Bi-allelic mutations of LONP1 encoding the mitochondrial LonP1 protease cause pyruvate dehydrogenase deficiency and profound neurodegeneration with progressive cerebellar atrophy.

LonP1 is crucial for maintaining mitochondrial proteostasis and mitigating cell stress. We identified a novel homozygous missense LONP1 variant, c.2282 C > T, (p.Pro761Leu), by whole-exome and Sanger sequencing in two siblings born to healthy consanguineous parents. Both siblings presented with stepwise regression during infancy, profound hypotonia and muscle weakness, severe intellectual disability and progressive cerebellar atrophy on brain imaging. Muscle biopsy revealed the absence of ragged-red fibers, however, scattered cytochrome c oxidase-negative staining and electron dense mitochondrial inclusions were observed. Primary cultured fibroblasts from the siblings showed normal levels of mtDNA and mitochondrial transcripts, and normal activities of oxidative phosphorylation complexes I through V. Interestingly, fibroblasts of both siblings showed glucose-repressed oxygen consumption compared to their mother, whereas galactose and palmitic acid utilization were similar. Notably, the siblings' fibroblasts had reduced pyruvate dehydrogenase (PDH) activity and elevated intracellular lactate:pyruvate ratios, whereas plasma ratios were normal. We demonstrated that in the siblings' fibroblasts, PDH dysfunction was caused by increased levels of the phosphorylated E1α subunit of PDH, which inhibits enzyme activity. Blocking E1α phosphorylation activated PDH and reduced intracellular lactate concentrations. In addition, overexpressing wild-type LonP1 in the siblings' fibroblasts down-regulated phosphoE1α. Furthermore, in vitro studies demonstrated that purified LonP1-P761L failed to degrade phosphorylated E1α, in contrast to wild-type LonP1. We propose a novel mechanism whereby homozygous expression of the LonP1-P761L variant leads to PDH deficiency and energy metabolism dysfunction, which promotes severe neurologic impairment and neurodegeneration.

Incidence of delayed intracranial hypertension in children with isolated sagittal synostosis following open calvarial vault reconstruction.

PURPOSE: Delayed intracranial hypertension (DIH) occurs most frequently in children with syndromic or multi-suture synostosis after surgical correction. The rarity of DIH in children with isolated non-syndromic sagittal synostosis (ISS) warrants follow-up evaluation by large craniofacial centers until skeletal maturity. This study reports the incidence of DIH in children following open repair for ISS by our center's craniofacial team. METHODS: A single-center retrospective study of patients who underwent open calvarial vault remodeling (CVR) for ISS at our institution between November 2000 and November 2012 was performed. Syndromic and multi-suture synostosis patients were excluded. Demographic and follow-up data were extracted from the medical record for analysis until July 2017. RESULTS: One hundred five patients with ISS were identified who had undergone CVR in the aforementioned timeframe. Average age at initial surgery was 11.7 ± 15.32 months. Mean follow-up in our craniofacial clinic was 4.94 ± 3.53 years, with 69 patients (65.7%) having follow-up in craniofacial clinic ≥ 3 years and 74 (70.5%) having follow-up ≥ 3 years in any clinic at our institution. Four patients (3.8%) had intracranial pressure (ICP) monitors placed for symptoms concerning for DIH, one of which (0.95%) had confirmed DIH and underwent a second surgical procedure at 7.4 years of age. The patient presented late initially, having his first operation at 1.56 years of age. CONCLUSION: One patient out of 105 (0.95%) developed DIH, confirmed by ICP monitoring, and required reoperation. The occurrence of DIH, albeit rare, remains an important topic to include in parental discussions and mandates long-term follow-up in this population.

Inhibition of CorA-Dependent Magnesium Homeostasis Is Cidal in Mycobacterium tuberculosis.

