Clinical usefulness and acceptability of small-bowel capsule endoscopy with panoramic imaging compared with axial imaging in Japanese patients.

Objectives: We aimed to evaluate the usefulness and acceptability of CapsoCam Plus (CapsoCam) in Japanese patients. Methods: This retrospective single-center study enrolled 930 patients with suspected small-bowel bleeding (SSBB) who underwent capsule endoscopy. Thirty-three patients using CapsoCam and PillCam SB3 (SB3) were matched using propensity score matching. The diagnostic yield and the acceptability of CapsoCam were evaluated. Results: There was no SSBB case where capsule endoscopy was performed within 48 h of bleeding. CapsoCam had a significantly higher observation rate of the entire small bowel (97% vs. 73%, p = 0.006) and Vater's papilla (82% vs. 15%, p < 0.001) than SB3. The reading time of CapsoCam was significantly longer than that of SB3 (30 vs. 25 min, p < 0.001), and CapsoCam's time from the capsule endoscopy swallowing to read completion was longer than that of SB3 (37 vs. 12 h, p < 0.001). The two groups showed no difference in the capsule endoscopy findings according to the P classification. Notably, 85% of the patients using CapsoCam reported examination distress as "not at all" or "almost not," and 94% reported swallowing difficulty as "very easy" or "easy." Conclusions: CapsoCam took time to read; however, it is a well-tolerated examination with a high observation rate of Vater's papilla and entire small-bowel mucosa. Detectability of bleeding sources was comparable in both modalities for cases of occult SSBB and overt SSBB more than 48 h after bleeding. CapsoCam is a useful modality for patients with SSBB.

Higher sensitivity of pericardial fluid cytology than biopsy in malignant effusions with potential explanation of false-negative cytology: A multi-institutional analysis.

OBJECTIVE: Malignant pericardial effusions are associated with a poor prognosis. Pericardial fluid cytology and pericardial biopsy are the primary methods for diagnosis. This study aimed to conduct a multi-institutional analysis to compare the diagnostic sensitivity of cytology and biopsy, and to investigate potential explanations for false-negative results in cytology. METHODS: A retrospective review of pericardial fluid cytology cases with concurrent biopsy was conducted across four different institutions. Results were compared using standard statistical methods with attention to sensitivity and histologic distribution. False-negative cytology cases were investigated for further exploration. RESULTS: A total of 309 cases were collected, of which 99 (32.0%) were confirmed malignant through repeat sampling or clinical history. Pericardial fluid cytology and biopsy identified 84 and 64 malignant cases, respectively. Our findings confirmed significantly higher sensitivity of cytology compared to biopsy (84.8% vs 65.7%). The most common sites of origin were lung, breast, and gastrointestinal, with adenocarcinoma being the most prevalent histologic subtype. Histologic review of 12 false-negative cytology cases revealed three key explanations; lymphoma was the most common missed diagnosis (33.3%); fibrinous pericarditis obscures neoplastic cells on the pericardial surface; and pericardial involvement can be seen without extension into the pericardial space. CONCLUSION: This study demonstrated diagnostic superiority of pericardial fluid cytology over biopsy in the evaluation of malignant pericardial effusions. We identified several limitations in fluid cytology causing false negatives. In the context of an underlying malignancy with pericardial effusion, pathologists should consider immunohistochemistry studies to aid on the diagnosis.

Fetal whole genome sequencing as a clinical diagnostic tool: Advantages, limitations and pitfalls.

Genome-wide sequencing, which includes exome sequencing and genome sequencing, has revolutionized the diagnostics of genetic disorders in both postnatal and prenatal settings. Compared to exome sequencing, genome sequencing enables the detection of many additional types of genomic variants, although this depends on the bioinformatics pipelines used. Variant classification might vary among laboratories. In the prenatal setting, variant classification may change if new fetal phenotypic features emerge as the pregnancy progresses. There is still a need to evaluate the incremental diagnostic yield of genome sequencing compared to exome sequencing in the prenatal setting. This article reviews the advantages and limitations of genome sequencing, with an emphasis on fetal diagnostics.

The Importance of Copy Number Variant Analysis in Patients with Monogenic Kidney Disease.

