Repurposing auranofin as an antifungal: In vitro activity against a variety of medically important fungi.

Virulence. 2017 Feb 17;8(2):138-142

Authors: Wiederhold NP, Patterson TF, Srinivasan A, Chaturvedi AK, Fothergill AW, Wormley FL, Ramasubramanian AK, Lopez-Ribot JL

Abstract
Repositioning old drugs can significantly decrease the time and effort that it takes to develop novel antifungal therapeutics, which represents a pressing and unmet clinical need due to the devastating nature of fungal infections. We have previously described the activity of auranofin, a gold thiol compound used to treat rheumatoid arthritis, against Candida albicans biofilms. Here we evaluate its antifungal spectrum of action and describe its activity against a variety of medically important fungi.

PMID: 27268469 [PubMed - indexed for MEDLINE]

Limb Amputation after Multiple Treatments of Tenosynovial Giant Cell Tumour: Series of 4 Dutch Cases.

Case Rep Orthop. 2017;2017:7402570

Authors: Mastboom MJL, Verspoor FGM, Gelderblom H, van de Sande MAJ

Abstract
In Tenosynovial Giant Cell Tumours (TGCT), previously named Pigmented Villonodular Synovitis (PVNS), a distinction is made between a single nodule (localized-type) and multiple nodules (diffuse-type). Diffuse-type is considered locally aggressive. Onset and extermination of this orphan disease remain unclear. Surgical resection is the most commonly performed treatment. Unfortunately, recurrences often occur (up to 92%), necessitating reoperations and adjuvant treatments. Once all treatments fail or if severe complications occur, limb amputation may become unavoidable. We describe four cases of above-knee amputation after TGCT diagnosis.

PMID: 28744388 [PubMed]

Brazilian guidelines for the diagnosis and treatment of cystic fibrosis.

J Bras Pneumol. 2017 May-Jun;43(3):219-245

Authors: Athanazio RA, Silva LVRFD, Vergara AA, Ribeiro AF, Riedi CA, Procianoy EDFA, Adde FV, Reis FJC, Ribeiro JD, Torres LA, Fuccio MB, Epifanio M, Firmida MC, Damaceno N, Ludwig-Neto N, Maróstica PJC, Rached SZ, Melo SFO, Grupo de Trabalho das Diretrizes Brasileiras de Diagnóstico e Tratamento da Fibrose Cística.

Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder characterized by dysfunction of the CFTR gene. It is a multisystem disease that most often affects White individuals. In recent decades, various advances in the diagnosis and treatment of CF have drastically changed the scenario, resulting in a significant increase in survival and quality of life. In Brazil, the current neonatal screening program for CF has broad coverage, and most of the Brazilian states have referral centers for the follow-up of individuals with the disease. Previously, CF was limited to the pediatric age group. However, an increase in the number of adult CF patients has been observed, because of the greater number of individuals being diagnosed with atypical forms (with milder phenotypic expression) and because of the increase in life expectancy provided by the new treatments. However, there is still great heterogeneity among the different regions of Brazil in terms of the access of CF patients to diagnostic and therapeutic methods. The objective of these guidelines was to aggregate the main scientific evidence to guide the management of these patients. A group of 18 CF specialists devised 82 relevant clinical questions, divided into five categories: characteristics of a referral center; diagnosis; treatment of respiratory disease; gastrointestinal and nutritional treatment; and other aspects. Various professionals working in the area of CF in Brazil were invited to answer the questions devised by the coordinators. We used the PubMed database to search the available literature based on keywords, in order to find the best answers to these questions. RESUMO A fibrose cística (FC) é uma doença genética autossômica recessiva caracterizada pela disfunção do gene CFTR. Trata-se de uma doença multissistêmica que ocorre mais frequentemente em populações descendentes de caucasianos. Nas últimas décadas, diversos avanços no diagnóstico e tratamento da FC mudaram drasticamente o cenário dessa doença, com aumento expressivo da sobrevida e qualidade de vida. Atualmente, o Brasil dispõe de um programa de ampla cobertura para a triagem neonatal de FC e centros de referência distribuídos na maior parte desses estados para seguimento dos indivíduos. Antigamente confinada à faixa etária pediátrica, tem-se observado um aumento de pacientes adultos com FC tanto pelo maior número de diagnósticos de formas atípicas, de expressão fenotípica mais leve, assim como pelo aumento da expectativa de vida com os novos tratamentos. Entretanto, ainda se observa uma grande heterogeneidade no acesso aos métodos diagnósticos e terapêuticos para FC entre as diferentes regiões brasileiras. O objetivo dessas diretrizes foi reunir as principais evidências científicas que norteiam o manejo desses pacientes. Um grupo de 18 especialistas em FC elaborou 82 perguntas clínicas relevantes que foram divididas em cinco categorias: características de um centro de referência; diagnóstico; tratamento da doença respiratória; tratamento gastrointestinal e nutricional; e outros aspectos. Diversos profissionais brasileiros atuantes na área da FC foram convidados a responder as perguntas formuladas pelos coordenadores. A literatura disponível foi pesquisada na base de dados PubMed com palavras-chave, buscando-se as melhores respostas às perguntas dos autores.