Mechanisms of magnesium homeostasis in Mycobacterium tuberculosis are poorly understood. Here, we describe the characterization of a pyrimidinetrione amide scaffold that disrupts magnesium homeostasis in the pathogen by direct binding to the CorA Mg2+/Co2+ transporter. Mutations in domains of CorA that are predicted to regulate the pore opening in response to Mg2+ ions conferred resistance to this scaffold. The pyrimidinetrione amides were cidal against the pathogen under both actively replicating and nonreplicating conditions in vitro and were efficacious against the organism during macrophage infection. However, the compound lacked efficacy in infected mice, possibly due to limited exposure. Our results indicate that inhibition of Mg2+ homeostasis by CorA is an attractive target for tuberculosis drug discovery and encourage identification of improved CorA inhibitors.

Comparison of Geriatric Trauma Outcomes When Admitted to a Medical or Surgical Service After a Fall.

BACKGROUND: Blunt trauma in the geriatric population is fraught with poor outcomes, with injury severity and comorbidities impacting morbidity and mortality. METHODS: We retrospectively reviewed 2172 patients aged ≥65 y who fell, requiring hospital admission between January 2012 and December 2016. There were 403 patients in the surgical arm (SA) and 1769 patients in the medical arm (MA). Ground-level falls were the only mechanism of injury included. We excluded all ICU admissions and deaths within 24 h. RESULTS: There were 5 deaths (1.24%) in the SA and 16 deaths (0.90%) in the MA (P = 0.57). The mean trauma injury severity score survival probability prediction in the SA was 96.9% versus 97.1% in the MA. MA patients had more comorbidities overall than SA patients. There was no difference in mortality between the SA and MA groups in multiple logistic regression models that accounted for trauma injury severity scores (TRISS) and comorbidities. Unadjusted hospital length of stay was 1 d shorter (median; 95% CI -1.4 to -0.6) in the SA and 0.5 d shorter (median; 95% CI -0.8 to -0.1) when adjusted for TRISS and comorbidities using multiple quantile regression. Finally, patients in the SA were 2.1 (95% CI 1.7 to 2.6) times more likely to be discharged home compared with patients in the MA, and this remained significant (OR 1.9; 95% CI 1.5 to 2.5) with simultaneous adjustment for TRISS and comorbidities using multiple logistic regression. CONCLUSIONS: Geriatric blunt trauma patients admitted to surgical services after mechanical falls have no difference in survival, a shorter median length of stay, and increased likelihood of being discharged home compared with patients admitted to medical services.

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test.

PurposeGenetic testing is an integral diagnostic component of pediatric medicine. Standard of care is often a time-consuming stepwise approach involving chromosomal microarray analysis and targeted gene sequencing panels, which can be costly and inconclusive. Whole-genome sequencing (WGS) provides a comprehensive testing platform that has the potential to streamline genetic assessments, but there are limited comparative data to guide its clinical use.MethodsWe prospectively recruited 103 patients from pediatric non-genetic subspecialty clinics, each with a clinical phenotype suggestive of an underlying genetic disorder, and compared the diagnostic yield and coverage of WGS with those of conventional genetic testing.ResultsWGS identified diagnostic variants in 41% of individuals, representing a significant increase over conventional testing results (24%; P = 0.01). Genes clinically sequenced in the cohort (n = 1,226) were well covered by WGS, with a median exonic coverage of 40 × ±8 × (mean ±SD). All the molecular diagnoses made by conventional methods were captured by WGS. The 18 new diagnoses made with WGS included structural and non-exonic sequence variants not detectable with whole-exome sequencing, and confirmed recent disease associations with the genes PIGG, RNU4ATAC, TRIO, and UNC13A.ConclusionWGS as a primary clinical test provided a higher diagnostic yield than conventional genetic testing in a clinically heterogeneous cohort.

The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.

Outcomes After Open Reduction With Internal Fixation of Mandible Fractures.