Introduction: Genetic testing can reveal monogenic causes of kidney diseases, offering diagnostic, therapeutic, and prognostic benefits. Although single nucleotide variants (SNVs) and copy number variants (CNVs) can result in kidney disease, CNV analysis is not always included in genetic testing. Methods: We investigated the diagnostic value of CNV analysis in 2432 patients with kidney disease genetically tested at the University Medical Centre Utrecht between 2014 and May 2022. We combined previous diagnostic testing results, encompassing SNVs and CNVs, with newly acquired results based on retrospective CNV analysis. The reported yield considers both the American College of Medical Genetics and Genomics (ACMG) classification and whether the genotype actually results in disease. Results: We report a diagnostic yield of at least 23% for our complete diagnostic cohort. The total diagnostic yield based solely on CNVs was 2.4%. The overall contribution of CNV analysis, defined as the proportion of positive genetic tests requiring CNV analysis, was 10.5% and varied among different disease subcategories, with the highest impact seen in congenital anomalies of the kidney and urinary tract (CAKUT) and chronic kidney disease at a young age. We highlight the efficiency of exome-based CNV calling, which reduces the need for additional diagnostic tests. Furthermore, a complex structural variant, likely a COL4A4 founder variant, was identified. Additional findings unrelated to kidney diseases were reported in a small percentage of cases. Conclusion: In summary, this study demonstrates the substantial diagnostic value of CNV analysis, providing insights into its contribution to the diagnostic yield and advocating for its routine inclusion in genetic testing of patients with kidney disease.

Pediatric Brainstem Tumor Biopsy: Surgical Planning and Execution for Maximal Safety and Tissue Yield.

Brainstem tumors account for 10-20% of pediatric brain tumors with a peak age of diagnosis between 7 and 9 years old and are often fatal. Historically, diagnosis of brainstem tumors has been largely based on imaging; however, recent studies have demonstrated the incongruities between preoperative MRI diagnosis and postoperative pathological findings highlighting the importance of brainstem biopsy for diagnostic accuracy. Stereotactic brainstem biopsy for pediatric brainstem tumors has been proven to be safe with a high diagnostic yield (96.1-97.4%) and relatively low morbidity and mortality. Successful pediatric brainstem tumor biopsy demands intricate knowledge of brainstem anatomy, cranial nerves and vasculature, and common pediatric brainstem tumors by the performing surgeon. Additionally, understanding of the surgical indications and techniques (e.g., frame-based versus frameless, robotic assistance, surgical approach, and targets selection) helps to ensure maximal safety and tissue yield. Pediatric brainstem biopsy permits histological conformation of brainstem lesions leading to accurate diagnosis and the potential for personalized treatment and future therapeutic research.

The Diagnostic Yield of Laboratory Tests in Chronic Constipation in Adults.

BACKGROUND: Chronic constipation is a common gastrointestinal complaint characterized by infrequent or difficult bowel movements, significantly affecting patients' quality of life. Laboratory markers offer potential diagnostic value in identifying physiological changes associated with chronic constipation, yet their effectiveness remains underexplored. OBJECTIVES: The objective of this study was to evaluate the diagnostic value of various laboratory tests in identifying the underlying causes of chronic constipation among adults. PATIENTS AND METHODS: A cross-sectional study was conducted at Kurdistan Private Hospital and Jeen Clinics in Duhok, Kurdistan, Iraq, from December 2022 to May 2024. A total of 132 patients meeting the Rome IV criteria for chronic constipation were included. Data collection involved demographic information, lifestyle factors, and laboratory tests, including complete blood count (CBC), thyroid stimulating hormone (TSH), serum calcium, serum potassium, serum glucose, serum creatinine, parathyroid hormone (PTH), and vitamin D levels. RESULTS: The study population consisted of 56 males (42.4%) and 76 females (57.6%) with a mean age of 46.5 years (SD=17 years) and a range of 18-81 years. Regular exercise was performed by only 56 (42.4%) patients, 85 (64.4%) patients were drinking less than 2 liters of water per day, and 108 (81.8%) were overweight or obese. Of the study population, hypothyroidism was detected in 27 (20.4%), hyperparathyroidism in 27 (20.4%), anemia in 58 (44%), leukocytosis in 24 (18.2%), renal impairment in 48 (36.4%), hypokalemia in four (3%), hyperkalemia in 12 (9.1%), hypocalcemia in 10 (7.6%), hypercalcemia in 12 (9.1%), impaired fasting glucose in 46 (34.8%), hyperglycemia in 21 (15.9%), and vitamin D deficiency in 80 (60.6%). Of the study population, 40 (30%) patients had normal laboratory investigations panel. CONCLUSION: In chronic constipation, laboratory tests have high diagnostic yield in adults and are essential for ruling out secondary causes of chronic constipation. Unhealthy lifestyles are prevalent in patients with chronic constipation.

