Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease.

Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

Toward clinical exomes in diagnostics and management of male infertility.

Infertility, affecting ∼10% of men, is predominantly caused by primary spermatogenic failure (SPGF). We screened likely pathogenic and pathogenic (LP/P) variants in 638 candidate genes for male infertility in 521 individuals presenting idiopathic SPGF and 323 normozoospermic men in the ESTAND cohort. Molecular diagnosis was reached for 64 men with SPGF (12%), with findings in 39 genes (6%). The yield did not differ significantly between the subgroups with azoospermia (20/185, 11%), oligozoospermia (18/181, 10%), and primary cryptorchidism with SPGF (26/155, 17%). Notably, 19 of 64 LP/P variants (30%) identified in 28 subjects represented recurrent findings in this study and/or with other male infertility cohorts. NR5A1 was the most frequently affected gene, with seven LP/P variants in six SPGF-affected men and two normozoospermic men. The link to SPGF was validated for recently proposed candidate genes ACTRT1, ASZ1, GLUD2, GREB1L, LEO1, RBM5, ROS1, and TGIF2LY. Heterozygous truncating variants in BNC1, reported in female infertility, emerged as plausible causes of severe oligozoospermia. Data suggested that several infertile men may present congenital conditions with less pronounced or pleiotropic phenotypes affecting the development and function of the reproductive system. Genes regulating the hypothalamic-pituitary-gonadal axis were affected in >30% of subjects with LP/P variants. Six individuals had more than one LP/P variant, including five with two findings from the gene panel. A 4-fold increased prevalence of cancer was observed in men with genetic infertility compared to the general male population (8% vs. 2%; p = 4.4 × 10-3). Expanding genetic testing in andrology will contribute to the multidisciplinary management of SPGF.

Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India.

BACKGROUND: Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS: 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION: We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Assessment of Advanced Diagnostic Bronchoscopy Outcomes for Peripheral Lung Lesions: A Delphi Consensus Definition of Diagnostic Yield and Recommendations for Patient-centered Study Designs. An Official American Thoracic Society/American College of Chest Physicians Research Statement.

Background: Advanced diagnostic bronchoscopy targeting the lung periphery has developed at an accelerated pace over the last two decades, whereas evidence to support introduction of innovative technologies has been variable and deficient. A major gap relates to variable reporting of diagnostic yield, in addition to limited comparative studies. Objectives: To develop a research framework to standardize the evaluation of advanced diagnostic bronchoscopy techniques for peripheral lung lesions. Specifically, we aimed for consensus on a robust definition of diagnostic yield, and we propose potential study designs at various stages of technology development. Methods: Panel members were selected for their diverse expertise. Workgroup meetings were conducted in virtual or hybrid format. The cochairs subsequently developed summary statements, with voting proceeding according to a modified Delphi process. The statement was cosponsored by the American Thoracic Society and the American College of Chest Physicians. Results: Consensus was reached on 15 statements on the definition of diagnostic outcomes and study designs. A strict definition of diagnostic yield should be used, and studies should be reported according to the STARD (Standards for Reporting Diagnostic Accuracy Studies) guidelines. Clinical or radiographic follow-up may be incorporated into the reference standard definition but should not be used to calculate diagnostic yield from the procedural encounter. Methodologically robust comparative studies, with incorporation of patient-reported outcomes, are needed to adequately assess and validate minimally invasive diagnostic technologies targeting the lung periphery. Conclusions: This American Thoracic Society/American College of Chest Physicians statement aims to provide a research framework that allows greater standardization of device validation efforts through clearly defined diagnostic outcomes and robust study designs. High-quality studies, both industry and publicly funded, can support subsequent health economic analyses and guide implementation decisions in various healthcare settings.

Significance of clinical-immunological patterns and diagnostic yield of biopsies in microscopic polyangiitis and granulomatosis with polyangiitis.