INTRODUCTION/HYPOTHESIS: Mandible fractures contribute substantially to morbidity after blunt trauma. Controversy exists surrounding the appropriate timing of surgical intervention and benefit from routine postreduction imaging. METHODS: The authors retrospectively reviewed 146 patients who sustained traumatic mandible fractures at a level 2 trauma center over a 5-year period, between January 2012 and December 2016. The authors excluded all patients who did not undergo surgery, underwent operative closed reduction only, sustained other significant maxillofacial injuries, penetrating mechanisms, and other major injuries based on injury severity scores (ISS) over 15. There were 51 patients meeting inclusion criteria. The authors reviewed admission face computed tomography (CT) scans and Panorex x-rays. Patients were divided into early (<72 hours) and late (>72 hours) open reduction with internal fixation (ORIF) groups. The authors reviewed demographics, mechanism of injury, postreduction imaging, and ISS. All statistical analyses were performed using Stata 15. RESULTS: There were 39 males (76%) and 12 females (24%) in the authors' study, with a mean age of 32 years. Twenty-eight patients (55%) underwent early ORIF and 23 patients (45%) underwent late ORIF, with no mortalities. There was no statistically significant difference in ISS between the 2 groups (P = 0.081). Preoperative face CT scans were performed in 49 patients (96%) and Panorex in 2 patients (4%). Eight patients (16%) had both modalities, with CT face identifying fractures in 5 patients not seen on Panorex, resulting in a change in operative approach. Postreduction imaging was obtained in 33 patients (65%), of whom 26 were Panorex X-rays. These demonstrated adequate reduction in 31 patients (94%) and did not change management in any instance. Complications occurred in 19 patients (37%), of whom there were 11 with uncontrolled pain after 1 week, 6 abscesses, 5 nonunions/malunions, 2 hardware extrusions, and 1 incisional dehiscence. A positive urine drug screen predicted uncontrolled pain (P < 0.05). There was no statistically significant difference in complications between the 2 groups. CONCLUSION: The authors' data suggest that CT scans of the face are superior to panoramic radiographs in traumatic mandible fracture evaluation, with no apparent benefit from routine postreduction imaging in detecting complications. Open reduction with internal fixation remains an effective treatment with favorable outcomes, and operative delays > 72 hours do not appear to increase complication rates.

High Frequency of Pathogenic Rearrangements in SPG11 and Extensive Contribution of Mutational Hotspots and Founder Alleles.

Biallelic loss-of-function mutations in SPG11 cause a wide spectrum of recessively inherited, neurodegenerative disorders including hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis, and Charcot-Marie-Tooth disease. By comprehensive screening of three large cohorts of HSP index patients, we identified 83 alleles with "small" mutations and 13 alleles that carry large genomic rearrangements. Including relevant data from previous studies, we estimate that copy number variants (CNVs) account for ∼19% of pathogenic SPG11 alleles. The breakpoints for all novel and some previously reported CNVs were determined by long-range PCR and sequencing. This revealed several Alu-associated recombination hotspots. We also found evidence for additional mutational mechanisms, including for a two-step event in which an Alu retrotransposition preceded the actual rearrangement. Apparently independent samples with identical breakpoints were analyzed by microsatellite PCRs. The resulting haplotypes suggested the existence of two rearrangement founder alleles. Our findings widen the spectra of mutations and mutational mechanisms in SPG11, underscore the pivotal role played by Alus, and are of high diagnostic relevance for a wide spectrum of clinical phenotypes including the most frequent form of recessive HSP.

Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes.