Device-assisted enteroscopy: Are we ready to dismiss the spiral?

Motorized spiral enteroscopy (MSE) is the latest advance in device-assisted enteroscopy. Adverse events related to MSE were discussed in a recent large systematic review and meta-analysis and were directly compared with those of balloon enteroscopy in a case-matched study and a randomized controlled trial. Following the real-life application of MSE, an unexpected safety issue emerged regarding esophageal injury and the technique has been withdrawn from the global market, despite encouraging results in terms of diagnostic and therapeutic yield. We conducted an Italian multicenter real-life prospective study, which was prematurely terminated after the withdrawal of MSE from the market. The primary goals were the evaluation of MSE performance (both diagnostic and therapeutic) and its safety in routine endoscopic practice, particularly in the early phase of introduction in the endoscopic unit. A subanalysis, which involved patients who underwent MSE after unsuccessful balloon enteroscopy, demonstrated, for the first time, the promising performance of MSE as a rescue procedure. Given its remarkable performance in clinical practice and its potential role as a backup technique following a previously failed enteroscopy, it may be more appropriate to refine and enhance MSE in the future rather than completely abandoning it.

Diagnostic Yield of Urine Xpert MTB/RIF Ultra in Adults With Suspected Extrapulmonary Tuberculosis.

We assessed the diagnostic yield of urine GeneXpert MTB/RIF Ultra and factors associated with a positive test among adult patients suspected to have extrapulmonary tuberculosis. Urine Ultra was positive in 14% of participants with definite or probable tuberculosis. Hospitalization, disseminated tuberculosis, and human immunodeficiency virus infection were associated with a positive result.

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.

The yield of genetic workup for middle-aged and elderly patients with neurological disorders in a real-world setting.

Genetic workup is becoming increasingly common in the clinical assessment of neurological disorders. We evaluated its yield among middle-aged and elderly neurological patients, in a real-world context. This retrospective study included 368 consecutive Israeli patients aged 50 years and older (202 [54.9%] males), who were referred to a single neurogenetics clinic between 2017 and mid-2023. All had neurological disorders, without a previous molecular diagnosis. Demographic, clinical and genetic data were collected from medical records. The mean age at first genetic counseling at the clinic was 62.3 ± 7.8 years (range 50-85 years), and the main indications for referral were neuromuscular, movement and cerebrovascular disorders, as well as cognitive impairment and dementia. Out of the 368 patients, 245 (66.6%) underwent genetic testing that included exome sequencing (ES), analysis of nucleotide repeat expansions, detection of specific mutations, targeted gene panel sequencing or chromosomal microarray analysis. Overall, 80 patients (21.7%) received a molecular diagnosis due to 36 conditions, accounting for 32.7% of the patients who performed genetic testing. The diagnostic rates were highest for neuromuscular (58/186 patients [31.2%] in this group, 39.2% of 148 tested individuals) and movement disorders (14/79 [17.7%] patients, 29.2% of 48 tested), but lower for other disorders. Testing of nucleotide repeat expansions and ES provided a diagnosis to 28/73 (38.4%) and 19/132 (14.4%) individuals, respectively. Based on our findings, genetic workup and testing are useful in the diagnostic process of neurological patients aged ≥50 years, in particular for those with neuromuscular and movement disorders.

Diagnostic yield of next-generation sequencing in suspect primary immunodeficiencies diseases: a systematic review and meta-analysis.

