Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy.

Ion channel mutations are an important cause of rare Mendelian disorders affecting brain, heart, and other tissues. We performed parallel exome sequencing of 237 channel genes in a well-characterized human sample, comparing variant profiles of unaffected individuals to those with the most common neuronal excitability disorder, sporadic idiopathic epilepsy. Rare missense variation in known Mendelian disease genes is prevalent in both groups at similar complexity, revealing that even deleterious ion channel mutations confer uncertain risk to an individual depending on the other variants with which they are combined. Our findings indicate that variant discovery via large scale sequencing efforts is only a first step in illuminating the complex allelic architecture underlying personal disease risk. We propose that in silico modeling of channel variation in realistic cell and network models will be crucial to future strategies assessing mutation profile pathogenicity and drug response in individuals with a broad spectrum of excitability disorders.

Do preoperative scapular fractures affect long-term outcomes after reverse shoulder arthroplasty?

BACKGROUND: Postoperative scapular stress fractures (SSFs) are a formidable problem after reverse shoulder arthroplasty (RSA). Less is known about patients who have these fractures preoperatively. The primary aim of this study was to examine postoperative satisfaction in patients undergoing primary RSA who have preoperative SSF and compared to a matched cohort without preoperative fracture. The secondary aim was to examine the differences in patient-reported outcomes between and within study cohorts. METHODS: A retrospective chart review of primary RSAs performed by a single surgeon from 2000 to 2020 was conducted. Patients diagnosed with cuff tear arthropathy (CTA), massive cuff tear (MCT), or rheumatoid arthritis (RA) were included. Five hundred twenty-five shoulders met inclusion criteria. Fractures identified on preoperative computed tomography scans were divided into 3 groups: (1) os acromiale, (2) multifragments (MFs), and (3) Levy types. Seventy-two shoulders had an occurrence of SSF. The remaining 453 shoulders were separated into a nonfractured cohort. American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form (ASES) and visual analog scale (VAS) scores were compared pre- and postoperatively in the total fracture group and the nonfractured group cohort. The multifragment subgroup was also compared to the pooled Os/Levy subgroup. RESULTS: The total incidence of SSF in all shoulders was 13.7%. There was a difference in satisfaction scores at all time points between the nonfracture (7.9 ± 2.8) and total fracture group (5.4 ± 3.6, P < .001, at last visit). There was also a greater ASES total score in the nonfractured group vs the total fracture group at the final visit (69.4 ± 23.4 and 62.1 ± 24.2; P = .02). The MF group had worse ASES functional or VAS functional scores than the Os/Levy group at all time points: at 1 year, ASES function: MF 24.2 ± 14.5 and Os/Levy 30.7 ± 14.2 (P = .045); at 2 years, ASES function: MF 21.4 ± 14.4 and Os/Levy 35.5 ± 10.6 (P < .001); and at last follow-up, VAS function: MF 4.8 ± 2.8 and Os/Levy 6.4 ± 3.2 (P = .023). DISCUSSION: Scapular fractures were proportionally most common in patients diagnosed with CTA (16.3%) compared with a 9.2% and 8.6% incidence in patients diagnosed with MCT and RA, respectively. Patients with preoperative SSF still see an improvement in ASES scores after RSA but do have lower satisfaction scores compared with the nonfractured cohort. The multifragment fracture group has lower functional and satisfaction scores at all postoperative time points compared with both the nonfracture and the Os/Levy fracture group.

Factors affecting risk of recurrence with periprosthetic infection in shoulder arthroplasty.