BACKGROUND: Phenotypic overlap among the inherited bone marrow failure syndromes (IBMFSs) frequently limits the ability to establish a diagnosis based solely on clinical features. >70 IBMFS genes have been identified, which often renders genetic testing prolonged and costly. Since correct diagnosis, treatment and cancer surveillance often depend on identifying the mutated gene, strategies that enable timely genotyping are essential. METHODS: To overcome these challenges, we developed a next-generation sequencing assay to analyse a panel of 72 known IBMFS genes. Cases fulfilling the clinical diagnostic criteria of an IBMFS but without identified causal genotypes were included. RESULTS: The assay was validated by detecting 52 variants previously found by Sanger sequencing. A total of 158 patients with unknown mutations were studied. Of 75 patients with known IBMFS categories (eg, Fanconi anaemia), 59% had causal mutations. Among 83 patients with unclassified IBMFSs, we found causal mutations and established the diagnosis in 18% of the patients. The assay detected mutant genes that had not previously been reported to be associated with the patient phenotypes. In other cases, the assay led to amendments of diagnoses. In 20% of genotype cases, the results indicated a cancer surveillance programme. CONCLUSIONS: The novel assay is efficient, accurate and has a major impact on patient care.

Whole-exome analysis of foetal autopsy tissue reveals a frameshift mutation in OBSL1, consistent with a diagnosis of 3-M Syndrome.

BACKGROUND: We report a consanguineous couple that has experienced three consecutive pregnancy losses following the foetal ultrasound finding of short limbs. Post-termination examination revealed no skeletal dysplasia, but some subtle proximal limb shortening in two foetuses, and a spectrum of mildly dysmorphic features. Karyotype was normal in all three foetuses (46, XX) and comparative genomic hybridization microarray analysis detected no pathogenic copy number variants. RESULTS: Whole-exome sequencing and genome-wide homozygosity mapping revealed a previously reported frameshift mutation in the OBSL1 gene (c.1273insA p.T425nfsX40), consistent with a diagnosis of 3-M Syndrome 2 (OMIM #612921), which had not been anticipated from the clinical findings. CONCLUSIONS: Our study provides novel insight into the early clinical manifestations of this form of 3-M syndrome, and demonstrates the utility of whole exome sequencing as a tool for prenatal diagnosis in particular when there is a family history suggestive of a recurrent set of clinical symptoms.

A high-resolution copy-number variation resource for clinical and population genetics.

PURPOSE: Chromosomal microarray analysis to assess copy-number variation has become a first-tier genetic diagnostic test for individuals with unexplained neurodevelopmental disorders or multiple congenital anomalies. More than 100 cytogenetic laboratories worldwide use the new ultra-high resolution Affymetrix CytoScan-HD array to genotype hundreds of thousands of samples per year. Our aim was to develop a copy-number variation resource from a new population sample that would enable more accurate interpretation of clinical genetics data on this microarray platform and others. METHODS: Genotyping of 1,000 adult volunteers who are broadly representative of the Ontario population (as obtained from the Ontario Population Genomics Platform) was performed with the CytoScan-HD microarray system, which has 2.7 million probes. Four independent algorithms were applied to detect copy-number variations. Reproducibility and validation metrics were quantified using sample replicates and quantitative-polymerase chain reaction, respectively. RESULTS: DNA from 873 individuals passed quality control and we identified 71,178 copy-number variations (81 copy-number variations/individual); 9.8% (6,984) of these copy-number variations were previously unreported. After applying three layers of filtering criteria, from our highest confidence copy-number variation data set we obtained >95% reproducibility and >90% validation rates (73% of these copy-number variations overlapped at least one gene). CONCLUSION: The genotype data and annotated copy-number variations for this largely Caucasian population will represent a valuable public resource enabling clinical genetics research and diagnostics.

Heterozygous mutations in ERF cause syndromic craniosynostosis with multiple suture involvement.