To determine the diagnostic yield of Next-generation sequencing (NGS) in suspect Primary Immunodeficiencies Diseases (PIDs). This systematic review was conducted following PRISMA criteria. Searching Pubmed and Web of Science databases, the following keywords were used in the search: ("Next-generation sequencing") OR "whole exome sequencing" OR "whole genome sequencing") AND ("primary immunodeficiency disease" OR "PIDs"). We used STARD items to assess the risk of bias in the included studies. The meta-analysis included 29 studies with 5847 patients, revealing a pooled positive detection rate of 42% (95% CI 0.29-0.54, P < 0.001) for NGS in suspected PID cases. Subgroup analyses based on family history demonstrated a higher detection rate of 58% (95% CI 0.43-0.71) in patients with a family history compared to 33% (95% CI 0.21-0.46) in those without (P < 0.001). Stratification by disease types showed varied detection rates, with Severe Combined Immunodeficiency leading at 58% (P < 0.001). Among 253 PID-related genes, RAG1, ATM, BTK, and others constituted major contributors, with 34 genes not included in the 2022 IUIS gene list. The application of NGS in suspected PID patients can provide significant diagnostic results, especially in patients with a family history. Meanwhile, NGS performs excellently in accurately diagnosing disease types, and early identification of disease types can benefit patients in treatment.

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.

Germline variant analysis from a cohort of patients with severe hypertriglyceridemia in Brazil.

Hypertriglyceridemia (HTG) is a common dyslipidemia associated with an increased risk of cardiovascular disease and pancreatitis. It is well stablished that the severe cases of disease often present with an underlying genetic cause. In this study, we determined the frequency and variation spectrum of genes involved in the triglyceride metabolism in a series of Brazilian patients with severe HTG. A total of 212 patients with very high HTG, defined with fasting triglycerides (TG) ≥ 880 mg/ dL, that underwent a multi-gene panel testing were included in this research. Germline deleterious variants (i.e. Pathogenic/Likely Pathogenic (P/LP) variants) were identified in 28 out of 212 patients, reflecting an overall diagnostic yield of 13% in our cohort. Variants of unknown significance (VUS) were identified in 87 patients, and represent 80% of detected variants in this dataset. We confirm the LPL as the most frequently mutated gene in patients with severe HTG, and we had only one suspected case of familial chylomicronemia syndrome, caused by a homozygous variant in LMF1, in our cohort. Notably, we report 16 distinct and novel variants (P/LP and VUS), each of them representing a single case, not previously reported in any public databases or other studies. Our data expand our knowledge of genetic variation spectrum in patients with severe HTG in the Brazilian population, often underrepresented in public genomic databases, being also a valuable clinical resource for genetic counseling and healthcare programs in the country.

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.

Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment.

OBJECTIVE: Whole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory. MATERIALS AND METHODS: We retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs). RESULTS: Among the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults. CONCLUSIONS: The proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.

Endoscopic Ultrasound-Guided Tissue Sampling for the Cytohistological Diagnosis of Focal Liver Lesions.

BACKGROUND: Focal liver lesions (FLL) often require cytohistological evaluation. Endoscopic Ultrasound (EUS)-guided tissue acquisition (EUS-TA) is highly accurate in diagnosing pancreatic and gastrointestinal malignancies. The aim of our study was to evaluate the role of EUS-TA in the characterization of FLL. METHODS: A retrospective analysis of a prospective database of patients who underwent EUS-TA for the evaluation of FLL. Diagnostic yield, adverse events and factors associated with diagnostic yield were evaluated as endpoints. The effect of variables such as needle size, lesion size, rapid on-site evaluation (ROSE) and the use of cytological or histological needles were analyzed. RESULTS: A total of 114 cases were included (mean age 68.05 ± 11.35 years, 64 male). A correct diagnosis was made using EUS-TA in 100 of the 114 cases (diagnostic yield of 88%). The EUS-TA of additional extrahepatic lesions during the same EUS procedure increased the diagnostic yield to 94%. No adverse events were reported. Multivariate analysis did not identify any factor influencing the diagnostic yield. CONCLUSIONS: EUS-TA is a highly accurate and safe technique for the differential diagnosis of FLL and could be considered as the primary approach in this setting.

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.

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.

Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing.

BACKGROUND: Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS: In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS: Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS: Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.

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.