BACKGROUND: Microscopic polyangiitis (MPA) and granulomatosis with polyangiitis (GPA) are the two major antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). OBJECTIVES: To characterize a homogenous AAV cohort and to assess the impact of clinicopathological profiles and ANCA serotypes on clinical presentation and prognosis. Clinical differences in GPA patients according to ANCA serotype and the diagnostic yield for vasculitis of biopsies in different territories were also investigated. RESULTS: This retrospective study (2000-2021) included 152 patients with AAV (77 MPA/75 GPA). MPA patients (96.1% myeloperoxidase [MPO]-ANCA and 2.6% proteinase 3 [PR3]-ANCA) presented more often with weight loss, myalgia, renal involvement, interstitial lung disease (ILD), cutaneous purpura, and peripheral nerve involvement. Patients with GPA (44% PR3-ANCA, 33.3% MPO, and 22.7% negative/atypical ANCA) presented more commonly with ear, nose, and throat and eye/orbital manifestations, more relapses, and higher survival than patients with MPA. GPA was the only independent risk factor for relapse. Poor survival predictors were older age at diagnosis and peripheral nerve involvement. ANCA serotypes differentiated clinical features in a lesser degree than clinical phenotypes. A mean of 1.5 biopsies were performed in 93.4% of patients in different territories. Overall, vasculitis was identified in 80.3% (97.3% in MPA and 61.8% in GPA) of patients. CONCLUSIONS: The identification of GPA presentations associated with MPO-ANCA and awareness of risk factors for relapse and mortality are important to guide proper therapeutic strategies in AAV patients. Biopsies of different affected territories should be pursued in difficult-to-diagnose patients based on their significant diagnostic yield.

Multi-gene panel sequencing in highly consanguineous families and patients with congenital forms of skeletal dysplasias.

Skeletal dysplasias (SKDs) are a heterogeneous group of more than 750 genetic disorders characterized by abnormal development, growth, and maintenance of bones or cartilage in the human skeleton. SKDs are often caused by variants in early patterning genes and in many cases part of multiple malformation syndromes and occur in combination with non-skeletal phenotypes. The aim of this study was to investigate the underlying genetic cause of congenital SKDs in highly consanguineous Pakistani families, as well as in sporadic and familial SKD cases from India using multigene panel sequencing analysis. Therefore, we performed panel sequencing of 386 bone-related genes in 7 highly consanguineous families from Pakistan and 27 cases from India affected with SKDs. In the highly consanguineous families, we were able to identify the underlying genetic cause in five out of seven families, resulting in a diagnostic yield of 71%. Whereas, in the sporadic and familial SKD cases, we identified 12 causative variants, corresponding to a diagnostic yield of 44%. The genetic heterogeneity in our cohorts was very high and we were able to detect various types of variants, including missense, nonsense, and frameshift variants, across multiple genes known to cause different types of SKDs. In conclusion, panel sequencing proved to be a highly effective way to decipher the genetic basis of SKDs in highly consanguineous families as well as sporadic and or familial cases from South Asia. Furthermore, our findings expand the allelic spectrum of skeletal dysplasias.

Diagnostic findings and yield of investigations for children with developmental regression.

Childhood conditions that feature developmental regression are poorly understood. Phenotype-genotype characterization and diagnostic yield data are needed to inform clinical decision-making. The aim of this study was to report the conditions featuring developmental regression and assess diagnostic yields of investigations. A retrospective chart review of children presenting with developmental regression to a tertiary pediatric genetic clinic between 2018 and 2021 was performed. Of 99 children, 30% (n = 30) had intellectual disability (ID), 21% (n = 21) were autistic, 39% (n = 39) were autistic with ID, and 9% (n = 9) did not have ID or autism. Thirty-two percent (n = 32) of children received a new diagnosis, including eight molecular findings not previously reported to feature developmental regression. Of the children investigated, exome sequencing (ES) provided the highest diagnostic yield (51.1%, n = 24/47), highest (63.6%, n = 14/22) for children with ID, 50% for autistic children with ID (n = 6/12) and children without autism or ID (n = 3/6), and 14.3% (n = 1/7) for autistic children without ID. We highlight the conditions that feature developmental regression and report on novel phenotypic expansions. The high diagnostic yield of ES, regardless of autism or ID diagnosis, indicates the presence of developmental regression as an opportunity to identify the cause, including for genetic differences not previously reported to include regression.

Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil.

In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.

Diagnostic reliability of monitoring for premature atrial and ventricular complexes.

AIMS: Short-term ambulatory electrocardiogram (ECG) monitoring is often used to assess premature atrial complex (PAC) and premature ventricular complex (PVC) frequency, but the diagnostic reliability is unknown. The objective of this study was to study the day-to-day variability of PAC and PVC frequency. METHODS AND RESULTS: We used 14-day full-disclosure mobile cardiac telemetry recordings without atrial fibrillation in 8245 US patients aged 17-103 years to calculate the diagnostic reliability of shorter ambulatory ECG recordings compared with 14-day averages. Over 14 days, 1853 patients had ≥500 PACs/day, 410 patients had ≥5000 PACs/day, and 197 patients had ≥10 000 PACs/day; 1640 patients had ≥500 PVCs/day, 354 patients had ≥5000 PVCs/day, and 175 patients had ≥10 000 PVCs/day. After 3 days, the estimated daily PAC frequency differed by ≥50% from the 14-day mean in 25% of patients; for PVCs, the corresponding duration was 7 days. Ten days of monitoring were needed to estimate PAC and PVC frequency within ±20% of the overall 14-day frequency in 80% of patients. For daily PAC and PVC frequencies ≥10 000, single-day estimation had a specificity of 99.3% [95% confidence interval (CI) 99.1-99.5] at a sensitivity of 76.6 (95% CI 70.1-80.4%) for PACs and a 99.6% (95% CI 99.4-99.7%) specificity at 79.4 (95% CI 72.7-85.2) sensitivity for PVCs. After 7 days, the sensitivity increased to 88.8% (95% CI 83.6-92.9) for PACs and 86.9% (95% CI 80.9-91.5%) for PVCs. CONCLUSION: While there is substantial daily variability across most PAC and PVC levels, findings of ≥10 000 PACs or PVCs are highly specific and do not need to be confirmed with longer recordings.

Shape-Sensing Robotic-Assisted Bronchoscopy in the Multiple Pulmonary Nodule Diagnosis during a Single Anesthetic Event.

INTRODUCTION: The widespread use of computed tomography as a screening tool for early lung cancer has increased detection of pulmonary lesions. It is common to encounter patients with more than one peripheral pulmonary nodule (PPN) of uncertain etiology. Shape-sensing robotic-assisted bronchoscopy (ssRAB) emerges as a potential alternative to biopsy multiple PPN, in addition to mediastinal staging in single anesthetic procedure. METHODS: This is a single-center, retrospective review of 22 patients who underwent ssRAB for evaluation of two or more PPN, between November 2021 and April 2023 at Mayo Clinic, FL, USA. RESULTS: A total of 46 PPNs were biopsied in 22 patients. All lesions were ≤2 cm with a median minimum and maximum cross-sectional lesion size of 1.40 cm and 1.05 cm, respectively. Diagnostic yield was 86.9% (n = 40), and target reach was 91.3% (n = 42). Most lesions were in the upper lobes, a solid pattern was found in 78.3% (n = 36), bronchus sign was present in 82.6% of cases (n = 38), 54.4% (n = 25) were malignant nodules, and 32.6% (n = 15) were benign. Fourteen patients had at least one malignant lesion out of two or more nodules sampled, and 10 patients had a malignant diagnosis for all sampled lesions. The complication rate was 9% (n = 2) with one case of bleeding and one of pneumothorax. CONCLUSION: This study is, to our knowledge, the first to assess the use and safety of ssRAB for diagnosis of multiple PPN in a single anesthetic event. This procedure will mainly impact management decisions and subsequently shorten the time from diagnosis to treatment.

Reanalysis of Trio Whole-Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half.

Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole-genome sequencing (trio-WGS). "Qualified" variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV), additionally, were present in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (p = 0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly through inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate a high yield of trio-WGS for revealing molecular diagnoses in ASD, which is greatly enhanced by reanalyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.

Limited Added Diagnostic Value of Whole Genome Sequencing in Genetic Testing of Inherited Retinal Diseases in a Swiss Patient Cohort.

The purpose of this study was to assess the added diagnostic value of whole genome sequencing (WGS) for patients with inherited retinal diseases (IRDs) who remained undiagnosed after whole exome sequencing (WES). WGS was performed for index patients in 66 families. The datasets were analyzed according to GATK's guidelines. Additionally, DeepVariant was complemented by GATK's workflow, and a novel structural variant pipeline was developed. Overall, a molecular diagnosis was established in 19/66 (28.8%) index patients. Pathogenic deletions and one deep-intronic variant contributed to the diagnostic yield in 4/19 and 1/19 index patients, respectively. The remaining diagnoses (14/19) were attributed to exonic variants that were missed during WES analysis due to bioinformatic limitations, newly described loci, or unclear pathogenicity. The added diagnostic value of WGS equals 5/66 (9.6%) for our cohort, which is comparable to previous studies. This figure would decrease further to 1/66 (1.5%) with a standardized and reliable copy number variant workflow during WES analysis. Given the higher costs and limited added value, the implementation of WGS as a first-tier assay for inherited eye disorders in a diagnostic laboratory remains untimely. Instead, progress in bioinformatic tools and communication between diagnostic and clinical teams have the potential to ameliorate diagnostic yields.

Search for small-bowel capsule diagnostic yield optimization conducted through observational analysis. / Búsqueda de optimización de la cápsula endoscópica mediante análisis observacional.

OBJECTIVES: To search for parameters susceptible to optimization when performing capsule endoscopy (CE) in a third level hospital with high volume and experience in this test. PATIENTS AND METHODS: Retrospective observational study, including 1325 CEs performed between 2017 and 2022. Overall diagnostic yield, effective diagnostic yield, by indication, place of request and waiting list, as well as complete examination rate and cleansing degree were analyzed. RESULTS: The overall diagnostic yield was 70.99%, while the effective diagnostic yield was 72.7%. Diagnostic yields varied between 60.2% and 77.9% depending on the indication and between 64.7% and 74.3% depending on the requesting center. The mean waiting list was 101.15 days, with a tendency to worse results when the waiting list was longer. A total of 77.8% of the examinations were complete. Completion rates were lower in patients >70 years of age (p=0.001), as well as in those with gastric transit >60minutes (p=0.000). A total of 77.3% were clean, with debris that did not impede diagnosis being found in 16.9% and debris that did impede diagnosis in 5.8%. There was a relationship, although not significant, between cleansing degree and age. CONCLUSIONS: The diagnostic yields of CE in our center are in line with those previously reported. Differences were found according to the place of request. Waiting list could also influence diagnostic yield. Completion rates are lower in >70 years of age and when gastric transit is >60minutes. Cleansing degree achieved is acceptable.

Diagnostic yield using electromagnetic navigation bronchoscopy for peripheral pulmonary nodules <2 cm.