Craniosynostosis is a clinically and genetically heterogeneous condition. Knowledge of the specific genetic diagnosis in patients presenting with this condition is important for surgical and medical management. The most common single gene causes of syndromic craniosynostosis are mutations in FGFR1, FGFR2, FGFR3, TWIST1, and EFNB1. Recently, a new single gene cause of craniosynostosis was published, together with phenotype data that highlight the clinical importance of making this specific molecular diagnosis. Phenotypic features of "ERF-related craniosynostosis" include sagittal or multiple-suture synostosis, Chiari malformation, and language delay. In order to determine the contribution of ERF mutations to genetically undiagnosed patients with craniosynostosis, we sequenced the coding regions of ERF in 40 patients with multi-suture or sagittal suture synostosis. We identified heterozygous ERF mutations in two individuals (5%). One mutation positive individual had pansynostosis, while the second had bilateral coronal and metopic synostosis. Both presented in infancy or childhood (age 3 months, and 6 years 9 months, respectively). One had CNS abnormalities including Chiari I malformation. Dysmorphic features included hypertelorism, proptosis, depressed nasal bridge, and retrognathia, in keeping with previously reported cases. The individuals did not require repeated cranial surgeries. ERF-related craniosynostosis should be suspected in patients presenting with multiple suture or sagittal synostosis.

Effectiveness and safety of autologous fat grafting to the soft palate alone.

BACKGROUND: Posterior pharyngeal augmentation is an accepted method of treating velopharyngeal insufficiency (VPI). Techniques using autologous fat harvest, preparation, and grafting are well described. Based on the complications from retropharyngeal injection, we performed augmentation of the nasal surface of the palate to reduce hypernasality with decreased risks. METHODS: After Institutional Review Board approval, a chart review from 2010 to 2013 identified 46 patients with cleft palate, subjective and nasoendoscopic evidence of VPI treated with autologous fat grafting to the soft palate. Speech evaluation of velopharyngeal function was compared before and after autologous fat grafting. RESULTS: A total of 61 autologous fat grafting procedures were performed in 46 patients. The average age of the study population is 5.59 ± 2.05 years. The majority underwent a single procedure (32/46 or 69.6%), 13 of 46 patients (28.2%) had 2 fat grafting procedures and only 1 patient (2.2%) had 3 fat grafting procedures. The fat was injected primarily in the soft palate. The recorded volume of fat grafted averaged 2.4 ± 1.1 mL. Average operative time was 39 ± 12.55 minutes. There were no local or donor site complications. Four patients were lost to follow-up. Of 34 patients with adequate speech follow-up, including Pittsburgh Weighted Speech Scale (PWSS) assessment, the average preoperative score of 8.17 ± 3.59 was reduced to 5.17 ± 3.14 postoperatively. Although 26 of 34 patients (76.5%) had an improvement in their PWSS score, only 13 of 34 patients (38.23%) saw an improvement in their PWSS category. CONCLUSIONS: Autologous fat grafting to the soft palate is a safe operation with minimal risks. Speech outcomes are subjectively enhanced in the majority of patients, with a full PWSS category improvement seen in 40% of the cases. Patient selection criteria to optimize results are provided.

The genome clinic: a multidisciplinary approach to assessing the opportunities and challenges of integrating genomic analysis into clinical care.

Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genetic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to guide health care decisions throughout life, to anticipate, diagnose, and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific, and clinical paradigms. The potential benefits of presymptomatic identification of at risk individuals, improved diagnostics, individualized therapy, accurate prognosis, and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models, and increased health care costs. Here, we review the challenges of integrating genomic analysis into clinical practice and describe a prototype for implementing genetic medicine. Our multidisciplinary team of bioinformaticians, health economists, ethicists, geneticists, genetic counselors, and clinicians has designed a "Genome Clinic" research project that addresses multiple challenges in genomic medicine-ranging from the development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference, and the ethics of consent.

Respiratory flexibility in response to inhibition of cytochrome C oxidase in Mycobacterium tuberculosis.

We report here a series of five chemically diverse scaffolds that have in vitro activities on replicating and hypoxic nonreplicating bacilli by targeting the respiratory bc1 complex in Mycobacterium tuberculosis in a strain-dependent manner. Deletion of the cytochrome bd oxidase generated a hypersusceptible mutant in which resistance was acquired by a mutation in qcrB. These results highlight the promiscuity of the bc1 complex and the risk of targeting energy metabolism with new drugs.