BACKGROUND: The goal of treating periprosthetic infection, besides its eradication, is to avoid recurrence. The purpose of this study was to evaluate the impact of increasing Infection Severity (IS) score (based on the 2018 International Consensus Meeting on Orthopedic Infections statement), single-stage revision, and pathogenicity of the infective organism on the risk of infection recurrence. METHODS: A database of 790 revisions performed by a single surgeon from 2004-2020 was reviewed for patients with minimum 2-year follow-up and ≥1 positive culture finding and/or pathology result from the revision surgical procedure. In total, 157 cases performed in 144 patients met the inclusion criteria. These cases were then categorized by infection probability (IS score) according to the 2018 consensus statement. Of 157 cases, 46 (29%) were classified as definitely or probably infected; 25 (16%), possibly infected; and 86 (55%), unlikely to be infected. Additionally, patients were grouped by single-stage surgery and pathogenicity of the infective organism. RESULTS: A recurrence in this study was classified as the growth of the same organism in any patient requiring revision surgery. The 86 cases in the group with unlikely infection showed a recurrence rate of 2.3%. The 25 cases in the group with possible infection showed a recurrence rate of 12%. The 46 cases in the group with definite or probable infection showed a recurrence rate of 17.4%. Patients in the definite/probable infection group had a higher rate of recurrence than those in the groups with possible infection and unlikely infection (P = .009). The IS score was higher in the recurrence group than the non-recurrence group (7.5 ± 4.3 vs. 3.9 ± 3.4, P < .001). Overall, patients who underwent 1-stage revision had a 5.0% recurrence rate, but among the 34 patients with an infection classification of definite or probable who underwent 1-stage revision, the recurrence rate was 5.9%. Cases of highly virulent methicillin-resistant Staphylococcus aureus also showed a recurrence rate of 30.8% compared with 4.0% and 5.9% for Cutibacterium acnes and coagulase-negative staphylococci, respectively (P = .005). CONCLUSION: Recurrent infection after treatment of a periprosthetic infection is associated with increasing severity scores, as defined in the 2018 consensus statement, and more aggressive microorganisms. However, a single-stage surgical procedure, even in patients with higher IS scores, did not impart a significantly increased risk of recurrence.

Surgical Options and Approaches for Septic Arthritis of the Native Hip and Knee Joint.

Septic arthritis (SA) of the adult knee and hip is a constantly evolving and urgent surgical issue. The epidemiology has shifted over the last few decades as have the most popular antibiotics and surgical treatments. SA of all types is increasing in the United States. There remains a high variability in the conservative and surgical management options available. This review will outline the most current understanding of the etiology and epidemiology of SA and will also discuss the distribution of causative organisms and appropriate treatments for each. A summary of evidence for different debridement and reconstructive techniques will also be presented in addition to novel areas of research to decrease the morbidity of this constantly growing problem.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

BACKGROUND: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS: Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS: Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Assessing structural variation in a personal genome-towards a human reference diploid genome.

BACKGROUND: Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods. RESULTS: We demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus. CONCLUSIONS: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.

Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing.

PURPOSE: We applied whole-genome sequencing (WGS) to children diagnosed with neoplasms and found to carry apparently balanced constitutional translocations to discover novel genic disruptions. METHODS: We applied the structural variation (SV) calling programs CREST, BreakDancer, SV-STAT, and CGAP-CNV, and we developed an annotative filtering strategy to achieve nucleotide resolution at the translocations. RESULTS: We identified the breakpoints for t(6;12)(p21.1;q24.31), disrupting HNF1A in a patient diagnosed with hepatic adenomas and maturity-onset diabetes of the young (MODY). Translocation as the disruptive event of HNF1A, a gene known to be involved in MODY3, has not been previously reported. In a subject with Hodgkin lymphoma and subsequent low-grade glioma, we identified t(5;18)(q35.1;q21.2), disrupting both SLIT3 and DCC, genes previously implicated in both glioma and lymphoma. CONCLUSION: These examples suggest that implementing clinical WGS in the diagnostic workup of patients with novel but apparently balanced translocations may reveal unanticipated disruption of disease-associated genes and aid in prediction of the clinical phenotype.

Device-based in vitro techniques for mechanical stimulation of vascular cells: a review.

The most common cause of death in the developed world is cardiovascular disease. For decades, this has provided a powerful motivation to study the effects of mechanical forces on vascular cells in a controlled setting, since these cells have been implicated in the development of disease. Early efforts in the 1970 s included the first use of a parallel-plate flow system to apply shear stress to endothelial cells (ECs) and the development of uniaxial substrate stretching techniques (Krueger et al., 1971, "An in Vitro Study of Flow Response by Cells," J. Biomech., 4(1), pp. 31-36 and Meikle et al., 1979, "Rabbit Cranial Sutures in Vitro: A New Experimental Model for Studying the Response of Fibrous Joints to Mechanical Stress," Calcif. Tissue Int., 28(2), pp. 13-144). Since then, a multitude of in vitro devices have been designed and developed for mechanical stimulation of vascular cells and tissues in an effort to better understand their response to in vivo physiologic mechanical conditions. This article reviews the functional attributes of mechanical bioreactors developed in the 21st century, including their major advantages and disadvantages. Each of these systems has been categorized in terms of their primary loading modality: fluid shear stress (FSS), substrate distention, combined distention and fluid shear, or other applied forces. The goal of this article is to provide researchers with a survey of useful methodologies that can be adapted to studies in this area, and to clarify future possibilities for improved research methods.