PMID: 28746534 [PubMed - in process]

Clinical care of children with primary ciliary dyskinesia.

Expert Rev Respir Med. 2017 Jul 26;:

Authors: Lucas JS, Alanin MC, Collins S, Harris A, Johansen HK, Nielsen KG, Papon JF, Robinson P, Walker WT

Abstract
INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare heterogeneous disorder, usually inherited as an autosomal recessive condition but X-linked inheritance is also described. Abnormal ciliary function in childhood leads to neonatal respiratory distress in term infants, persistent wet cough, bronchiectasis, chronic rhinosinusitis, and hearing impairment; approximately 50% of patients have situs inversus. There is a paucity of evidence for treating PCD, hence consensus guidelines are predominantly influenced by knowledge from cystic fibrosis (CF). Extrapolation of evidence from other diseases is inappropriate since differences in pathophysiology, morbidity and prognosis risk treatment failure and lack of adherence. Areas covered: Review authors searched PubMed and Cochrane databases for publications relating to management of children with PCD. Because of the paucity of data, we emphasise the need for well-designed clinical trials with PCD patients rather than reliance on evidence from other diseases. Expert commentary: The evidence for treatment of PCD is poor, and management is often extrapolated from studies of patients with CF or chronic rhinosinusitis. However, much work is underway to improve the situation and international consortia and networks are conducting well-designed projects to inform the management of children with PCD.

PMID: 28745925 [PubMed - as supplied by publisher]

Relative resistance index (RRI) - a scoring system for antibiotic resistance in Pseudomonas aeruginosa.

Br J Biomed Sci. 2017 Jul 26;:1-5

Authors: Ewing J, McCaughan J, Moore J, Fairley D, Sutherland B, Reid A, Downey D

Abstract
BACKGROUND: There is a need to measure antibiotic resistance of Pseudomonas aeruginosa (PA) in cystic fibrosis (CF), either qualitatively or quantitatively, to inform patient management. The aim of this study was to develop a simple method by which resistance can be quantified by calculating a relative resistance index (RRI), and to assess correlation of RRIs with clinical variables.
METHODS: In our model, RRIs were calculated based on resistance to aztreonam, ceftazidime, ciprofloxacin, colistin, meropenem, tazocin, temicillin and tobramycin. Eighty-five adults with CF and chronic PA colonisation were identified. For each, all PA cultures were allocated a score of 0 for susceptible, 0.5 for intermediate resistance or 1 for resistance for each antibiotic listed above, and the RRI calculated by dividing the sum of these by the number of antibiotics, giving a maximum score of 1. The mean RRIs for all cultures were correlated with key clinical variables monitored in CF patients (including age, FEV1, IV antibiotic days and BMI).
RESULTS: RRIs for non-mucoid PA exhibited moderate positive correlation with total number of IV days (r = 0.405; p < 0.001) and moderate negative correlation with FEV1 % predicted (r = -0.437; p < 0.001). RRIs were not significantly correlated with duration of colonisation, typing (clonal vs other strain) or BMI. Median RRIs were significantly higher for females (0.26, IQR 0.13-0.54) than males (0.18, IQR 0.07-0.37) for non-mucoid PA only (p = 0.03).
CONCLUSIONS: RRI is an easily calculated measure that correlates with other clinical variables in CF patients and enables quantitative monitoring of resistance.

