of an accelerated discharge (AD) pathway. METHODS: A retrospective review of children with non-ambulatory CP treated at 2 centers with posterior spinal fusion (PSF) for NMS was performed. One institution uses a standardized AD post-operative pathway for NMS patients, whereas the second institution had no standard pathway. A post-operative fever was defined as temperature > 38.5 °C. Target outcome variables included the development of a fever as well as re-admission within 90 days of surgery. RESULTS: A total of 122 non-ambulatory children were identified (82% GMFCS V, mean 14.3 ± 3.4 years at surgery). A post-operative fever was documented in 75.4% of patients (N = 92) and all additional culture studies reported negative results. Children admitted to the PICU were more likely to undergo a fever workup (P < 0.001) and more likely to receive additional or extended antibiotic therapy (P < 0.001). Children treated at the AD pathway had a significantly lower rate of PICU admission (P < 0.001). Post-operative PICU admission was associated with a post-operative fever (49.5% vs 25%, P = 0.03). CONCLUSION: Non-ambulatory CP children with NMS undergoing PSF have a 75.4% rate of developing early post-operative fevers. Reflexive fever work-ups provided limited clinical utility while increasing the hospital length of stay and potentially exposing patients to antibiotic-related complications.

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

Droplet digital PCR measurement of HER2 copy number alteration in formalin-fixed paraffin-embedded breast carcinoma tissue.

BACKGROUND: Human epidermal growth factor receptor 2 (HER2) testing is routinely performed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) analyses for all new cases of invasive breast carcinoma. IHC is easier to perform, but analysis can be subjective and variable. FISH offers better diagnostic accuracy and added confidence, particularly when it is used to supplement weak IHC signals, but it is more labor intensive and costly than IHC. We examined the performance of droplet digital PCR (ddPCR) as a more precise and less subjective alternative for quantifying HER2 DNA amplification. METHODS: Thirty-nine cases of invasive breast carcinoma containing ≥30% tumor were classified as positive or negative for HER2 by IHC, FISH, or both. DNA templates for these cases were prepared from formalin-fixed paraffin-embedded (FFPE) tissues to determine the HER2 copy number by ddPCR. ddPCR involved emulsifying hydrolysis probe-based PCR reaction mixtures containing the ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian); also known as HER2] gene and chromosome 17 centromere assays into nanoliter-sized droplets for thermal cycling and analysis. RESULTS: ddPCR distinguished, through differences in the level of HER2 amplification, the 10 HER2-positive samples from the 29 HER2-negative samples with 100% concordance to HER2 status obtained by FISH and IHC analysis. ddPCR results agreed with the FISH results for the 6 cases that were equivocal by IHC analyses, confirming 2 of these samples as positive for HER2 and the other 4 as negative. CONCLUSIONS: ddPCR can be used as a molecular-analysis tool to precisely measure copy number alterations in FFPE samples of heterogeneous breast tumor tissue.

Is there a valid and reliable assessment of diagnostic knee arthroscopy skill?

BACKGROUND: The Basic Arthroscopic Knee Skill Scoring System (BAKSSS) has construct validity as an objective measure of arthroscopic proficiency when used to assess the task of performing arthroscopic meniscectomies on cadaver knees. The reliability of this instrument is unknown. QUESTIONS/PURPOSE: We asked whether (1) a simple modification of the BAKSSS would show construct validity similar to that in the initial BAKSSS study, (2) this assessment would be reliable, and (3) this assessment could be used as a high-stakes pass or fail test. METHODS: Twenty-three orthopaedic residents performed diagnostic knee arthroscopies on cadaveric knee specimens. Their competency was assessed by three live raters using the modified BAKSSS. Interrater reliability was assessed by comparing the scores given by each rater to each subject. RESULTS: The modified BAKSSS showed construct validity with junior residents achieving lower scores (mean score, 20) than senior residents (mean score, 33). The modified BAKSSS had an interrater reliability of kappa = 0.685-0.852. The modified BAKSSS had a kappa = 0.543 when used as a proficiency test for diagnostic arthroscopy. CONCLUSIONS: The modified BAKSSS is useful for assessing diagnostic knee arthroscopy proficiency. Future scoring systems should be designed to be generalizable so they can be applied to multiple procedures without the need for modification, allow for video-based assessment, and must be rigorously tested for reliability and other types of validity (eg, face validity, content validity, and criterion-related validity). CLINICAL RELEVANCE: Having a valid and reliable assessment of basic arthroscopic procedures may allow educators to more adequately evaluate individual residents and the effectiveness of various training modalities.

The uniqueome: a mappability resource for short-tag sequencing.

SUMMARY: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the 'uniqueome', a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data. AVAILABILITY: Files, scripts and supplementary data are available from http://grimmond.imb.uq.edu.au/uniqueome/; the ISAS uniqueome aligner is freely available from http://www.imagenix.com/.