In vitro biomechanical comparison of 3.5 mm LC-DCP/intramedullary rod and 5 mm clamp-rod internal fixator (CRIF)/intramedullary rod fixation in a canine femoral gap model.

OBJECTIVE: To compare the biomechanical properties of clamp rod internal fixation (CRIF)/rod and LC-DCP/rod constructs in a canine femoral gap model. STUDY DESIGN: Cadaveric biomechanical study. SAMPLE POPULATION: Canine femora (n = 10 pair). METHODS: Femora with 40 mm ostectomies were assigned to LC-DCP/rod or CRIF/rod treatment groups. Five construct pairs had 4-point bending and 5 pairs had torsional loading. Construct stiffness, strength, and bending angle at failure or permanent angular deformation (torsional loading) were determined. Statistical comparisons were performed using Student t tests; significance was set at P ≤ .05. RESULTS: There was significantly greater permanent angular deformation, or residual twist, in the CRIF/rod constructs (23.1 ± 0.89°) compared with LC-DCP/rod constructs (7.47 ± 2.08°). Whereas there was no significant difference in torsional stiffness of these constructs at torsional loads <4.92 N m (P = .819), LC-DCP/rod constructs had significantly greater torsional stiffness (0.303 ± 0.079 N m/°) and strength (11.546 ± 2.79 N m) than CRIF/rod construct stiffness (0.06 ± 0.013 N m/°) and strength (6.078 ± 0.527 N m) at torsional loads >4.92 N m. Differences in stiffness and strength in 4-point bending were not statistically significant. CONCLUSIONS: LC-DCP/rod constructs had significantly less permanent angular deformation than CRIF/rod constructs. CRIF/rod constructs became less stiff as torsional load was increased, thus the LC-DCP/rod constructs had significantly greater torsional stiffness and strength under high torsional loads. LC-DCP/rod and CRIF/rod constructs performed similarly under 4-point bend loading conditions.

Analyzing Consequence Variables Within the High-Probability Instructional Sequence for a Child Diagnosed With CHARGE Syndrome.

Many individuals with developmental disabilities exhibit noncompliance during intensive instruction. As a treatment for noncompliance, the high-probability instructional sequence (high-p sequence) consists of delivering several high-p instructions before a low-p instruction. The purpose of this study was to extend the research on comparing consequences for high-p demands-namely, praise, edibles, and videos-with an 11-year-old girl diagnosed with CHARGE syndrome. CHARGE syndrome is a rare medical condition often resulting in multisensory impairments and developmental delays. In Treatment Analysis 1, we compared praise versus edibles as consequences for compliance with high- and low-p instructions. Results showed the edibles were initially more effective than praise, but the effects did not maintain. In Treatment Analysis 2, we changed the consequence for compliance with high- and low-p instructions to a music video and then attempted to fade the number of high-p instructions. We replicated the efficacy of the high-p sequence but failed to fade the number of high-p instructions and failed to achieve maintenance. Therefore, in Treatment Analysis 3, we conducted presession preference assessments of music videos in order to use a selected video as the consequence for compliance. This "varied reinforcement" intervention resulted in high levels of compliance. Results are discussed in terms of motivating operations and recommendations for practice.

Noncontingent reinforcement: Arbitrary versus maintaining reinforcers for escape-maintained problem behavior.

Noncontingent reinforcement (NCR) involves the delivery of maintaining reinforcers on a time-dependent schedule and often includes extinction. However, arbitrary reinforcers may be equally efficacious during NCR without extinction for treating escape-maintained problem behavior. The purpose of this study was to extend previous research on NCR by evaluating the relative efficacy of NCR without extinction and comparing maintaining versus arbitrary reinforcers for 4 individuals with escape-maintained problem behavior. Two different NCR conditions, NCR using the maintaining reinforcer (escape) and NCR using an arbitrary reinforcer (an edible), were evaluated using multielement and reversal designs. Treatment effects varied across participants. Results for 2 participants showed a reduction in problem behavior during NCR without extinction with both the arbitrary and maintaining reinforcers. For 1 participant, results showed a reduction in problem behavior with both the arbitrary and maintaining reinforcers only when extinction was added to NCR. For the 4th participant, the maintaining reinforcer was effective during NCR without extinction, but the arbitrary reinforcer was ineffective.