PMID: 28745144 [PubMed - as supplied by publisher]

Increased prevalence of colonic adenomas in patients with cystic fibrosis.

J Cyst Fibros. 2017 Jul 22;:

Authors: Hegagi M, Aaron SD, James P, Goel R, Chatterjee A

Abstract
BACKGROUND: Cystic fibrosis (CF) is the most common lethal genetic illness in the Caucasian population. Studies have shown that CF patients are at an elevated risk of developing colon cancer. Colonic adenomas are the precursors of colon cancer. This study aims to determine the prevalence of adenomas in patients with cystic fibrosis.
METHODS: All patients were recruited prospectively at The Ottawa Hospital Cystic Fibrosis Clinic from 2010 through 2015. Baseline demographic and cystic fibrosis disease characteristics were collected from the clinic's CF patient database. Upon presentation at the endoscopy unit, and after a brief history and physical exam, a colonoscopy was performed. Polyps were resected if detected and sent to the pathology department for characterization. Findings were compared with a control group (pairing each CF patient with 5 age and sex-matched controls) of near-average risk patients who underwent a colonoscopy at the same center.
RESULTS: Of the 33 patients that provided informed consent to participate in the study, 30 patients underwent colonoscopy and 13/30 (43.3%) were found to have colonic adenomas compared to 7 (4.7%) of the 150 control patients. The relative risk ratio for adenoma detection in a CF patient as compared to a matched control patient was 9.29 (95% CI 4.04-21.31), p<0.01.
CONCLUSIONS: Colonic adenomas are more prevalent in CF patients compared to the general population. This study suggests the need for additional research to support recently published screening guidelines for CF patients.

PMID: 28743561 [PubMed - as supplied by publisher]

Whole exome sequencing unveils a frameshift mutation in CNGB3 for cone dystrophy: A case report of an Indian family.

Medicine (Baltimore). 2017 Jul;96(30):e7490

Authors: Gupta S, Chaurasia A, Pathak E, Mishra R, Chaudhry VN, Chaudhry P, Mukherjee A, Mutsuddi M

Abstract
RATIONALE: Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES).
PATIENT CONCERNS: In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood. Fundus examination disclosed vascular attenuation and macular retinal pigment epithelium (RPE) changes in all the affected siblings, signifying degeneration of photoreceptor cells.
DIAGNOSIS: Complete clinical investigation and electroretinography studies led to the diagnosis of cone dystrophy in three siblings of the family.
INTERVENTIONS: Detailed ophthalmic examination, including family history, visual function testing, and retinal imaging, was performed. We captured and sequenced exomes of 2 affected siblings and their mother using SureSelect Human All Exon V5 Kit on Illumina HiSeq 2000/2500 platform with 100 bp paired-end sequencing method. Candidates after data analysis were screened by segregation analysis and Sanger sequencing. Considering recessive inheritance and consanguinity in the pedigree, we attempted to map large loci homozygous by descent in the genome of patients using exome sequencing variants. Extensive protein modeling was carried out to assess possible consequences of the identified variant on the 3-dimensional structure of the protein.
OUTCOMES: WES generated more than 65,000 variants for each individual. Assuming recessive inheritance, 13,026 variants were selected. Further filtering on the basis of their position in gene, class, and minor allele frequency constricted the huge list to 12 rare variants. Finally, we ascertained a single base deletion c.1148delC (p.Thr383fs) in the gene CNGB3 as the causal variant. This is a recurrent frameshift mutation resulting in truncated CNGB3 protein. We mapped a large 15-Mb stretch of homozygous markers spanning the causal variant in the proband. The gene CNGB3 encodes modulatory subunit of cyclic nucleotide-gated channels in cone photoreceptors. Protein modeling reveals loss of 2 transmembrane helices and conserved CAP_ED domain in truncated CNGB3, which eventually is predicted to form nonfunctional channels and hamper phototransduction.
LESSONS: We have identified a recurrent mutation c.1148delC (p.Thr383fs) in CNGB3 for autosomal recessive CD. The present report provides the first description of CNGB3 mutation from India. It is also the foremost investigation of familial CD in Indian patients; therefore, it presents the primary genetic etiology of CD in India.