High-throughput droplet digital PCR system for absolute quantitation of DNA copy number.

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ~2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.

Flexible Intramedullary Nailing of Pediatric Femoral Fractures.

BACKGROUND: Flexible intramedullary nailing is performed for femoral fractures in pediatric patients who may be too large for spica cast immobilization but who have substantial growth remaining and who are not a candidate for rigid intramedullary nailing. Flexible nailing allows the surgeon to obtain correct alignment of the femur fracture so as to allow for healing without a lower extremity deformity. DESCRIPTION: The patient is positioned on a radiolucent table, flexible nails are chosen according to the diameter of the medullary canal, medial and lateral incisions are made along the distal aspect of the thigh, and access to the canal is obtained with use of a drill-bit of the appropriate size. Flexible nails are contoured to place the apex at the location of the fracture site and then passed 1 at a time up to the fracture through the medial and lateral corticotomies. Fracture reduction is obtained, and the nails are passed across the fracture 1 at a time. Leave a small amount of nail prominent at the entry site; the nails are then cut and advanced with a tamp. ALTERNATIVES: Spica cast immobilization, rigid intramedullary nailing, external fixation, and submuscular plating. RATIONALE: Flexible nailing provides relative stability of a femoral fracture similar to external fixation, submuscular plating, and rigid nailing; however, external fixators come with pin-track complications and infections, as well as a bulky device external to the thigh. Submuscular plating is beneficial for length-unstable fractures but is a longer procedure and implant removal is more difficult. In an older child with growth remaining, a rigid femoral nail is an option with similar outcomes to flexible nailing; however, the implant is harder to remove. Flexible nailing provides a cosmetic incision with reliable relative fixation in length-stable fractures, and easy removal of implants with equal or even improved outcomes compared with other surgical techniques. EXPECTED OUTCOMES: The outcomes of this procedure are excellent. Most pediatric femoral fractures treated with flexible nailing heal well with few complications. Angulation at the fracture site is the most common complication and is more common in fractures of the proximal or distal third of the femur1. Worse outcomes occur in older children and children who are heavier1. Outcomes are improved when flexible nailing is done in length-stable fractures; however, postoperative immobilization in a single-leg spica cast or knee immobilizer can augment fixation in fractures that are not stable. Implant irritation can occur at the insertion site; however, the implants are easy to remove once the fracture has healed. There is a substantially lower rate of malunion when stainless-steel nails (6%) are utilized compared with titanium nails (23%). Consideration should therefore be given to the use of stainless-steel nails for pediatric femoral fractures2. IMPORTANT TIPS: Use a radiolucent table with either a post or a sheet for counter-traction aids during reductionUse stainless-steel nailsPass the easier nail firstAdvance into the femoral neck or trochanteric apophysisDo not wrap rods around each otherCut off the machined tip of the nail and custom-contour the nail in patients with poor bone quality.

Reduction in Diameter of Hamstring Autograft With Additional Circumferential Preconditioning During ACL Reconstruction in a Pediatric Population.

BACKGROUND: Over 130,000 anterior cruciate ligament (ACL) reconstructions (ACLRs) are performed annually in the United States. Previous studies have shown that circumferential preconditioning reduces the diameter of fresh-frozen allografts, but no studies have described the effect in ACL autografts used during ACLR. PURPOSE: To characterize the changes in the hamstring autograft diameter as a result of preparatory circumferential preconditioning. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: A total of 135 patients with ACLR, with a median age of 15 years (interquartile range, 14-16 years; 50.4% boys), were identified in 2 pediatric hospitals. Three orthopaedic surgeons recorded hamstring autograft diameters at 2 time points during graft preparation. Hamstring tendons were prepared using a standardized procedure, tensioned to 15 to 20 lbs, and measured using cylindrical sizing guides. The graft was left with passive compression in the smallest initial rigid sizing guide for 10 minutes on both the tibial and femoral sides and then measured again immediately before implantation. Tunnels were drilled based on the second measurement of graft size. Comparisons were made between the graft diameter before and after circumferential preconditioning. A random-effects regression model and a linear regression model were performed to capture any unexplained variance on the linear predictor scale and determine correlations between demographics and graft characteristics. RESULTS: The median initial diameter for both femoral and tibial sides was 9.5 mm. After longitudinal tension and circumferential preconditioning, the median autograft diameter of both sides decreased by 1 mm (P < .001) to 8.5 mm. In the random-effects model, decreased patient height was a significant predictor of greater reduction in graft diameter. Increased height was a significant predictor for greater initial graft diameter (average beta coefficient = 3.08; P < .01). No intraoperative complications were noted with implantation of the preconditioned grafts in smaller diameter tunnels. CONCLUSION: The median diameter of hamstring ACL autografts decreases by 1 mm after circumferential preconditioning within standard cylindrical sizing guides. This allowed for drilling of tunnels that were an average of 1 mm smaller without any noted intraoperative complications with graft insertion.