BACKGROUND: Although electromagnetic navigation bronchoscopy (ENB) is highly sensitive in the diagnosis of peripheral pulmonary nodules (PPNs), its diagnostic yield for subgroups of smaller PPNs is under evaluation. OBJECTIVES: Diagnostic yield evaluation of biopsy using ENB for PPNs <2 cm. DESIGN: The diagnostic yield, sensitivity, specificity, positive predictive value, and negative predictive value of the ENB-mediated biopsy for PPNs were evaluated. METHODS: Patients who had PPNs with diameters <2 cm and underwent ENB-mediated biopsy between May 2015 and February 2020 were consecutively enrolled. The final diagnosis was made via pathological examination after surgery. RESULTS: A total of 82 lesions from 65 patients were analyzed. The median tumor size was 11 mm. All lesions were subjected to ENB-mediated biopsy, of which 29 and 53 were classified as malignant and benign, respectively. Subsequent segmentectomy, lobectomy, or wedge resection, following pathological examinations were performed on 64 nodules from 57 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value for nodules <2 cm were 53.3%, 91.7%, 92.3%, and 51.2%, respectively. The receiver operating curve showed an area under the curve of 0.721 (p < 0.001). Additionally, the sensitivity, specificity, positive predictive value, and negative predictive value were 62.5%, 100%, 100%, and 42.9%, respectively, for nodules with diameters equal to or larger than 1 cm; and 30.8%, 86.7%, 66.7%, and 59.1%, respectively, for nodules less than 1 cm. In the subgroup analysis, neither the lobar location nor the distance of the PPNs to the pleura affected the accuracy of the ENB diagnosis. However, the spiculated sign had a negative impact on the accuracy of the ENB biopsy (p = 0.010). CONCLUSION: ENB has good specificity and positive predictive value for diagnosing PPNs <2 cm; however, the spiculated sign may negatively affect ENB diagnostic accuracy. In addition, the diagnostic reliability may only be limited to PPNs equal to or larger than 1 cm.

Genome sequencing reanalysis increases the diagnostic yield in dystonia.

PURPOSE: We investigated the contribution of genomic data reanalysis to the diagnostic yield of dystonia patients who remained undiagnosed after prior genome sequencing. METHODS: Probands with heterogeneous dystonia phenotypes who underwent initial genome sequencing (GS) analysis in 2019 were included in the reanalysis, which was performed through gene-specific discovery collaborations and systematic genomic data reanalysis. RESULTS: Initial GS analysis in 2019 (n = 111) identified a molecular diagnosis in 11.7 % (13/111) of cases. Reanalysis between 2020 and 2023 increased the diagnostic yield by 7.2 % (8/111); 3.6 % (4/111) through focused gene-specific clinical correlation collaborative efforts [VPS16 (two probands), AOPEP and POLG], and 3.6 % (4/111) by systematic reanalysis completed in 2023 [NUS1 (two probands) and DDX3X variants, and a microdeletion encompassing VPS16]. Seven of these patients had a high phenotype-based dystonia score ≥3. Notable unverified findings in four additional cases included suspicious variants of uncertain significance in FBXL4 and EIF2AK2, and potential phenotypic expansion associated with SLC2A1 and TREX1 variants. CONCLUSION: GS data reanalysis increased the diagnostic yield from 11.7 % to 18.9 %, with potential extension up to 22.5 %. While optimal timing for diagnostic reanalysis remains to be determined, this study demonstrates that periodic re-interrogation of dystonia GS datasets can provide additional genetic diagnoses, which may have significant implications for patients and their families.

Safety and Diagnostic Yield of Medical Pleuroscopy (MP) Performed under Balanced Analgosedation by a Pneumological Team Compared to Video-Assisted Thoracic Surgery (VATS): A Retrospective Controlled Real-Life Study (TORAPO).