PMID: 28746191 [PubMed - in process]

Whole-exome sequencing of Finnish hereditary breast cancer families.

Eur J Hum Genet. 2016 Jan;25(1):85-93

Authors: Määttä K, Rantapero T, Lindström A, Nykter M, Kankuri-Tammilehto M, Laasanen SL, Schleutker J

Abstract
A remarkable proportion of factors causing genetic predisposition to breast cancer (BC) are unknown in non-BRCA1/2 families. Exome sequencing was performed for 13 high-risk Finnish hereditary breast and/or ovarian cancer (HBOC) families to detect variants contributing to BC susceptibility. After filtering, 18 candidate variants in DNA damage response (DDR) pathway genes were screened in 129 female HBOC patients, up to 989 female controls, and 31 breast tumours by Sanger sequencing/TaqMan assays. In addition, two variants were further studied in 49 male BC patients and 909 male controls. Second, all variants predicted to affect function in six early-onset BC patients were analysed in detail. Variants in ATM, MYC, PLAU, RAD1, and RRM2B were enriched in female HBOC patients compared with controls (odds ratio 1.16-2.16). A rare nonsynonymous variant in RAD50 was detected in a male BC patient. In addition, a very rare BRCA1 variant was identified in a single high-risk family. None of the variants showed wild-type allele loss in breast tumours. Furthermore, novel variants predicted to affect function were detected in early-onset patients in genes, which target DNA repair and replication, signalling, apoptosis, and cell cycle pathways. Family-specific enrichment of multiple DDR pathway gene defects likely explains BC predisposition in the studied families. These findings provide new information on potential BC-related pathways and an excellent premise for future studies.

PMID: 27782108 [PubMed - indexed for MEDLINE]

A genotypic ascertainment approach to refute the association of MYO1A variants with non-syndromic deafness.

Eur J Hum Genet. 2016 Jan;25(1):147-149

Authors: Patton J, Brewer C, Chien W, Johnston JJ, Griffith AJ, Biesecker LG

Abstract
Variants in the unconventional myosin gene, MYO1A, have been reported to cause non-syndromic sensorineural hearing loss with a pattern of autosomal dominant inheritance. Others have challenged this association. We used a genotypic ascertainment study design to test the association of MYO1A variants with hearing loss. We evaluated MYO1A variants from a cohort of 951 individuals with exome sequencing who were not ascertained for hearing loss. Five individuals had one of two variants claimed to be associated with sensorineural hearing loss in a prior study and 33 individuals had one of 13 predicted deleterious variants. We obtained audiology evaluations for 12 individuals with these variants of interest. The hearing acuity of the participants was compared with age- and sex-matched controls and published age- and sex-specific reference ranges from a large population of otologically screened adults. None of the participants had bilateral sensorineural hearing loss of moderate or greater severity. These data do not support a causal relationship of variants in MYO1A to sensorineural hearing loss. We suggest that the genotypic ascertainment method is useful to objectively evaluate gene-phenotype associations.

PMID: 27759032 [PubMed - indexed for MEDLINE]

Variants in SKP1, PROB1, and IL17B genes at keratoconus 5q31.1-q35.3 susceptibility locus identified by whole-exome sequencing.