High frequency of copy number variations (CNVs) in the chromosome 11p15 region in patients with Beckwith-Wiedemann syndrome.

Beckwith-Wiedemann syndrome (BWS), an overgrowth and tumor predisposition syndrome is clinically heterogeneous. Its variable presentation makes molecular diagnosis particularly important for appropriate counseling of patients with respect to embyronal tumor risk and recurrence risk. BWS is characterized by macrosomia, omphalocele, and macroglossia. Additional clinical features can include hemihyperplasia, embryonal tumors, umbilical hernia, and ear anomalies. BWS is etiologically heterogeneous arising from dysregulation of one or both of the chromosome 11p15.5 imprinting centers (IC) and/or imprinted growth regulatory genes on chromosome 11p15.5. Most BWS cases are sporadic and result from loss of maternal methylation at imprinting center 2 (IC2), gain of maternal methylation at imprinting center 1 (IC1) or paternal uniparental disomy (UPD). Heritable forms of BWS (15 %) have been attributed mainly to mutations in the growth suppressor gene CDKN1C, but have also infrequently been identified in patients with copy number variations (CNVs) in the chromosome 11p15.5 region. Four hundred and thirty-four unrelated BWS patients referred to the molecular diagnostic laboratory were tested by methylation-specific multiplex ligation-dependent probe amplification. Molecular alterations were detected in 167 patients, where 103 (62 %) showed loss of methylation at IC2, 23 (14 %) had gain of methylation at IC1, and 41 (25 %) showed changes at both ICs usually associated with paternal UPD. In each of the three groups, we identified patients in whom the abnormalities in the chromosome 11p15.5 region were due to CNVs. Surprisingly, 14 patients (9 %) demonstrated either deletions or duplications of the BWS critical region that were confirmed using comparative genomic hybridization array analysis. The majority of these CNVs were associated with a methylation change at IC1. Our results suggest that CNVs in the 11p15.5 region contribute significantly to the etiology of BWS. We highlight the importance of performing deletion/duplication testing in addition to methylation analysis in the molecular investigation of BWS to improve our understanding of the molecular basis of this disorder, and to provide accurate genetic counseling.

Does extensive genotyping and nasal potential difference testing clarify the diagnosis of cystic fibrosis among patients with single-organ manifestations of cystic fibrosis?

BACKGROUND: The phenotypic spectrum of cystic fibrosis (CF) has expanded to include patients affected by single-organ diseases. Extensive genotyping and nasal potential difference (NPD) testing have been proposed to assist in the diagnosis of CF when sweat testing is inconclusive. However, the diagnostic yield of extensive genotyping and NPD and the concordance between NPD and the sweat test have not been carefully evaluated. METHODS: We evaluated the diagnostic outcomes of genotyping (with 122 mutations included as disease causing), sweat testing and NPD in a prospectively ascertained cohort of undiagnosed patients who presented with chronic sino-pulmonary disease (RESP), chronic/recurrent pancreatitis (PANC) or obstructive azoospermia (AZOOSP). RESULTS: 202 patients (68 RESP, 42 PANC and 92 AZOOSP) were evaluated; 17.3%, 22.8% and 59.9% had abnormal, borderline and normal sweat chloride results, respectively. Only 17 (8.4%) patients were diagnosable as having CF by genotyping. Compared to sweat testing, NPD identified more patients as having CF (33.2%) with fewer borderline results (18.8%). The level of agreement according to kappa statistics (and the observed percentage of agreement) between sweat chloride and NPD in RESP, PANC and AZOOSP subjects was 'moderate' (65% observed agreement), 'poor' (33% observed agreement) and 'fair' (28% observed agreement), respectively. The degree of agreement only improved marginally when subjects with borderline sweat chloride results were excluded from the analysis. CONCLUSIONS: The diagnosis of CF or its exclusion is not always straightforward and may remain elusive even with comprehensive evaluation, particularly among individuals who present at an older age with single-organ manifestations suggestive of CF.