INTRODUCTION: Medical pleuroscopy (MP) is an invasive technique that provides access to the pleural space with a rigid or semi-rigid work instrument, allowing for visualization and the obtaining of bioptic pleural samples. Using pulmonologist-based analgosedation to perform pleuroscopy is still debated for safety reasons. The aim of this real-life study is to demonstrate the safety and diagnostic yield of MP performed under balanced analgosedation by a pulmonologist team with expertise in the management of critically ill patients in the respiratory intensive care unit (RICU) and interventional pulmonology unit as compared to video-assisted thoracic surgery (VATS) performed by a thoracic surgeon team under anesthesiologist-based analgosedation. METHODS: In this multicentric retrospective controlled study, the inclusion criteria were patients older than 18 years old with pleural effusion of unknown diagnosis consecutively admitted in the years 2017-2022 to the pulmonology unit and RICU of San Donato Hospital in Arezzo (Italy, Tuscany) and to the thoracic surgery unit of Santa Maria Le Scotte in Siena (Italy, Tuscany) to undergo, respectively, MP under balanced propofol-based analgosedation on spontaneous breathing with local anesthesia provided by a pulmonologist team (Group A), and VATS provided by a surgeon team under propofol-based analgosedation managed by an anesthesiologist using invasive mechanical ventilation (IMV) via endotracheal intubation (ETI) (Group B). The primary endpoints were (1) a comparison between the two groups in terms of the diagnostic yield of pleural effusion, and (2) major and minor complications of pleuroscopic procedures. The secondary endpoints were (1) the length of the pleuroscopic procedure; (2) the duration of hospitalization; (3) propofol doses; and (4) the patient's comfort after the procedure assessed using the Visual Analogue Scale (VAS). RESULTS: We enrolled 91 patients in Group A and 116 patients in Group B. A conclusive diagnosis was obtained in 97.8% of Group A vs. 100% of Group B (p = 0.374). Malignant effusion was diagnosed in 59.3% of Group A and in 55.1% of Group B; p = 0.547. No intraoperative or postoperative mortality events or major complications were observed in Group A. The major complications observed in Group B were three major bleeding events (p = 0.079) and one exitus (p = 0.315) not related to the interventional procedure. No significant difference emerged between the two groups in terms of minor complications. The duration of the intervention was significantly lower in Group A (40.0 min ± 12.6 versus 51.5 ± 31.0; p = 0.001). Pain control and, therefore, patient comfort were better in Group A, with an average VAS of 0.34 ± 0.65 versus 2.58 ± 1.26, p < 0.001. The duration of hospitalization was lower in Group B (5.1 ± 2.6 vs. 15.5 ± 8.0, p < 0.001). The average overall dose of propofol administered was significantly lower in Group A (65.6 ± 35.8 mg versus 280 ± 20.0 mg; p < 0.001). CONCLUSIONS: This real-life study shows that the MP performed under propofol-based analgosedation by an independent pneumologist team is a safe and well-tolerated procedure with a diagnostic yield and complication rates similar to those obtained with VATS.

Early comparison robotic bronchoscopy versus electromagnetic navigational bronchoscopy for biopsy of pulmonary nodules in a thoracic surgery practice.

Pulmonary nodules are frequently encountered in high-risk patients. Often these require biopsy which can be challenging. We relate our experience comparing use of electromagnetic navigational bronchoscopy (ENB) to a robotic bronchoscopy system (RB). A retrospective review of patients undergoing bronchoscopic biopsy from 2015 to 2021. The timeframe overlapped with transition from ENB using Veran SPiN system to RB using Ion system by Intuitive. Patient and nodule characteristics were collected. Primary end point was overall diagnostic yield which was defined by pathologic confirmation of malignancy or benign finding. Secondary outcomes included diagnostic yield based on overall size of nodules and need for further work up and testing. 116 patients underwent ENB or RB of 134 nodules. No perioperative complications occurred. Diagnostic yield of ENB was 49.5% (41/91 nodules) versus 86.1% (37/43 nodules) for RB. Average nodule size for ENB was 2.55 cm versus 1.96 cm for RB. When divided based on size, ENB had a 30% diagnostic yield for nodules 1-2 cm (11/37 nodules, mean size 1.46 cm) and 64% yield for nodules 2-3 cm (14/22 nodules, mean size 2.38 cm). RB had an 81% yield for nodules 1-2 cm (mean size 1.41 cm) and 100% yield for nodules 2-3 cm (mean 2.3 cm). RB showed superiority over ENB in early implementation trials for biopsy of suspicious pulmonary nodules. It is a safe technology allowing for increased access to all lung fields and utilization in the thoracic surgical practice will be paramount to advancing the field.

Diagnostic yield of postmortem brain examination following premortem brain biopsy for neoplastic and nonneoplastic disease.