Defining the volume of consultations for musculoskeletal infection encountered by pediatric orthopaedic services in the United States.

OBJECTIVE: Adequate resources are required to rapidly diagnose and treat pediatric musculoskeletal infection (MSKI). The workload MSKI consults contribute to pediatric orthopaedic services is unknown as prior epidemiologic studies are variable and negative work-ups are not included in national discharge databases. The hypothesis was tested that MSKI consults constitute a substantial volume of total consultations for pediatric orthopaedic services across the United States. STUDY DESIGN: Eighteen institutions from the Children's ORthopaedic Trauma and Infection Consortium for Evidence-based Study (CORTICES) group retrospectively reviewed a minimum of 1 year of hospital data, reporting the total number of surgeons, total consultations, and MSKI-related consultations. Consultations were classified by the location of consultation (emergency department or inpatient). Culture positivity rate and pathogens were also reported. RESULTS: 87,449 total orthopaedic consultations and 7,814 MSKI-related consultations performed by 229 pediatric orthopaedic surgeons were reviewed. There was an average of 13 orthopaedic surgeons per site each performing an average of 154 consultations per year. On average, 9% of consultations were MSKI related and 37% of these consults yielded positive cultures. Finally, a weak inverse monotonic relationship was noted between percent culture positivity and percent of total orthopedic consults for MSKI. CONCLUSION: At large, academic pediatric tertiary care centers, pediatric orthopaedic services consult on an average of ~3,000 'rule-out' MSKI cases annually. These patients account for nearly 1 in 10 orthopaedic consultations, of which 1 in 3 are culture positive. Considering that 2 in 3 consultations were culture negative, estimating resources required for pediatric orthopaedic consult services to work up and treat children based on culture positive administrative discharge data underestimates clinical need. Finally, ascertainment bias must be considered when comparing differences in culture rates from different institution's pediatric orthopaedics services, given the variability in when orthopaedic physicians become involved in a MSKI workup.

Surgeon Agreement on the Presence of Pathologic Anterior Instability on Shoulder Imaging Studies.

BACKGROUND: In the setting of anterior shoulder instability, it is important to assess the reliability of orthopaedic surgeons to diagnose pathologic characteristics on the 2 most common imaging modalities used in clinical practice: standard plain radiographs and magnetic resonance imaging (MRI). PURPOSE: To assess the intra- and interrater reliability of diagnosing pathologic characteristics associated with anterior shoulder instability using standard plain radiographs and MRI. STUDY DESIGN: Cohort study (diagnosis); Level of evidence, 3. METHODS: Patient charts at a single academic institution were reviewed for anterior shoulder instability injuries. The study included 40 sets of images (20 radiograph sets, 20 MRI series). The images, along with standardized evaluation forms, were distributed to 22 shoulder/sports medicine fellowship-trained orthopaedic surgeons over 2 points in time. Kappa values for inter- and intrarater reliability were calculated. RESULTS: The overall response rate was 91%. For shoulder radiographs, interrater agreement was fair to moderate for the presence of glenoid lesions (κ = 0.49), estimate of glenoid lesion surface area (κ = 0.59), presence of a Hill-Sachs lesion (κ = 0.35), and estimate of Hill-Sachs surface area (κ = 0.50). Intrarater agreement was moderate for radiographs (κ = 0.48-0.57). For shoulder MRI, interrater agreement was fair to moderate for the presence of glenoid lesions (κ = 0.44), glenoid lesion surface area (κ = 0.35), Hill-Sachs lesion (κ = 0.33), Hill-Sachs surface area (κ = 0.28), humeral head edema (κ = 0.41), and presence of a capsulolabral injury (κ = 0.36). Fair agreement was found for specific type of capsulolabral injury (κ = 0.21). Intrarater agreement for shoulder MRI was moderate for the presence of glenoid lesion (κ = 0.59), presence of a Hill-Sachs lesion (κ = 0.52), estimate of Hill-Sachs surface area (κ = 0.50), humeral head edema (κ = 0.51), and presence of a capsulolabral injury (κ = 0.53), and agreement was substantial for glenoid lesion surface area (κ = 0.63). Intrarater agreement was fair for determining the specific type of capsulolabral injury (κ = 0.38). CONCLUSION: Fair to moderate agreement by surgeons was found when evaluating imaging studies for anterior shoulder instability. Agreement was similar for identifying pathologic characteristics on radiographs and MRI. There was a trend toward better agreement for the presence of glenoid-sided injury. The lowest agreement was observed for specific capsulolabral injuries.

A robust targeted sequencing approach for low input and variable quality DNA from clinical samples.