Identification of deleterious synonymous variants in human genomes.

MOTIVATION: The prioritization and identification of disease-causing mutations is one of the most significant challenges in medical genomics. Currently available methods address this problem for non-synonymous single nucleotide variants (SNVs) and variation in promoters/enhancers; however, recent research has implicated synonymous (silent) exonic mutations in a number of disorders. RESULTS: We have curated 33 such variants from literature and developed the Silent Variant Analyzer (SilVA), a machine-learning approach to separate these from among a large set of rare polymorphisms. We evaluate SilVA's performance on in silico 'infection' experiments, in which we implant known disease-causing mutations into a human genome, and show that for 15 of 33 disorders, we rank the implanted mutation among the top five most deleterious ones. Furthermore, we apply the SilVA method to two additional datasets: synonymous variants associated with Meckel syndrome, and a collection of silent variants clinically observed and stratified by a molecular diagnostics laboratory, and show that SilVA is able to accurately predict the harmfulness of silent variants in these datasets. AVAILABILITY: SilVA is open source and is freely available from the project website: http://compbio.cs.toronto.edu/silva CONTACT: silva-snv@cs.toronto.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genetic, cell biological, and clinical interrogation of the CFTR mutation c.3700 A>G (p.Ile1234Val) informs strategies for future medical intervention.

PURPOSE: The purpose of this study was to determine the molecular consequences of the variant c.3700 A>G in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, a variant that has been predicted to cause a missense mutation in the CFTR protein (p.Ile1234Val). METHODS: Clinical assays of CFTR function were performed, and genomic DNA from patients homozygous for c.3700 A>G and their family members was sequenced. Total RNA was extracted from epithelial cells of the patients, transcribed into complementary DNA, and sequenced. CFTR complementary DNA clones containing the missense mutation p.Ile1234Val or a truncated exon 19 (p.Ile1234_Arg1239del) were constructed and heterologously expressed to test CFTR protein synthesis and processing. RESULTS: In vivo functional measurements revealed that the individuals homozygous for the variant c.3700 A>G exhibited defective CFTR function. We show that this mutation in exon 19 activates a cryptic donor splice site 18 bp upstream of the original donor splice site, resulting in deletion of six amino acids (r.3700_3717del; p.Ile1234_Arg1239del). This deletion, similar to p.Phe508del, causes a primary defect in folding and processing. Importantly, Lumacaftor (VX-809), currently in clinical trial for cystic fibrosis patients with the major cystic fibrosis-causing mutation, p.Phe508del, partially ameliorated the processing defect caused by p.Ile1234_Arg1239del. CONCLUSION: These studies highlight the need to verify molecular and clinical consequences of CFTR variants to define possible therapeutic strategies.

Impact of Safety Device Features Upon Motor Vehicle Collision Facial Fracture Traumas: A Five-Year Retrospective Study in the Appalachian Tri-State Area.

Motor vehicle collisions (MVCs) represent a significant public health concern, contributing to substantial morbidity and mortality globally. Despite advancements in vehicle safety technology, the impact of safety measures on facial fractures in MVCs remains poorly understood, especially in regions with diverse road conditions like the Appalachian tri-state area. This retrospective study analyzed data from two regional level II trauma centers in Appalachia, focusing on MVC-related facial fractures and safety device usage from January 2017 to December 2021. Descriptive statistics and logistic regression models were employed to assess associations between safety devices and injury outcomes. The study comprised 85 participants, categorized into groups based on safety device usage. Results indicated no significant differences in demographic characteristics, injury severity, surgical intervention rates, or specific facial fractures among groups. These findings challenge some previous research suggesting the protective effects of safety devices on facial fractures in MVCs, underscoring the complex nature of injury prevention in this context. While limitations such as retrospective data collection and sample size constrain generalizability, this study contributes valuable insights for informing injury prevention strategies and trauma care practices in Appalachia and beyond.