Eur J Hum Genet. 2016 Jan;25(1):73-78

Authors: Karolak JA, Gambin T, Pitarque JA, Molinari A, Jhangiani S, Stankiewicz P, Lupski JR, Gajecka M

Abstract
Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in impairment of visual function. The extreme genetic heterogeneity makes it difficult to discover factors unambiguously influencing the KTCN phenotype. In this study, we used whole-exome sequencing (WES) and Sanger sequencing to reduce the number of candidate genes at the 5q31.1-q35.3 locus and to prioritize other potentially relevant variants in an Ecuadorian family with KTCN. We applied WES in two affected KTCN individuals from the Ecuadorian family that showed a suggestive linkage between the KTCN phenotype and the 5q31.1-q35.3 locus. Putative variants identified by WES were further evaluated in this family using Sanger sequencing. Exome capture discovered a total of 173 rare (minor allele frequency <0.001 in control population) nonsynonymous variants in both affected individuals. Among them, 16 SNVs were selected for further evaluation. Segregation analysis revealed that variants c.475T>G in SKP1, c.671G>A in PROB1, and c.527G>A in IL17B in the 5q31.1-q35.3 linkage region, and c.850G>A in HKDC1 in the 10q22 locus completely segregated with the phenotype in the studied KTCN family. We demonstrate that a combination of various techniques significantly narrowed the studied genomic region and reduced the list of the putative exonic variants. Moreover, since this locus overlapped two other chromosomal regions previously recognized in distinct KTCN studies, our findings suggest that this 5q31.1-q35.3 locus might be linked with KTCN.

PMID: 27703147 [PubMed - indexed for MEDLINE]

Congenital protein losing enteropathy: an inborn error of lipid metabolism due to DGAT1 mutations.

Eur J Hum Genet. 2016 Aug;24(9):1268-73

Authors: Stephen J, Vilboux T, Haberman Y, Pri-Chen H, Pode-Shakked B, Mazaheri S, Marek-Yagel D, Barel O, Di Segni A, Eyal E, Hout-Siloni G, Lahad A, Shalem T, Rechavi G, Malicdan MC, Weiss B, Gahl WA, Anikster Y

Abstract
Protein-losing enteropathy (PLE) is a clinical disorder of protein loss from the gastrointestinal system that results in hypoproteinemia and malnutrition. This condition is associated with a wide range of gastrointestinal disorders. Recently, a unique syndrome of congenital PLE associated with biallelic mutations in the DGAT1 gene has been reported in a single family. We hypothesize that mutations in this gene are responsible for undiagnosed cases of PLE in infancy. Here we investigated three children in two families presenting with severe diarrhea, hypoalbuminemia and PLE, using clinical studies, homozygosity mapping, and exome sequencing. In one family, homozygosity mapping using SNP arrays revealed the DGAT1 gene as the best candidate gene for the proband. Sequencing of all the exons including flanking regions and promoter regions of the gene identified a novel homozygous missense variant, p.(Leu295Pro), in the highly conserved membrane-bound O-acyl transferase (MBOAT) domain of the DGAT1 protein. Expression studies verified reduced amounts of DGAT1 in patient fibroblasts. In a second family, exome sequencing identified a previously reported splice site mutation in intron 8. These cases of DGAT1 deficiency extend the molecular and phenotypic spectrum of PLE, suggesting a re-evaluation of the use of DGAT1 inhibitors for metabolic disorders including obesity and diabetes.

PMID: 26883093 [PubMed - indexed for MEDLINE]

De novo PIK3R2 variant causes polymicrogyria, corpus callosum hyperplasia and focal cortical dysplasia.

Eur J Hum Genet. 2016 Aug;24(9):1359-62

Authors: Terrone G, Voisin N, Abdullah Alfaiz A, Cappuccio G, Vitiello G, Guex N, D'Amico A, James Barkovich A, Brunetti-Pierri N, Del Giudice E, Reymond A

Abstract
We report an 8-year-old boy with a complex cerebral malformation, intellectual disability, and complex partial seizures. Whole-exome sequencing revealed a yet unreported de novo variant in the PIK3R2 gene that was recently associated with megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome and bilateral perisylvian polymicrogyria (BPP). Our patient showed cerebral abnormalities (megalencephaly, perisylvian polymicrogyria, and mega corpus callosum) that were consistent with these conditions. Imaging also showed right temporal anomalies suggestive of cortical dysplasia. Until now, only three variants (c.1117G>A (p.(G373R)), c.1126A>G (p.(K376E)) and c.1202T>C (p.(L401P))) affecting the SH2 domain of the PIK3R2 protein have been reported in MPPH and BPP syndromes. In contrast to the variants reported so far, the patient described herein exhibits the c.1669G>C (p.(D557H)) variant that affects a highly conserved residue at the interface with the PI3K catalytic subunit α. The phenotypic spectrum associated with variants in this gene and its pathway are likely to continue to expand as more cases are identified.