Next-generation deep sequencing of gene panels is being adopted as a diagnostic test to identify actionable mutations in cancer patient samples. However, clinical samples, such as formalin-fixed, paraffin-embedded specimens, frequently provide low quantities of degraded, poor quality DNA. To overcome these issues, many sequencing assays rely on extensive PCR amplification leading to an accumulation of bias and artifacts. Thus, there is a need for a targeted sequencing assay that performs well with DNA of low quality and quantity without relying on extensive PCR amplification. We evaluate the performance of a targeted sequencing assay based on Oligonucleotide Selective Sequencing, which permits the enrichment of genes and regions of interest and the identification of sequence variants from low amounts of damaged DNA. This assay utilizes a repair process adapted to clinical FFPE samples, followed by adaptor ligation to single stranded DNA and a primer-based capture technique. Our approach generates sequence libraries of high fidelity with reduced reliance on extensive PCR amplification-this facilitates the accurate assessment of copy number alterations in addition to delivering accurate single nucleotide variant and insertion/deletion detection. We apply this method to capture and sequence the exons of a panel of 130 cancer-related genes, from which we obtain high read coverage uniformity across the targeted regions at starting input DNA amounts as low as 10 ng per sample. We demonstrate the performance using a series of reference DNA samples, and by identifying sequence variants in DNA from matched clinical samples originating from different tissue types.

The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.

Effects of DNA secondary structure on oligonucleotide probe binding efficiency.

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable "window size" around target sites that is as small as possible without compromising folding algorithm prediction accuracy.

Arthroscopic training resources in orthopedic resident education.

The purpose of this study was to determine the frequency of use, perceived effectiveness, and preference for arthroscopic surgical skill training resources. An electronic survey was sent to orthopedics residents, residency program directors, and orthopedic sports medicine attending physicians in the United States. The frequency and perceived effectiveness of 10 types of adjunctive arthroscopic skills training was assessed. Residents and faculty members were asked to rate their confidence in resident ability to perform common arthroscopic procedures. Surveys were completed by 40 of 152 (26.3%) orthopedic residency program directors, 70 of 426 (16.4%) sports medicine faculty, and 235 of 3,170 (7.4%) orthopedic residents. The use of adjunctive methods of training varied from only 9.8% of programs with virtual reality training to 80.5% of programs that used reading of published materials to develop arthroscopic skill. Practice on cadaveric specimens was viewed as the most effective and preferred adjunctive method of training. Residents trained on cadaveric specimens reported increased confidence in their ability to perform arthroscopic procedures. The resources for developing arthroscopic surgical skill vary considerably across orthopedic residency programs in the United States. Adjunctive training methods were perceived to be effective at supplementing traditional training in the operating room.

A rapid molecular approach for chromosomal phasing.

Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).

Using the arthroscopic surgery skill evaluation tool as a pass-fail examination.

BACKGROUND: Examination of arthroscopic skill requires evaluation tools that are valid and reliable with clear criteria for passing. The Arthroscopic Surgery Skill Evaluation Tool was developed as a video-based assessment of technical skill with criteria for passing established by a panel of experts. The purpose of this study was to test the validity and reliability of the Arthroscopic Surgery Skill Evaluation Tool as a pass-fail examination of arthroscopic skill. METHODS: Twenty-eight residents and two sports medicine faculty members were recorded performing diagnostic knee arthroscopy on a left and right cadaveric specimen in our arthroscopic skills laboratory. Procedure videos were evaluated with use of the Arthroscopic Surgery Skill Evaluation Tool by two raters blind to subject identity. Subjects were considered to pass the Arthroscopic Surgery Skill Evaluation Tool when they attained scores of ≥ 3 on all eight assessment domains. RESULTS: The raters agreed on a pass-fail rating for fifty-five of sixty videos rated with an interclass correlation coefficient value of 0.83. Ten of thirty participants were assigned passing scores by both raters for both diagnostic arthroscopies performed in the laboratory. Receiver operating characteristic analysis demonstrated that logging more than eighty arthroscopic cases or performing more than thirty-five arthroscopic knee cases was predictive of attaining a passing Arthroscopic Surgery Skill Evaluation Tool score on both procedures performed in the laboratory. CONCLUSIONS: The Arthroscopic Surgery Skill Evaluation Tool is valid and reliable as a pass-fail examination of diagnostic arthroscopy of the knee in the simulation laboratory. CLINICAL RELEVANCE: This study demonstrates that the Arthroscopic Surgery Skill Evaluation Tool may be a useful tool for pass-fail examination of diagnostic arthroscopy of the knee in the simulation laboratory. Further study is necessary to determine whether the Arthroscopic Surgery Skill Evaluation Tool can be used for the assessment of multiple arthroscopic procedures and whether it can be used to evaluate arthroscopic procedures performed in the operating room.