Intra-articular Fracture Pattern in Intercondylar Distal Femur Fractures: An Analysis of Frequency and Major Fracture Fragments.

INTRODUCTION: The treatment of intercondylar distal femur fractures requires anatomic reduction of intra-articular fragments and absolute fixation. Preoperative planning is necessary to understand fracture morphology. All fracture lines need to be recognized as the primary implant may not capture all articular fragments, mainly when coronal plane fractures are present. Oftentimes, independent interfragmentary compression screws are necessary. No recent studies have visually mapped out the distal femur articular fracture fragments necessary for absolute fixation. The objectives of this study are to determine the frequency of coronal plane fractures in intercondylar distal femur fractures and describe the pattern of intra-articular fracture fragments. MATERIALS AND METHODS: The hospital's trauma registry was queried for distal femur ORIF CPT codes logged in the past four years. A retrospective chart review was performed using the EMR and CT scans. Demographics and mechanisms of injury were analyzed. Fracture fragments were surveyed and drawn out by hand on a template for easy organization. Patients' fractures were categorized into the following groups: fractures with no intra-articular coronal plane fractures, those with medial coronal fractures, those with lateral coronal fractures, or those with both medial and lateral coronal fractures. Major fracture fragments were identified. RESULTS: A total of 55 patients were included. 26 patients (47%) were found to have no intra-articular coronal plane fractures; 6 patients (11%) were found to have medial coronal plane fractures; 15 patients (27%) were found to have lateral coronal plane fractures, and 8 patients (15%) had medial and lateral coronal plane fractures. Collectively, intra-articular coronal plane fractures were identified in 29 patients (53%) with intercondylar distal femur fractures. Four major fracture fragments along with intercondylar and condylar comminution sites were identified. DISCUSSION: Distal femur intra-articular coronal plane fractures can yield large anterior and posterior condylar fracture fragments of either the medial condyle, lateral condyle, or both condyles. Coronal plane fracture fragments must be identified to obtain absolute fixation. Our study found a higher coronal plane fracture line frequency (52.7%) than prior commonly cited studies. Surgeons must be on the lookout for anterior fracture fragments, posterior fracture fragments, and articular comminution when treating intercondylar femur fractures.

Flexor Tenosynovectomy for Recurrent Carpal Tunnel Syndrome: A Retrospective Case Series of 108 Hands.

Background: The etiology of recurrent carpal tunnel syndrome (CTS) is unclear, and outcomes following secondary surgery in this demographic have been poorer than primary surgery. Fibrosis and hypertrophy have been identified in the flexor tenosynovium in these patients. The authors use flexor tenosynovectomy (FTS) for recurrent CTS after primary carpal tunnel release and present a review of these patients. Methods: A retrospective chart review was performed of 108 cases of FTS for recurrent CTS from 1995 to 2015 by 4 attending surgeons at one institution. Demographic information, symptoms, and outcomes were among the data recorded. A phone survey was conducted on available patients where the shortened version of the Disabilities of the Arm, Shoulder and Hand Questionnaire (QuickDASH) and satisfaction were assessed. Results: Average office follow-up was 12 months. Average age was 57.5 years. A total of 104 (96%) reported symptom improvement and 48 (44%) reported complete symptom resolution. Forty patients were available for long-term follow-up at an average 6.75 years postoperatively via phone interview. Average QuickDASH score was 31.2 in these patients. Thirty-six (90%) of 40 patients were initially satisfied at last office visit, and 31 (78%) of 40 were satisfied at average 6.9 years, a maintenance of satisfaction of 86%. Satisfied patients were older (58 years) than unsatisfied patients (51 years). Conclusion: Both long-term satisfaction and QuickDASH scores in our cohort are consistent with or better than published results from nerve-shielding procedures. The authors believe a decrease in both carpal tunnel volume and potential adhesions of fibrotic or inflammatory synovium contributes to the benefits of this procedure. This remains our procedure of choice for recurrent CTS.

Trampoline-Related Injuries: A Comparison of Injuries Sustained at Commercial Jump Parks Versus Domestic Home Trampolines.

