Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

The primary objective of this study was to create a genome-wide high resolution map (i.e., .100 bp) of ‘rearrangement hotspots’ which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs) into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a ‘seed and extend’ approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (186 coverage), including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs). These regions are correlated with increased nonallelic homologous recombination (NAHR) event frequency which presumably represents the origin of copy number variations (CNVs) and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of ‘rearrangement hotspots’, which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s) for development of constitutional and acquired diseases

Accuracy of free-hand placement of thoracic pedicle screws in adolescent idiopathic scoliosis: how much of a difference does surgeon experience make?

The use of thoracic pedicle screws for the treatment of adolescent idiopathic scoliosis (AIS) has gained widespread popularity. However, the placement of pedicle screws in the deformed spine poses unique challenges, and surgeons experience a learning curve. The in vivo accuracy as determined by computed tomography (CT) of placement of thoracic pedicle screws in the deformed spine as a function of surgeon experience is unknown. We undertook a retrospective review to determine the effect of surgeon experience on the accuracy of thoracic pedicle screw placement in AIS. In 2005, we started to obtain routine postoperative CT scans on patients undergoing a spinal fusion. From a database of these patients, we selected AIS patients, who underwent a posterior spinal fusion. Fifteen consecutive patients for each of the following three groups stratified by attending surgeon experience were selected (N = 45): A) less than 20 cases of all pedicle screw constructs for AIS (surgeons <2 years of practice), B) 20–50 cases (surgeons 2–5 years of practice), and C) greater than 50 cases (surgeons greater than 5 years of practice). Intraoperative evaluation of all screws included probing of the pedicle screw tract, neurophysiologic monitoring, and fluoroscopic confirmation. A total of 856 thoracic pedicle screws were studied. Postoperative CT scans were evaluated by two spine surgeons and a consensus read established as follows: (1) In: intraosseous placement or ≤2-mm breach, (2) Out: >2-mm breach, either medial or lateral. Of the 856 screws, 104 demonstrated a >2-mm breach, for an overall rate of 12.1% (medial = 55, lateral = 49, P = 0.67). When the breach rates were stratified by surgeon experience, there was a trend toward decreased rate of breach for the most experienced surgeons, although this did not attain statistical significance (Group A: 12.7%, Group B: 12.9%, Group C: 10.8%, P = 0.58). However, the most experienced group (C) had a markedly decreased rate of medial breaches (3.5 vs. 7.4% and 8.4% for groups A and B, respectively, P < 0.01). The breach rate for the concave periapical screws was not statistically different from the overall breach rate (13.0% vs. 12.1%, P = 0.93). In conclusion, the overall accuracy of placement of pedicle screws in the deformed spine was 87.9%, with no neurologic, vascular, or visceral complications. Meticulous technique allows spine surgeons with a range of surgical experience to accurately and safely place thoracic pedicle screws in the deformed spine. The most experienced surgeons demonstrated the lowest rate of medial breaches