PMID: 26860062 [PubMed - indexed for MEDLINE]

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pharmacogenomics

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"systems biology"

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"systems biology"

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Single Nucleotide Polymorphisms in Genes MACC1, RAD18, MMP7 and SDF-1a As Prognostic Factors in Resectable Colorectal Cancer.

Radiol Oncol. 2017 Jun;51(2):151-159

Authors: Horvat M, Potocnik U, Repnik K, Kavalar R, Zadnik V, Potrc S, Stabuc B

Abstract
BACKGROUND: Colorectal cancer (CRC) represents one of the most common malignancies worldwide. Research has indicated that functional gene changes such as single nucleotide polymorphism (SNP) influence carcinogenesis and metastasis and might have an influence on disease relapse. The aim of our study was to evaluate the role of SNPs in selected genes as prognostic markers in resectable CRC.
PATIENTS AND METHODS: In total, 163 consecutive patients treated surgically for CRC of stages I, II and III at the University Medical Centre in Maribor in 2007 and 2008 were investigated. DNA was isolated from formalin-fixed paraffin-embedded CRC tissue from the Department of Pathology and SNPs in genes SDF-1a, MMP7, RAD18 and MACC1 were genotyped using polymerase chain reaction followed by high resolution melting curve analysis or restriction fragment length polymorphism.
RESULTS: We found worse disease-free survival (DFS) for patients with TT genotype of SNP rs1990172 in gene MACC1 (p = 0.029). Next, we found worse DFS for patients with GG genotype for SNP rs373572 in gene RAD18 (p = 0.020). Higher frequency of genotype GG of MMP7 SNP rs11568818 was found in patients with T3/T4 stage (p = 0.014), N1/N2 stage (p = 0.041) and with lymphovascular invasion (p = 0.018). For MACC1 rs1990172 SNP we found higher frequency of genotype TT in patients with T3/T4 staging (p = 0.024). Higher frequency of genotype GG of RAD18 rs373572 was also found in patients with T1/T2 stage with disease relapse (p = 0.041).
CONCLUSIONS: Our results indicate the role of SNPs as prognostic factors in resectable CRC.

PMID: 28740450 [PubMed]

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2017/07/26

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Endocrine aspects in cystic fibrosis.

J Pediatr Endocrinol Metab. 2017 Jul 25;:

Authors: Kiess W, Penke M, Kobelt L, Lipek T, Henn C, Gausche R, Vogel M, Prenzel F

PMID: 28742522 [PubMed - as supplied by publisher]

Sensitivity and specificity of cystic fibrosis-related diabetes screening methods: which test should be the reference method?

J Pediatr Endocrinol Metab. 2017 Jul 25;:

Authors: Boudreau V, Lehoux Dubois C, Desjardins K, Mailhot M, Tremblay F, Rabasa-Lhoret R

PMID: 28742521 [PubMed - as supplied by publisher]

Unilateral Lung Agenesis, Aplasia or Hypoplasia - which one is it?

Congenit Anom (Kyoto). 2017 Jul 25;:

Authors: Nguyen KM, Vala S, Milla S, Guglani L

Abstract
Congenital lung malformations can lead to symptoms in the immediate newborn period or early childhood, but may also be diagnosed incidentally on routine imaging or autopsy, especially if the individual has remained asymptomatic. We report a case where incidental detection of abnormal intrathoracic structures led to a different diagnosis while being evaluated for scoliosis.

PMID: 28742269 [PubMed - as supplied by publisher]