Medical autopsies have decreased in frequency due in part to advances in radiological techniques and increased availability of molecular and other ancillary testing. However, premortem diagnosis of CNS disease remains challenging; while ∼90% of brain tumor biopsies are diagnostic, only 20%-70% of biopsies for presumed nonneoplastic disease result in a specific diagnosis. The added benefits of performing an autopsy following surgical brain biopsy are not well defined. A retrospective analysis was performed of patients who underwent brain biopsy and autopsy at Brigham and Women's Hospital from 2003 to 2022. A total of 135 cases were identified, including 95 (70%) patients with primary CNS neoplasms, 16 (12%) with metastatic tumors, and 24 (18%) with nonneoplastic neurological disease. Diagnostic concordance between biopsy and autopsy diagnosis was excellent both for primary CNS neoplasms (98%) and metastatic tumors (94%). Conversely, patients with nonneoplastic disease received definitive premortem diagnoses in 7/24 (29%) cases. Five (21%) additional patients received conclusive diagnoses following autopsy; 8 (33%) received a more specific differential diagnosis compared to the biopsy. Overall, autopsy confirmed premortem diagnoses or provided new diagnostic information in 131/135 (97%) cases, highlighting the value in performing postmortem brain examination in patients with both neoplastic and nonneoplastic diseases.

Evaluation of Paroxysmal Events in Critically Ill Patients: Relationship of Primary Diagnosis to Long-Term Electroencephalogram Yield.

Continuous EEG (cEEG) is indicated for the workup of paroxysmal events. We aimed to assess whether primary admission diagnoses predict the yield of cEEG when ordered for evaluating paroxysmal events. We identified patients in the ICU who underwent at least 6 hours of cEEG monitoring to evaluate paroxysmal events. Primary admission diagnoses were categorized into neurological or non-neurological conditions. cEEG results were dichotomized into presence or absence of epileptiform discharges. We identified 159 recordings that were obtained for the evaluation of paroxysmal events. Most patients (n = 100, 63%) were admitted with primary admission diagnoses of neurological disorders, such as ischemic stroke, or intracranial hemorrhage. We found that patients with primary neurological conditions were more likely to have brain surgeries, abnormal brain imaging, and focal neurological deficits on examination compared to those with primary non-neurological conditions. However, there was no significant difference in the prevalence of epileptiform discharges in cEEG among patients with primary diagnoses of neurological or non-neurological disorders. These results suggest that cEEG is often necessary to evaluate paroxysmal events, even among patients without primary neurological disorders.

Early Onset Inherited Peripheral Neuropathies: The Experience of a Specialized Referral Center for Genetic Diagnosis Achievement.

BACKGROUND: Charcot-Marie-Tooth disease (CMT) is a heterogeneous group of inherited peripheral neuropathies. Although the typical disease onset is reported in the second decade, earlier onsets are not uncommon. To date, few studies on pediatric populations have been conducted and the achievement of molecular diagnosis remains challenging. METHODS: During the last 24 years we recruited 223 patients with early-onset hereditary peripheral neuropathies (EOHPN), negative for PMP22 duplication, 72 of them referred by a specialized pediatric hospital. Genetic testing for CMT-associated genes has been carried out with a range of different techniques. RESULTS: Of the 223 EOHPN cases, 43% were classified as CMT1 (demyelinating), 49% as CMT2 (axonal), and 8% as CMTi (intermediate). Genetic diagnosis was reached in 51% of patients, but the diagnostic yield increased to 67% when focusing only on cases from the specialized pediatric neuromuscular centers. Excluding PMP22 rearrangements, no significant difference in diagnostic rate between demyelinating and axonal forms was identified. De novo mutations account for 38% of cases. CONCLUSIONS: This study describes an exhaustive picture of EOHPN in an Italian referral genetic center and analyzes the molecular diagnostic rate of a heterogeneous cohort compared with one referred by a specialized pediatric center. Our data identify MPZ, MFN2, GDAP1, and SH3TC2 genes as the most frequent players in EOHPN. Our study underlines the relevance of a specific neurological pediatric expertise to address the genetic testing and highlights its importance to clarify possible unexpected results when neuropathy is only a secondary clinical sign of a more complex phenotype.