INTRODUCTION: The nature of trampoline injuries may have changed with the increasing popularity of recreational jump parks. METHODS: A retrospective review was performed evaluating domestic trampoline and commercial jump park injuries over a 2-year period. RESULTS: There were 439 trampoline injuries: 150 (34%) at jump parks versus 289 (66%) on home trampolines. Fractures and dislocations accounted for 55% of jump park injuries versus 44% of home trampoline injuries. In adults, fractures and dislocations accounted for 45% of jump park injuries versus 17% of home trampoline injuries. More lower extremity fractures were seen at jump parks versus home trampolines in both children and adults. Adults had a 23% surgical rate with jump park injuries versus a 10% surgical rate on home trampolines. DISCUSSION: Trampoline-related injury distribution included a higher percentage of fractures/dislocations, lower extremity fractures, fractures in adults, and surgical interventions associated with jump parks versus home trampolines. LEVEL OF EVIDENCE: Level III.

Stargazin and other transmembrane AMPA receptor regulating proteins interact with synaptic scaffolding protein MAGI-2 in brain.

The spatial coordination of neurotransmitter receptors with other postsynaptic signaling and structural molecules is regulated by a diverse array of cell-specific scaffolding proteins. The synaptic trafficking of AMPA receptors by the stargazin protein in some neurons, for example, depends on specific interactions between the C terminus of stargazin and the PDZ [postsynaptic density-95 (PSD-95)/Discs large/zona occludens-1] domains of membrane-associated guanylate kinase scaffolding proteins PSD-93 or PSD-95. Stargazin [Cacng2 (Ca2+ channel gamma2 subunit)] is one of four closely related proteins recently categorized as transmembrane AMPA receptor regulating proteins (TARPs) that appear to share similar functions but exhibit distinct expression patterns in the CNS. We used yeast two-hybrid screening to identify MAGI-2 (membrane associated guanylate kinase, WW and PDZ domain containing 2) as a novel candidate interactor with the cytoplasmic C termini of the TARPs. MAGI-2 [also known as S-SCAM (synaptic scaffolding molecule)] is a multi-PDZ domain scaffolding protein that interacts with several different ligands in brain, including PTEN (phosphatase and tensin homolog), dasm1 (dendrite arborization and synapse maturation 1), dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, and NMDA receptors. We confirmed that MAGI-2 coimmunoprecipitated with stargazin in vivo from mouse cerebral cortex and used in vitro assays to localize the interaction to the C-terminal -TTPV amino acid motif of stargazin and the PDZ1, PDZ3, and PDZ5 domains of MAGI-2. Expression of stargazin recruited MAGI-2 to cell membranes and cell-cell contact sites in transfected HEK-293T cells dependent on the presence of the stargazin -TTPV motif. These experiments identify MAGI-2 as a strong candidate for linking TARP/AMPA receptor complexes to a wide range of other postsynaptic molecules and pathways and advance our knowledge of protein interactions at mammalian CNS synapses.

Somatic cancer variant curation and harmonization through consensus minimum variant level data.

BACKGROUND: To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD). MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice. METHODS: We developed MVLD through a consensus approach by i) reviewing clinical actionability interpretations from institutions participating in the WG, ii) conducting extensive literature search of clinical somatic interpretation schemas, and iii) survey of cancer variant web portals. A forthcoming guideline on cancer variant interpretation, from the Association of Molecular Pathology (AMP), can be incorporated into MVLD. RESULTS: Along with harmonizing standardized terminology for allele interpretive and descriptive fields that are collected by many databases, the MVLD includes unique fields for cancer variants such as Biomarker Class, Therapeutic Context and Effect. In addition, MVLD includes recommendations for controlled semantics and ontologies. The Somatic WG is collaborating with ClinVar to evaluate MVLD use for somatic variant submissions. ClinVar is an open and centralized repository where sequencing laboratories can report summary-level variant data with clinical significance, and ClinVar accepts cancer variant data. CONCLUSIONS: We expect the use of the MVLD to streamline clinical interpretation of cancer variants, enhance interoperability among multiple redundant curation efforts, and increase submission of somatic variants to ClinVar, all of which will enhance translation to clinical oncology practice.

SV-STAT accurately detects structural variation via alignment to reference-based assemblies.

BACKGROUND: Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich source of information in which to detect breakpoints of structural variations at base-pair resolution. However, accurate prediction of SVs remains challenging, and existing informatics tools predict rearrangements with significant rates of false positives or negatives. RESULTS: To address this challenge, we developed 'Structural Variation detection by STAck and Tail' (SV-STAT) which implements a novel scoring metric. The software uses this statistic to quantify evidence for structural variation in genomic regions suspected of harboring rearrangements. To demonstrate SV-STAT, we used targeted and genome-wide approaches. First, we applied a custom capture array followed by Roche/454 and SV-STAT to three pediatric B-lineage acute lymphoblastic leukemias, identifying five structural variations joining known and novel breakpoint regions. Next, we detected SVs genome-wide in paired-end Illumina data collected from additional tumor samples. SV-STAT showed predictive accuracy as high as or higher than leading alternatives. The software is freely available under the terms of the GNU General Public License version 3 at https://gitorious.org/svstat/svstat. CONCLUSIONS: SV-STAT works across multiple sequencing chemistries, paired and single-end technologies, targeted or whole-genome strategies, and it complements existing SV-detection software. The method is a significant advance towards accurate detection and genotyping of genomic rearrangements from DNA sequencing data.

Focused Analysis of Exome Sequencing Data for Rare Germline Mutations in Familial and Sporadic Lung Cancer.

INTRODUCTION: The association between smoking-induced chronic obstructive pulmonary disease (COPD) and lung cancer (LC) is well documented. Recent genome-wide association studies (GWAS) have identified 28 susceptibility loci for LC, 10 for COPD, 32 for smoking behavior, and 63 for pulmonary function, totaling 107 nonoverlapping loci. Given that common variants have been found to be associated with LC in genome-wide association studies, exome sequencing of these high-priority regions has great potential to identify novel rare causal variants. METHODS: To search for disease-causing rare germline mutations, we used a variation of the extreme phenotype approach to select 48 patients with sporadic LC who reported histories of heavy smoking-37 of whom also exhibited carefully documented severe COPD (in whom smoking is considered the overwhelming determinant)-and 54 unique familial LC cases from families with at least three first-degree relatives with LC (who are likely enriched for genomic effects). RESULTS: By focusing on exome profiles of the 107 target loci, we identified two key rare mutations. A heterozygous p.Arg696Cys variant in the coiled-coil domain containing 147 (CCDC147) gene at 10q25.1 was identified in one sporadic and two familial cases. The minor allele frequency (MAF) of this variant in the 1000 Genomes database is 0.0026. The p.Val26Met variant in the dopamine ß-hydroxylase (DBH) gene at 9q34.2 was identified in two sporadic cases; the minor allele frequency of this mutation is 0.0034 according to the 1000 Genomes database. We also observed three suggestive rare mutations on 15q25.1: iron-responsive element binding protein neuronal 2 (IREB2); cholinergic receptor, nicotinic, alpha 5 (neuronal) (CHRNA5); and cholinergic receptor, nicotinic, beta 4 (CHRNB4). CONCLUSIONS: Our results demonstrated highly disruptive risk-conferring CCDC147 and DBH mutations.

Genetic disruption of cortical interneuron development causes region- and GABA cell type-specific deficits, epilepsy, and behavioral dysfunction.

The generation of properly functioning circuits during brain development requires precise timing of cell migration and differentiation. Disruptions in the developmental plan may lead to neurological and psychiatric disorders. Neocortical circuits rely on inhibitory GABAergic interneurons, the majority of which migrate from subcortical sources. We have shown that the pleiotropic molecule hepatocyte growth factor/scatter factor (HGF/SF) mediates interneuron migration. Mice with a targeted mutation of the gene encoding urokinase plasminogen activator receptor (uPAR), a key component in HGF/SF activation and function, have decreased levels of HGF/SF and a 50% reduction in neocortical GABAergic interneurons at embryonic and perinatal ages. Disruption of interneuron development leads to early lethality in most models. Thus, the long-term consequences of such perturbations are unknown. Mice of the uPAR-/- strain survive until adulthood, and behavior testing demonstrates that they have an increased anxiety state. The uPAR-/- strain also exhibits spontaneous seizure activity and higher susceptibility to pharmacologically induced convulsions. The neocortex of the adult uPAR-/- mouse exhibits a dramatic region- and subtype-specific decrease in GABA-immunoreactive interneurons. Anterior cingulate and parietal cortical areas contain 50% fewer GABAergic interneurons compared with wild-type littermates. However, interneuron numbers in piriform and visual cortical areas do not differ from those of normal mice. Characterization of interneuron subpopulations reveals a near complete loss of the parvalbumin subtype, with other subclasses remaining intact. These data demonstrate that a single gene mutation can selectively alter the development of cortical interneurons in a region- and cell subtype-specific manner, with deficits leading to long-lasting changes in circuit organization and behavior.

The somatic genomic landscape of chromophobe renal cell carcinoma.

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations.