Search

Expanded carrier screening (ECS) is a preventive genetic test that enables couples to know their risk of having a child affected by certain monogenetic diseases. This study aimed to evaluate the carrier frequency for rare monogenic diseases in the general Chinese population and the impacts of ECS on their reproductive decisions and pregnancy outcomes.This single-center study was conducted between September 2022 and April 2023. An ECS panel containing 224 recessive genes was offered to 1,499 Chinese couples from the general population who were at early gestational ages or planned to conceive.Overall, 55.0 % of the individuals carried for at least one recessive condition. There were 16 autosomal recessive (AR) genes with a carrier frequency of ≥1/100 and 22 AR genes with a carrier frequency of <1/100 to ≥1/200. The most common AR and X-linked diseases were GJB2-related non-syndromic hearing loss, and hemolytic anemia, respectively. Fifty-five couples (3.67 %; 1 in 27.3) were at increased risk of having an affected child with 19 pregnant at the time of testing. Of these, 10 opted for amniocentesis, and four affected pregnancies were identified, with three of them being terminated.This study not only provides valuable information about the recessive genetic landscape, but also establishes a solid foundation for couple-based ECS in a real clinical setting. [ABSTRACT FROM AUTHOR]

Background: Autosomal recessive polycystic kidney disease (ARPKD) is a genetically inherited pediatric disorder. It is caused by a mutation in the PKHD1 gene located on chromosome 6. The predominant phenotype is characterized by early-onset bilateral enlarged kidneys, as well as fibrocystic changes in the kidney and liver. Fetuses or infants usually present with Potter syndrome, and they are more likely to develop severe renal insufficiency. Generally, patients die perinatally or in infancy. Liver involvement has been reported in adults with ARPKD who have survived the neonatal period and childhood. However, renal involvement is rarely expected in adulthood. The case is being presented for its clinical rarity, in addition to emphasize the critical role of NGS approaches in diagnosis. Case presentation: We hereby describe a 33-year-old female with adult-onset proteinuria and nephromegaly. She had a rare homozygous missense mutation of the PKHD1 gene with autosomal recessive inheritance. The proband has consanguineous heterozygote parents. The mutation was identified by whole-exome sequencing, and the results were confirmed by segregation analysis. Conclusion: Here, we reported a thorough literature review of late-onset autosomal recessive polycystic kidney disease. Furthermore, we explored the importance of genetic work-up in families with genetic disorders and consanguineous marriages, particularly in underdeveloped countries. [ABSTRACT FROM AUTHOR]

Objective: To investigate the genetic mutations in patients with papillary thyroid carcinoma (PTC) and their clinicopathological features by next generation sequencing (NGS). Methods: NGS technology was used to detect genetic mutations in PTC patients, and clinicopathological features were collected. Results: ①Among 855 PTC patients, 810 patients had genetic mutations, and 45 patients had no genetic mutation. ②BRAF mutation was associated with tumor diameter (P < 0.001) and histological subtypes (P = 0.002). The abundance of V600E mutation was associated with gender (P = 0.004), tumor diameter (P < 0.001), bilateral presentation (P = 0.001), extrathyroidal extension (P < 0.001), lymphatic metastasis (P < 0.001), histological subtypes (P = 0.002) and TNM staging (P = 0.000); The different mutation abundance of V600E was associated with tumor diameter (P < 0.001), multifocal presentation (P = 0.047), bilateral presentation (P = 0.001), extrathyroidal extension (P = 0.001), lymphatic metastasis (P < 0.001), histological subtypes (P = 0.022) and TNM staging (P = 0.000). ③RET fusion was associated with tumor diameter (P < 0.001) and lymphatic metastasis (P = 0.005). ④TERT mutation was associated with gender (P = 0.043), tumor diameter (P < 0.001), extrathyroidal extension (P = 0.028) and TNM staging (P = 0.017). ⑤RAS mutation was associated with histological subtypes (P < 0.001). ⑥NTRK and PIK3CA mutations were not associated with clinicopathological features. Conclusion: NGS technology can comprehensively analyze the genetic mutations in PTC patients, which provides important prompts for the occurrence, development, diagnosis and treatment of PTC. In addition, BRAF V600E mutation, RET fusion and TERT mutation are associated with a number of high-risk clinicopathological features. Detection of genetic mutations in PTC patients by NGS is of great significance. [ABSTRACT FROM AUTHOR]

Introduction: Liquid biopsy is gaining momentum for diagnosis and surveillance of cancer patients. Indeed, head and neck squamous cell carcinoma (HNSCC) is burdened with poor prognosis and high recurrence rates after treatment. It is therefore crucial to be able to detect minimal residual disease early after radical treatment or relapse, so surgery can be performed when the disease is still resectable. In this scenario, aim of this study is to create a liquid biopsy-based pipeline able to detect somatic tumor mutations in a cohort of HNSCC-affected patients undergoing follow-up after surgical intervention. Methods: Our cohort included 17 patients diagnosed with HNSCC over 4 years. The first saliva sample was collected before surgery while the rest were collected during the subsequent visits, according to the follow-up schedule. Salivary DNA (sDNA) was extracted, and a 52-gene next generation sequencing (NGS)-based panel was used for somatic variants detection. Results: 41.2% of samples collected before surgery bore a deleterious variant (n=7/17). Overall, 29.2% of samples harbored at least a pathogenic variant (n=21/72). The most frequently mutated genes were TP53 (80%), FBXW7 (8%), PDGFRA (4%) and PTEN (4%). Finally, three patients experienced a loco-regional relapse by clinical evaluations, anticipated in 67% of cases by the molecular one (n=2/3). Discussion: Our data indicate that sDNA could aid in the monitoring of patients' follow-up as low-frequency somatic mutations could be assessed from the saliva of HNSCC patients. Prospectively, these results suggest that salivary-based liquid biopsy might pave the way for personalized molecular therapies based on mutational data. [ABSTRACT FROM AUTHOR]

Purposes: Osimertinib, one of the third-generation EGFR-tyrosine kinase inhibitors (TKIs) designed to target EGFR T790M mutation, significantly improves the prognosis of lung cancer. However, drug resistance still happens and MET amplification is responsible for one of the main causes. Fluorescence in situ hybridization (FISH) is the gold standard for MET amplification detection, but fundamentally limited by observer subjectivity. Herein, we assessed the value of next-generation sequencing (NGS) method in MET amplification detection in non-small cell lung cancer (NSCLC), as well as revealed the mutation profiling of NSCLC patients with osimertinib resistance to provide some valuable clues to the mechanisms of resistance. Methods: A total of 317 cancer tissue samples from 317 NSCLC patients at time of progression following osimertinib were submitted to NGS and only 96 tissues were tested by FISH simultaneously. With FISH results as gold standard, enumeration algorithm was applied to establish the optimal model for identifying MET amplification using gene copy number (GCN) data. Results: The optimal model for identifying MET amplification was constructed based on the GCN of MET, BRAF, CDK6 and CYP3A4, which achieved a 74.0% overall agreement with FISH and performed well in identifying MET amplification except polysomy with a sensitivity of 85.7% and a specificity of 93.9%. The inconsistency between NGS and FISH occurred mainly in polysomy subtype, while MET GCN ≥ 5 could be reliably recognized by NGS. Moreover, the most frequently mutated genes in NSCLC patients with osimertinib resistance were EGFR (59.94%), followed by TP53 (43.85%), NRG1 (9.46%), PIK3CA (6.31%), and ATM (5.36%). The known resistance mechanisms, including MET amplification, EGFR (C797S, L718Q/R), TP53, CDK4, CDK6, CDKN2A, BRAF, KRAS, NRAS and PIK3CA mutations were also disclosed in our cohort. Conclusions: NGS assay can achieve a high concordance with FISH in MET amplification detection and has advantages in portraying various genetic alterations, which is of worthy in clinical promotion. [ABSTRACT FROM AUTHOR]

Next generation sequencing (NGS) or massively parallel sequencing (MPS) is a high‐throughput technology that can be used to analyze DNA and RNA molecules with greater sensitivity, scalability, and speed than traditional Sanger sequencing. NGS systems are slowly gaining popularity in forensic science and may eventually become the future of forensic DNA analysis. The data generated can be utilized to conduct an array of forensic biology analyses such as short tandem repeats (STR) profiling, forensic genetic genealogy, predictive DNA phenotyping, and more. However, the adoption of NGS for forensic casework is associated with a lot of ethical, social, and legal concerns. This article provides a comprehensive review of NGS systems, data analysis, and forensic applications. It also provides policy considerations that aim to reduce harm and bias, while promoting informed consent, standardization, transparency, and accountability. This article is categorized under:Forensic Biology > Interpretation of Biological EvidenceForensic Biology > Ethical and Social ImplicationsForensic Biology > Forensic DNA Technologies [ABSTRACT FROM AUTHOR]

Background/Objectives: Metastatic colorectal cancer remains a fatal disease, with a 5-year survival rate lower than 15%. The most common metastatic sites are the lungs and the liver, while skin metastases are very rare and often indicate a poor prognosis with a lower survival rate. Methods. Herein, we present the clinical case of a 62-year-old female patient with rectal cancer metastases to the skin of the anogenital and abdominal regions, diagnosed 2 years after completion of treatment of the underlying disease. Results: Histological examination of the skin lesions revealed adenocarcinoma, and expression of the same immunohistochemical markers was also found in the primary tumor and in the cutaneous metastases. However, next-generation sequencing demonstrated differences in the mutational profiles of the primary tumor and metastasis to the skin. Somatic mutations in the APC, TP53, and PTPN11 genes were revealed in primary rectal adenocarcinoma, but another pathogenic TP53 mutation and a frameshift variant in the DYNC1I1 gene were found in cutaneous metastases. The patient underwent several courses of FOLFOX6 chemotherapy in combination with bevacizumab, but the treatment was unsuccessful. An analysis of 50 clinical cases from the literature concerning various manifestations of cutaneous metastases of rectal cancer showed a median survival of 8.5 months from the time of detection of the skin lesions. Conclusions: In this regard, careful skin examination of patients with rectal cancer and timely detection of cutaneous metastases are essential steps in the follow-up of patients who have undergone treatment of the primary tumor. [ABSTRACT FROM AUTHOR]

Mesonephric adenocarcinomas (MAs) with spindle cell components are rare malignant cervical tumours. In the present study, a retrospective analysis of these tumours was performed. Clinicopathological data were gathered from electronic surgical pathology records, and both immunohistochemistry and targeted next-generation sequencing (NGS) were performed. The present study included three postmenopausal female patients diagnosed with primary uterine cervical MA with prominent spindle cell components, aged 51-60 years. All patients underwent hysterectomy with bilateral salpingo-oophorectomy and pelvic lymph node dissection. There were no recurrences or deaths after surgery. NGS analysis identified KRAS mutations in 2 cases and a PIK3-catalytic subunit α (PIK3CA) mutation in another. Spindle cell components may indicate MAs at an advanced stage. Spindle cell components in MAs are diagnostic pitfalls, and the use of immunohistochemical panels and molecular detection cases with overlapping morphological features is recommended. While KRAS mutations are the most common types of mutations in MAs with spindle cell components, the present study demonstrates that PIK3CA mutations can also occur independently in cases without KRAS mutations. [ABSTRACT FROM AUTHOR]

Mutation profiling by next-generation sequencing (NGS) has facilitated understanding of the molecular pathogenesis of acute myeloid leukemia (AML), and has been incorporated into the new disease classification (International Consensus Classification; ICC) and risk classification (European LeukemiaNet [ELN] 2022; ELN2022). We compared disease subtypes between the previous disease classification (4th edition of the WHO classification; WHO-4) and the ICC in 91 patients with AML diagnosed at our institution. We also compared disease risk classifications using the previous risk classification (ELN2017) and the ELN2022. Targeted sequencing of bone marrow samples was conducted at Kyoto University. We found that entities under AML with recurrent genetic abnormalities were well-established, with almost no change from the WHO-4 to the ICC. In contrast, 16.7% of cases of AML, not otherwise specified in the WHO-4 were reclassified into AML with mutated TP53, and 36.7% were reclassified into AML with myelodysplasia-related gene mutations or cytogenetic abnormalities per the ICC. Meanwhile, the ELN2017 and ELN2022 showed no difference in concordance indexes in multivariate Cox regression analysis for progression-free and overall survival. The superiority of the ELN2022 over the ELN2017 could not be confirmed in our single-center retrospective study, and further investigation including multicenter prospective studies is needed. [ABSTRACT FROM AUTHOR]

Objective: Establishing the cause of hearing loss (HL) is important and rewarding, though not without its challenges. While our ability to identify the etiology for HL has improved with advances in scientific knowledge, a significant proportion of cases remain of unknown etiology. Recent protocol changes within the NHS Genomic Medicine Service support the utilization of the HL gene panel test, rather than individual gene tests. In light of these changes, determining the yield of these more extensive panel tests is important in informing future practice. Study Design: Retrospective study. Setting: The Cochlear Implant (CI) Department at Great Ormond Street Hospital (GOSH). Methods: Four hundred seventy‐six children with profound HL were identified from a database of referrals to the GOSH CI Department. Data on etiology of HL including genetic diagnosis was collected from hospital notes on an electronic patient records system and hospital genetics database. Results: We identified a positive result in 163/476 (34%) cases through the gene panel test, representing an additional 19% yield to current level 1 investigations. Genetic HL, including both syndromic (including those not covered by the HL gene panel) and nonsyndromic (209/476, 44%) was the most common etiology in our cohort. Perinatal, intrauterine, ototoxicity, meningitis, and encephalitis categories altogether comprised 97/476 (20%) cases. Conclusion: Gene panel testing provides significant additional yield over current level 1 investigations which include GJB2 testing only. This has far‐reaching implications for how we optimize investigations into HL in children and counsel families, and for future early interventions. [ABSTRACT FROM AUTHOR]

Introduction: From 2020, with advent of COVID-19 pandemic, Tripura has experienced SARS-CoV-2 viral evolution in accordance with other parts of India. Since January 2022, the Omicron variant of SARS-CoV-2 virus became the predominant lineage circulating in India and neighboring countries. This study characterizes the viral genome of the omicron variant circulating in the state since its inception to June, 2023. Methods and results: The current study was performed on nasopharyngeal and oropharyngeal samples received from the various departments of AGMC, as well as eight district hospitals from Tripura. The positive samples with a cycle threshold value of 25 or less for the E and/or N gene were considered for whole genome sequencing using Illumina Miseq NGS platform. Majority of the sequences belonged to Clade 21 L, with BA.5.2 being the major sub variant detected during the study period. Majority of the mutations were detected in the Spike protein region, including L24-, P25-, P26-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, S477N, T478K, Q498R, Y505H, Q954H and N969K. All the sequences uniquely showed the mutations A27S and G142D in N terminal domain in Spike protein, not being reported from other Indian sequences like BA.5 variants. T9I, A63T and P13L were major substitutions in E, M and N protein regions respectively. Escape of mutants from vaccine induced immunity was mostly observed in BA.2 sub variants, majority endowed with the triplet mutation of K417N + E484K + N501Y. Conclusion: The current study indicates that Omicron variants circulating in the state of Tripura is comparable to other regions of India and the neighbouring country of Bangladesh. Genetic mutations increasing viral transmissibility have been identified in the circulating viral genomes. [ABSTRACT FROM AUTHOR]

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase approximately 50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important. [ABSTRACT FROM AUTHOR]

In the last two decades, next-generation sequencing (NGS) has facilitated enormous progress in cancer medicine, in both diagnosis and treatment. However, the usefulness of NGS in older cancer patients is unclear. To determine the role of NGS in older cancer patients, we retrospectively assessed demographic, clinicopathologic, and disease-specific data from 100 randomly selected cancer patients (any subtype/stage) who underwent NGS testing in 2020 at our institution and compared the treatment outcomes (progression-free survival [PFS] and overall survival [OS]) in the younger and older patient cohorts (A [n = 34] and B [n = 66]: age < 70 and ≥70 years, respectively). Overall, 27% had targetable mutations, and 8% received NGS-determined targeted therapy (45% and 19% of patients with a targetable mutation in cohorts A and B, respectively; p = 0.2), of whom 38% (3% of the whole cohort) benefited from the therapy (PFS > 6 months). The median OS (from diagnosis) was 192 and 197 weeks in cohorts A and B, respectively (p = 0.08). This pilot study revealed no significant age-stratified difference in the diagnostic approach and treatment strategy. A small, but relevant, proportion of the cohort (3%) benefited from NGS-determined treatment. Nevertheless, older cancer patients with targetable mutations less frequently received targetable therapies. [ABSTRACT FROM AUTHOR]

Background: In the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability. Results and discussion: In this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10− 43 and 1-1.6 × 10− 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods. Conclusions: In summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution. [ABSTRACT FROM AUTHOR]

AbstractIntroductionMethodsResultsConclusionParticulate matter (PM) air pollution is associated with an increased incidence of lung diseases, but the underlying mechanisms have not been fully elucidated. In this study, a mouse model of subacute lung inflammation was employed to investigate the cellular responses and gene expression changes induced by exposure to natural ambient air pollution.C57BL/6J mice were exposed to road dust (primarily PM10) at 150 µg/m³ for 21 days (8 h/day) through a nose-only inhalation exposure system. Lung tissues were analyzed for the expression of proinflammatory signaling, oxidative stress, and fibrosis markers. RNA-sequencing analysis was conducted to identify differentially expressed genes (DEGs). A gene ontology over-representation analysis was performed to identify the altered genetic pathways.Elevated levels of proinflammatory cytokines, including IL-1β, IL-6, and TNF-α, and an increase in phosphorylated MAPK were determined in the road dust exposure group compared to the control group. Histopathological examinations revealed more severe lung inflammation and damage in the exposed mice, including fibrosis and bronchiolar hyperplasia. Gene expression profiling identified 108 DEGs, with decreases in most except genes such as Krt15 and Reg3g. The protein–protein interaction network analysis together with text-mining identified 18 key hub genes, associated with fatty acid oxidation, lipid metabolism, and peroxisomes.This study identified key genes, signaling pathways, and cellular responses in mouse lung affected by road dust exposure. These findings contribute to a deeper understanding of the transcriptional and cellular responses induced by subacute exposure to the PM in road dust. [ABSTRACT FROM AUTHOR]

Background: Error-corrected next-generation sequencing (ecNGS) technologies have enabled the direct evaluation of genome-wide mutations after exposure to mutagens. Previously, we reported an ecNGS methodology, Hawk-Seq™, and demonstrated its utility in evaluating mutagenicity. The evaluation of technical transferability is essential to further evaluate the reliability of ecNGS-based assays. However, cutting-edge sequencing platforms are continually evolving, which can affect the sensitivity of ecNGS. Therefore, the effect of differences in sequencing instruments on mutation data quality should be evaluated. Results: We assessed the performance of four sequencing platforms (HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400) with the Hawk-Seq™ protocol for mutagenicity evaluation using DNA samples from mouse bone marrow exposed to benzo[a]pyrene (BP). The overall mutation (OM) frequencies per 106 bp in vehicle-treated samples were 0.22, 0.36, 0.46, and 0.26 for HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400, respectively. The OM frequency of NextSeq2000 was significantly higher than that of HiSeq2500, suggesting the difference to be based on the platform. The relatively higher value in NextSeq2000 was a consequence of the G:C to C:G mutations in NextSeq2000 data (0.67 per 106 G:C bp), which was higher than the mean of the four platforms by a ca. of 0.25 per 106 G:C bp. A clear dose-dependent increase in G:C to T:A mutation frequencies was observed in all four sequencing platforms after BP exposure. The cosine similarity values of the 96-dimensional trinucleotide mutation patterns between HiSeq and the three other platforms were 0.93, 0.95, and 0.92 for NovaSeq, NextSeq, and DNBSeq, respectively. These results suggest that all platforms can provide equivalent data that reflect the characteristics of the mutagens. Conclusions: All platforms sensitively detected mutagen-induced mutations using the Hawk-Seq™ analysis. The substitution types and frequencies of the background errors differed depending on the platform. The effects of sequencing platforms on mutagenicity evaluation should be assessed before experimentation. [ABSTRACT FROM AUTHOR]

AbstractThe support of the p-value corresponding to a discrete test-statistic is a finite isolated subset of the unit interval. In differential gene expression studies with RNA-sequence datasets, multiple discrete tests are performed. The objective of such studies are to identify differentially expressed genes with a control over a measure of false discoveries. We suggest to remove hypotheses corresponding to the p-values having minimum support-point greater than the threshold of that overall measure. We argue this suggestion and present methods of filtering the set of hypotheses for two useful testing scenarios. Simulation experiments show gain in power of the multiple testing procedures when applied to the filtered set of hypotheses. We also demonstrate the method with two real datasets, related to the study of HIV and mammary gland. [ABSTRACT FROM AUTHOR]

Background and Objectives: Leprosy foot ulcers (LFU) tend to become chronic due to secondary bacterial infections, leading to subsequent disfigurement and disability. Treatment modality for infected plantar ulcers thus so far is majorly based on conventional approach of empirical antibacterial therapy. However, this approach tends to overlook unconventional pathogens which are likely to be present in the LFU. Materials and Methods: Twenty-six leprosy patients (17 males and 9 females) who had completed multidrug therapy (MDT) and those are suffering from foot ulcer were included. Using sterile cotton swabs, two wound swabs were collected, of these; one for bacterial culture and another for NGS (Next Generation Sequencing). Results: Out of 26 samples tested on conventional bacterial culture, Streptococcus spp. (50%) was predominant organism. On NGS, 09/26 (34.61%) showed Streptococcus-dysgalactiae-subsp.-equisimilis-GGS 12 as the most abundant single organism, along with some unknown and unclassified organisms; 03/26 (11.5%) were Arcanobacterium-haemolyticum-DSM-20595 alone and 02/26 (7.69%) were Streptococcus-pyogenes alone. A combination of Arcanobacterium-haemolyticum-DSM-20595 and Streptococcus-dysgalactiae-subsp.-equisimilis-GGS 124 was found in nine (34.61%) specimens. Conclusion: Polymicrobial infection with conventional and unconventional pathogenic bacteria is another notable finding suggesting appropriate interventions. The study findings also reiterate the need for understanding the polymicrobial infections and their role in the clinical progression of the LFU. [ABSTRACT FROM AUTHOR]

Studies have demonstrated the susceptibility of companion animals to natural infection with SARS-CoV-2. Using quantitative reverse transcription polymerase chain reaction and sequencing analyses, this study investigated SARS-CoV-2 RNA excretion in pets in households with infected owners. Oropharyngeal and rectal swabs were collected from dogs and cats in Parana, Southern Brazil, between October 2020 and April 2021. Viral RNA was detected in 25% of cats and 0.98% of dog oropharyngeal swabs; however, systemic, respiratory, and gastrointestinal signs were absent. Complete viral genomes belonged to the Gamma lineage. Phylogenetic analyses indicated that pet samples were probably derived from human-positive cases in Parana. Viral excretion in the oropharynx was more frequent in cats than in dogs. Mutations in the S protein characteristic of Gamma strains were present in all sequenced SARS-CoV-2 strains. The receptor-binding domain of these Brazilian strains did not show any additional mutations not reported in the Gamma strains. Mutations in NSP6, NSP12, and N proteins previously mapped to strains that infect deer or minks were detected. This study highlights the importance of actively monitoring the SARS-CoV-2 strains that infect pets with continued viral exposure. Monitoring genetic changes is crucial because new variants adapted to animals may pose human health risks. [ABSTRACT FROM AUTHOR]

Papillomaviruses (PVs) are oncogenic and infect the skin and mucosa of various host species. Considering the recent advances in research on PVs using rolling circle amplification (RCA) followed by high-throughput sequencing (HTS), in this study, we aimed to investigate the bovine papillomavirus (BPV) types associated with proliferative lesions in the upper alimentary tract of an affected bull and characterize the viral strains through complete genome sequencing using this strategy. We analyzed the PV strains associated with two hyperplastic esophageal lesions through PCR using degenerate primer pairs and RCA, followed by HTS. HTS of the libraries generated using RCA products provided the whole genome sequence of BPV4 present in squamous papilloma, whereas the complete genome sequence of BPV2 and subgenomic fragments of BPV4 were identified in carcinoma in situ (CIS). For the first time, we have sequenced BPV2 identified from the CIS of the bovine upper alimentary canal. Additionally, RCA followed by HTS allowed characterization of the mixed infection by BPV2 and BPV4 in this lesion. These data reveal that BPV4 is not the only BPV type present in CIS of the esophageal mucous membrane; moreover, a mixed infection caused by BPV2 and BPV4 at the tested anatomical site was demonstrated. [ABSTRACT FROM AUTHOR]

Primary liver tumours, including benign liver tumours, hepatocellular carcinoma and cholangiocarcinoma, present a multifaceted challenge, necessitating a collaborative approach, as evidenced by the role of the multidisciplinary tumour board (MDTB). The approach to managing primary liver tumours involves specialised teams, including surgeons, radiologists, oncologists, pathologists, hepatologists, and radiation oncologists, coming together to propose individualised treatment plans. The evolving landscape of primary liver cancer treatment introduces complexities, particularly with the expanding array of systemic and locoregional therapies, alongside the potential integration of molecular biology and artificial intelligence (AI) into MDTBs in the future. Precision medicine demands collaboration across disciplines, challenging traditional frameworks. In the next decade, we anticipate the convergence of AI, molecular biology, pathology, and advanced imaging, requiring adaptability in MDTB structure to incorporate these cutting-edge technologies. Navigating this evolution also requires a focus on enhancing basic, translational, and clinical research, as well as boosting clinical trials through an upgraded use of MDTBs as hubs for scientific collaboration and raising literacy about AI and new technologies. In this review, we will delineate the current unmet needs in the clinical management of primary liver cancers, discuss our perspective on the future role of MDTBs in primary liver cancers ("next generation" MDTBs), and unravel the potential power and limitations of novel technologies that may shape the multidisciplinary care landscape for primary liver cancers in the coming decade. [ABSTRACT FROM AUTHOR]

The current genetic diagnostic workup of congenital cataract (CC) is mainly based on NGS panels, whereas exome sequencing (ES) has occasionally been employed. In this multicentre study, we investigated by ES the detection yield, mutational spectrum and genotype–phenotype correlations in a CC cohort recruited between 2020 and mid‐2022. The cohort consisted of 67 affected individuals from 51 unrelated families and included both non‐syndromic (75%) and syndromic (25%) phenotypes, with extra‐CC ocular/visual features present in both groups (48% and 76%, respectively). The functional effect of variants was predicted by 3D modelling and hydropathy properties changes. Variant clustering was used for the in‐depth assessment of genotype–phenotype correlations. A diagnostic (pathogenic or likely pathogenic) variant was identified in 19 out of 51 probands/families (~37%). In a further 14 probands/families a candidate variant was identified: in 12 families a VUS was detected, of which 9 were considered plausibly pathogenic (i.e., 4 or 5 points according to ACMG criteria), while in 2 probands ES identified a single variant in an autosomal recessive gene associated with CC. Eighteen probands/families, manifesting primarily non‐syndromic CC (15/18, 83%), remained unsolved. The identified variants (8 P, 12 LP, 10 VUS‐PP, and 5 VUS), half of which were unreported in the literature, affected five functional categories of genes involved in transcription/splicing, lens formation/homeostasis (i.e., crystallin genes), membrane signalling, cell–cell interaction, and immune response. A phenotype‐specific variant clustering was observed in four genes (KIF1A, MAF, PAX6, SPTAN1), whereas variable expressivity and potential phenotypic expansion in two (BCOR, NHS) and five genes (CWC27, KIF1A, IFIH1, PAX6, SPTAN1), respectively. Finally, ES allowed to detect variants in six genes not commonly included in commercial CC panels. These findings broaden the genotype–phenotype correlations in one of the largest CC cohorts tested by ES, providing novel insights into the underlying pathogenetic mechanisms and emphasising the power of ES as first‐tier test. [ABSTRACT FROM AUTHOR]

Autoimmune lymphoproliferative syndrome (ALPS) is a rare genetic disorder featuring chronic lymphadenopathy, splenomegaly, cytopenias, and increased lymphoma risk. Differentiating ALPS from immunodeficiencies with overlapping symptoms is challenging. This study evaluated the performance and the diagnostic yield of a 15-gene NGS panel for ALPS at Cincinnati Children’s Hospital Medical Center. Samples from 802 patients submitted for ALPS NGS panel were studied between May 2014 and January 2023. A total of 62 patients (7.7%) had a definite diagnosis: 52/62 cases (84%) showed 37 unique pathogenic/likely pathogenic germline FAS variants supporting ALPS diagnosis (6.5%, 52/802). The ALPS diagnostic yield increased to 30% in patients who additionally fulfilled abnormal ALPS immunology findings criteria. 17/37 (46%) diagnostic FAS variants were novel variants reported for the first time in ALPS. 10/802 cases (1.2%) showed diagnostic findings in five genes (ADA2, CTLA4, KRAS, MAGT1, NRAS) which are related to autoimmune lymphoproliferative immunodeficiency (ALPID). Family studies enabled the reclassification of variants of unknown significance (VUS) and also the identification of at-risk family members of FAS-positive patients, which helped in the follow-up diagnosis and treatment. Alongside family studies, complete clinical phenotypes and abnormal ALPS immunology and Fas-mediated apoptosis results helped clarify uncertain genetic findings. This study describes the largest cohort of genetic testing for suspected ALPS in North America and highlights the effectiveness of the ALPS NGS panel in distinguishing ALPS from non-ALPS immunodeficiencies. More comprehensive assessment from exome or genome sequencing could be considered for undefined ALPS-U patients or non-ALPS immunodeficiencies after weighing cost, completeness, and timeliness of different genetic testing options. [ABSTRACT FROM AUTHOR]

Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients’ long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers. [ABSTRACT FROM AUTHOR]

Much attention is placed on organohalide-respiring bacteria (OHRB), such as Dehalococcoides, during the design and performance monitoring of chlorinated solvent bioremediation systems. However, many OHRB cannot function effectively without the support of a diverse group of other microbial community members (MCMs), who play key roles fermenting organic matter into more readily useable electron donors, producing corrinoids such as vitamin B12, or facilitating other important metabolic processes or biochemical reactions. While it is known that certain MCMs support dechlorination, a metric considering their contribution to bioremediation performance has yet to be proposed. Advances in molecular biology tools offer an opportunity to better understand the presence and activity of specific microbes, and their relation to bioremediation performance. In this paper, we test the hypothesis that a specific microbial consortium identified within 16S ribosomal ribonucleic acid (rRNA) gene next generation sequencing (NGS) data can be predictive of contaminant degradation rates. Field-based data from multiple contaminated sites indicate that increasing relative abundance of specific MCMs correlates with increasing first-order degradation rates. Based on these results, we present a framework for computing a simplified metric using NGS data, the Microbial Community Structure Index, to evaluate the adequacy of the microbial ecosystem during assessment of bioremediation performance. [ABSTRACT FROM AUTHOR]

Rationale: Isoniazid-resistant tuberculosis (Hr-TB) is often overlooked in diagnostic algorithms because of reliance on first-line molecular assays testing only for rifampicin resistance. Objectives: To determine the prevalence, outcomes, and molecular mechanisms associated with rifampin-susceptible, isoniazid-resistant TB (Hr-TB) in the Eastern Cape, South Africa. Methods: Between April 2016 and October 2017, sputum samples were collected from patients with rifampin-susceptible TB at baseline and at Weeks 7 and 23 of drug-susceptible TB treatment. We performed isoniazid phenotypic and genotypic drug susceptibility testing, including FluoroTypeMTBDR, Sanger sequencing, targeted next-generation sequencing, and whole-genome sequencing. Results: We analyzed baseline isolates from 766 patients with rifampin-susceptible TB. Of 89 patients (11.7%) who were found to have Hr-TB, 39 (44%) had canonical katG or inhA promoter mutations; 35 (39%) had noncanonical katG mutations (including 5 with underlying large deletions); 4 (5%) had mutations in other candidate genes associated with isoniazid resistance. For 11 (12.4%), no cause of resistance was found. Conclusions: Among patients with rifampin-susceptible TB who were diagnosed using first-line molecular TB assays, there is a high prevalence of Hr-TB. Phenotypic drug susceptibility testing remains the gold standard. To improve the performance of genetic-based phenotyping tests, all isoniazid resistance–associated regions should be included, and such tests should have the ability to identify underlying mutations. [ABSTRACT FROM AUTHOR]

The pathogenic strains of Escherichia coli (E. coli) are frequent cause of urinary tract infections including catheter-associated, soft tissue infections and sepsis. The growing antibiotic resistance in E. coli is a major health concern. Bacteriophages are specific for their bacterial host, thus providing a novel and effective alternatives. This study focuses on isolation of bacteriophages from urban sewage treatment plants. Initially 50 different bacteriophages have been isolated against non-resistant reference E. coli strain and fifty multidrug resistant clinical isolates of extraintestinal infections. Out of which only thirty-one lytic phages which gave clear plaques were further analysed for different physico-chemical aspects such as thermal inactivation, pH, effect of organic solvents and detergents. Two bacteriophages, ASEC2201 and ASEC2202, were selected for their ability to withstand temperature fluctuation from −20 to 62 °C and a pH range from 4 to 10. They also showed good survival (40–94%) in the presence of organic solvents like ethanol, acetone, DMSO and chloroform or ability to form plaques even after the treatment with detergents like SDS, CTAB and sarkosyl. Both efficiently killed reference strain and 40–44% of multidrug resistant clinical isolates of E. coli. Later ASEC2201 and ASEC2202 were subjected to morphological characterisation through transmission electron microscopy, which revealed them to be tailed phages. The genomic analysis confirmed them to be Escherichia phages which belonged to family Drexlerviridae of Caudovirales. [ABSTRACT FROM AUTHOR]

Purpose of Review: Myelofibrosis (MF) includes prefibrotic primary MF (pre-PMF), overt-PMF and secondary MF (SMF). Median overall survival (OS) of pre-PMF, overt-PMF and SMF patients is around 14 years, seven and nine years, respectively. Main causes of mortality are non-clonal progression and transformation into blast phase. Recent Findings: Discoveries on the impact of the biological architecture on OS have led to the design of integrated scores to predict survival in PMF. For SMF, OS estimates should be calculated by the specific MYSEC-PM (MYelofibrosis SECondary-prognostic model). Information on the prognostic role of the molecular landscape in SMF is accumulating. Crucial treatment decisions for MF patients could be now supported by multivariable predictive algorithms. OS should become a relevant endpoint of clinical trials. Summary: Prognostic models guide prediction of OS and treatment planning in MF, therefore, their timely application is critical in the personalized approach of MF patients. [ABSTRACT FROM AUTHOR]

Spontaneous forward–reverse mutations were reported by us earlier in clinical samples from various types of cancers and in HeLa cells under normal culture conditions. To investigate the effects of chemical stimulations on such mutation cycles, the present study examined single nucleotide variations (SNVs) and copy number variations (CNVs) in HeLa and A549 cells exposed to wogonin-containing or acidic medium. In wogonin, both cell lines showed a mutation cycle during days 16–18. In acidic medium, both cell lines displayed multiple mutation cycles of different magnitudes. Genomic feature colocalization analysis suggests that CNVs tend to occur in expanded and unstable regions, and near promoters, histones, and non-coding transcription sites. Moreover, phenotypic variations in cell morphology occurred during the forward–reverse mutation cycles under both types of chemical treatments. In conclusion, chemical stresses imposed by wogonin or acidity promoted cyclic forward–reverse mutations in both HeLa and A549 cells to different extents. [ABSTRACT FROM AUTHOR]

Objective: To investigate the clinical utility of Next Generation Sequencing (NGS) in molecular typing of endometrial carcinoma and its combined screening for Lynch Syndrome (LS). Methods: 90 patients diagnosed with endometrial carcinoma (EC) and receiving treatment at the Third Affiliated Hospital of Zhengzhou University between March 2022 and December 2023 were included in this study. Molecular typing and germline evaluation for LS were conducted using NGS on the Illumina platform. A retrospective analysis was performed to examine the clinical pathological characteristics, molecular mutation spectrum, and LS screening outcomes among patients with four distinct molecular subtyping categories. Results: Among the 90 cases of EC, 11 cases (12.2%) of POLE mut type, 19 cases (21.1%) of MMRd type, 6 cases (6.7%) of p53 abn type, and 54 cases (60%) of NSMP type were detected, with detailed analysis of their respective molecular characteristics. LS screening identified 9 cases (10%) of pathogenic germline mutations in MMR genes, including 3 cases of MLH1 germline mutations, 2 cases of PMS2, 2 of MSH2, and 2 of MSH6. Of the 9 LS patients, 7 were MMRd type and 2 NSMP type, with 7 cases showing abnormal MMR protein expression. Additionally, 6 cases with germline variants of uncertain significance in MMR genes were detected, including 2 MLH1, 1 MSH6, 2 MSH6, 1 PMS2, and 1 EPCAM. Conclusion: NGS enables precise molecular typing of endometrial carcinoma through the identification of mutations in the POLE, TP53, and MMR genes. Conducting germline mutation testing for MMR genes in all patients with endometrial carcinoma can effectively prevent instances of overlooked LS diagnoses. Nevertheless, the extensive expenses associated with NGS necessitate additional validation and investigation before its clinical implementation can be fully endorsed. [ABSTRACT FROM AUTHOR]

Background: Presence of Germline mutations in the BRCA1 and BRCA2 genes is the most significant epidemiological factor for breast cancer (BC), where germline BRCA1 (gBRCA 1) mutation increases the risk for BC by 59–87% and gBRCA 2 mutation increases the risk by 38–80%. In this retrospective study, we have analyzed NGS-based genetic data for samples received at our laboratory for genetic testing over a three-year period to understand the prevalence and pattern if any of BRCA1 and BRCA2 mutations in Indian breast cancer patients. Results: BRCA gene sequencing using NGS was performed in 395 consecutive cases of BC referred for testing to our lab between 2021 and 2023. Genetic analysis of mutations BRCA 1 and BRCA 2 genes resulted in 115 (29%) positive patients. Out of 115 patients, 79 reported BRCA1 mutations, whereas 36 had BRCA2 mutations. Exon 10 (57.3%) of BRCA1 and exon 11 (52%) of BRCA2 were the most mutated exons observed in this study. The c.1961delA (26.4%) variant, followed by the c.68_69delAG (22.7%) variant in BRCA1, and the c.6373delA (20.5%) variant in BRCA2, were the most common mutations found in our study. Our data shows positive correlation of younger age group (20–45 years) with BRCA positive status (Chi-square p value = 0.001). Conclusion: BRCA mutation prevalence was 29.1% in our data which is higher than Western countries. Based on our findings BRCA screening looks imperative for women with BC especially younger women (< 50 years), as family history based BRCA testing would miss out many BRCA positive candidates which could benefit from PARP therapy options. [ABSTRACT FROM AUTHOR]

In this study, total RNA high-throughput sequencing (HTS) of a single symptomatic Phytolacca americana plant enabled the obtention of a nearly complete genome of two new isolates of turnip yellows virus (TuYV), named TuYV-ITA1 and TuYV-ITA2, and revealed a mixed infection with a new variant of citrus exocortis viroid (CEVd), named CEVd-ITA1. The TuYV-ITA2 isolate diverged from the known virus isolates of TuYV and showed variability in the P0 and P5 readthrough domain. Recombination analysis revealed its recombinant nature between TuYV and an unidentified polerovirus. The putative recombination event was identified in the P5 readthrough domain of the TuYMV-ITA2 isolate. Our results thus represent the first report of TuYV in Italy and some molecular evidence for the possible natural co-existence of TuYV and CEVd in a new natural host for both infectious entities. This study is adding further knowledge about the role of weed plants as virus reservoirs, and thus additional biological and impact studies would be desirable to determine in particular the role of P. americana in the spread of TuYV and if this virus should be considered a new threat for the susceptible Italian crops. [ABSTRACT FROM AUTHOR]

Background: Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collecting ctDNA is minimally invasive and reflects the entire genetic makeup of a patient's cancer. ctDNA variants in NGS data can be difficult to distinguish from sequencing and PCR artefacts due to low abundance, particularly in the early stages of cancer. Unique Molecular Identifiers (UMIs) are short sequences ligated to the sequencing library before amplification. These sequences are useful for filtering out low frequency artefacts. The utility of ctDNA as a cancer biomarker depends on accurate detection of cancer variants. Results: In this study, we benchmarked six variant calling tools, including two UMI-aware callers for their ability to call ctDNA variants. The standard variant callers tested included Mutect2, bcftools, LoFreq and FreeBayes. The UMI-aware variant callers benchmarked were UMI-VarCal and UMIErrorCorrect. We used both datasets with known variants spiked in at low frequencies, and datasets containing ctDNA, and generated synthetic UMI sequences for these datasets. Variant callers displayed different preferences for sensitivity and specificity. Mutect2 showed high sensitivity, while returning more privately called variants than any other caller in data without synthetic UMIs – an indicator of false positive variant discovery. In data encoded with synthetic UMIs, UMI-VarCal detected fewer putative false positive variants than all other callers in synthetic datasets. Mutect2 showed a balance between high sensitivity and specificity in data encoded with synthetic UMIs. Conclusions: Our results indicate UMI-aware variant callers have potential to improve sensitivity and specificity in calling low frequency ctDNA variants over standard variant calling tools. There is a growing need for further development of UMI-aware variant calling tools if effective early detection methods for cancer using ctDNA samples are to be realised. [ABSTRACT FROM AUTHOR]

Background/aim: Autosomal recessive polycystic kidney disease is an inherited kidney disease. This study aims to detect rare and common DNA variants of the PKHD1 gene using next-generation sequencing (NGS) and to classify them in terms of being pathogenic according to The American College of Medical Genetics and Genomics. Materials and methods: NGS analysis was performed on the DNA of 304 patients who were referred to Ege University Molecular Medicine Laboratory with suspected polycystic kidney disease. Results: As a result, a total of 82 different DNA variants, 16 of which were novel, were detected. The breakdown of the variants found is as follows: 73 (89.02%) were missense variants, six (7.32%) nonsense variants, two (2.44%) frameshift deletions, and one (1.22%) nonframeshift deletion. According to The American College of Medical Genetics and Genomics classification of these variants, 26 were benign (Class 5), two were likely benign (Class 4), 36 were of uncertain significance (Class 3), and nine were likely pathogenic (Class 2), nine of which are pathogenic variants (Class 1). Heterozygosity was found in 39 (63.9%) patients, homozygosity in six (9.8%) patients, compound heterozygosity in 12 (19.7%) patients, and complex genotype in four (6.6%) patients in which variants in Class 1, Class 2 and Class 3 were determined according to ACMG classification. When the exon distributions of the DNA variants detected in the PKHD1 gene were analyzed, the most common exons of the DNA variant are exon 32 (n = 9), exon 58 (n = 8), exon 67 (n = 6), exon 61 (n = 5), 30 exons (n = 4). Conclusion: This fast and economical molecular diagnostic approach will provide a reliable prenatal diagnostic option, enabling definitive disease diagnosis and the identification of carriers. [ABSTRACT FROM AUTHOR]

The "limón sutil" (Citrus aurantifolia) has been widely cultivated and well established for many years in Piura, northwestern Peru, because of its exceptional climate and soil conditions. However, decline and death of C. aurantifolia trees caused by different phytopathogens remain a common problem which has been observed in the last decades. It is known that the microbiota of soil plays an important role with their host and could be the starting point to understand the causes of citrus decline. In this study, we identified through culture-independent methods the bacterial and fungal microbiota associated to C. aurantifolia, C. jambhiri and C. volkameriana rhizospheres in the main areas of Piura. By using a 16S rRNA and ITS-metabarcoding analysis, we evaluated the taxonomic diversity between healthy trees and with decline symptoms and how this diversity could influence the health status of citrus trees. More than 600 and 200 bacterial and fungal ASVs were identified, respectively. Our metabarcoding analysis was able to identify Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidota and Acidobacteriota prokaryotic phyla, while fungal phyla included Ascomycota, Basidiomycota and Glomeromycota. In addition, there were differences between microbial diversity indices in rhizospheres evaluated. Finally, bacterial and fungal genera were shared among the different citrus rhizospheres. These results have allowed us to obtain a preliminary identification of microbiota in the citrus rhizospheres of healthy trees and with decline symptoms. [ABSTRACT FROM AUTHOR]

Introduction: Genetic factors play an important role in the etiopathogenesis of autism spectrum disorder (ASD). The Pogo Transposable Element with ZNF Domain protein (POGZ) gene (MIM*614787) has been reported to be one of the most frequently mutated genes associated with ASD. This study aims to analyze the exonic regions of the POGZ gene in individuals diagnosed with non-syndromic ASD. Methods: Fifty-one non-syndromic cases diagnosed with ASD according to the DSM-V diagnostic criteria, aged 2-18 years, were included in the study. The healthy control group consisted of 50 children of similar age groups without neurodevelopmental problems. Amplicons produced using deep intronic primers covering the mRNA-encoded regions of the POGZ gene from at least 50 base pairs were sequenced by Next Generation Sequencing Analysis. Results: No pathogenic or likely pathogenic variants reported in open-access databases (ClinVar, HGMD, etc.) were detected in the case group. In the ASD and healthy control groups, rs113396244, rs11204811, rs779479223, rs772352054, rs3831142, rs112072925, rs227453 and rs142860188 variants were determined. The rs3831142, rs112072925, rs2274535, rs142860188 variants were found statistically significant in the ASD group. The distribution of the cases with detected single nucleotide polymorphisms (SNPs) according to gender was not statistically significant. Conclusion: The variants identified as statistically significant within the patient group are situated in regions that encompass both the HP1-ZNF and DDE domains of the protein. Given the crucial role that the DDE domain plays, particularly in fetal brain development and neurogenesis, these four variants may potentially possess modifying and/or predisposing effects in the context of ASD. [ABSTRACT FROM AUTHOR]

Ovarian cancer is the 6th most common cancer in women. The main epithelial subtypes of ovarian cancer include high grade serous carcinoma, low grade serous carcinoma, endometrioid ovarian carcinoma, clear cell ovarian carcinoma and mucinous ovarian carcinoma. Our knowledge of the molecular basis of ovarian cancer has exponentially increased in the last few decades such that each subtype is now regarded as a distinct disease with specific morphological, immunohistochemical and molecular characteristics that allow for more personalized treatment. This article provides a comprehensive overview of the molecular pathology of the commonest types of epithelial ovarian carcinomas. This includes discussion of the scope of current molecular testing available in diagnostic practice and future avenues for testing as a result of translational studies. We also discuss the importance of pathologist involvement in molecular testing pathways, tumour board discussion and trial conduct with respect to ovarian cancer. [ABSTRACT FROM AUTHOR]

Identifying the underlying etiology of developmental delay/intellectual disability (DD/ID) is challenging but important. The genetic diagnosis of unexplained DD/ID helps in the treatment and prognosis of the disability in patients. In this study, we reported our experience of using whole exome sequencing (WES) of children with unexplained DD/ID. We conducted a retrospective analysis of WES results of children under 19 years of age with unexplained DD/ID between January 2020 and December 2021. The demographic data of all patients and variants identified through WES were evaluated. Furthermore, we evaluated the clinical characteristics that influenced the identification of genetic causes. Forty-one patients with DD/ID were included, of whom 21 (51.2 %) were male. The average age at symptom onset was 1.6 ± 1.3 years, and the duration from symptom onset to diagnosis was 3.1 ± 3.7 years. Hypotonia was the most common symptom (17 patients, 41.5 %), and epilepsy was confirmed in 10 patients (24.4 %). Twenty-two pathogenic/likely pathogenic variants were identified in 20 patients, and three variants of uncertain significance were identified in three patients. Family-based trio Sanger sequencing for candidate variants of 12 families was conducted; 10 variants were de novo , one variant paternally inherited, and two variants compound heterozygous. The diagnostic yield of WES for DD/ID was 48.8 % and was significantly high in patients with an early onset of DD/ID and facial dysmorphism. In contrast, patients with autism spectrum disorder (ASD) were more likely to have negative WES results compared with others without ASD. The diagnostic yield of WES was 48.8 %. We conclude that patients' characteristics, such as dysmorphic features and the age of symptom onset, can predict the likelihood that WES will identify a causal variant of a phenotype. [ABSTRACT FROM AUTHOR]

Despite several therapeutic advancements, the proportion of patients with advanced biliary tract cancers (BTC) surviving 5 years from diagnosis remains dismal. The increasing recognition of targetable genetic alterations in BTCs has ushered in a new era in the treatment of these patients. Newer therapeutic agents targeting mutations such as isocitrate dehydrogenase (IDH), fibroblastic growth factor receptor (FGFR), human epidermal growth factor receptor (HER), and so on have established a new standard of care for treatment upon progression on frontline therapy in patients with disease harboring these mutations. The current review aims to concisely summarize progress with various targeted therapy options for BTC. We also briefly discuss future directions in clinical and translational research for the adoption of a personalized approach for the treatment of unresectable or advanced BTC. Several new agents continue to emerge as feasible treatment options for patients with advanced BTC harboring targetable mutations. There is a growing need to identify mechanisms to conquer primary and acquired resistance to these agents. The identification of potential biomarkers that predict response to targeted therapy may be helpful in adopting a more tailored approach. All patients receiving treatment for advanced BTC should undergo tissue genomic profiling at diagnosis. [ABSTRACT FROM AUTHOR]

Copyright of Neurologie Pro Praxi is the property of SOLEN sro and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary: Tumor profiling techniques have become an essential tool in cancer diagnostics creating an opportunity for individualized cancer care. Interpretation of results of molecular analyses and their integration into clinical practice, however, can be challenging. Molecular tumor boards play a key role in translating molecular findings into cancer treatment recommendations. In this short review we address important questions regarding the molecular tumor board set-up and highlight aspects of interest and challenges ahead. [ABSTRACT FROM AUTHOR]

Background/Aim: The application of next generation sequencing (NGS) technology in the genetic investigation of hereditary cancer is important for clinical surveillance, therapeutic approach, and reducing the risk of developing new malignancies. The aim of the study was to explore genetic predisposition in individuals referred for hereditary cancer. Materials and Methods: A total of 8,261 individuals were referred for multigene genetic testing, during the period 2020-2023, in the laboratory, and underwent multigene genetic testing using NGS. Among the examined individuals, 56.17% were diagnosed with breast cancer, 6.77% with ovarian cancer, 2.88% with colorectal cancer, 1.91% with prostate cancer, 6.43% were healthy with a significant family history of cancer, while 3.06% had a different type of cancer and 0.21% had not provided any information. Additionally, in 85 women with breast cancer we performed whole exome sequencing analysis. Results: 20% of the examined individuals carried a pathogenic variant. Specifically, 54.8% of the patients had a pathogenic variant in a clinically significant gene (BRCA1, BRCA2, PALB2, RAD51C, PMS2, CDKN2A, MLH1, MSH2, TP53, MSH6, APC, RAD51D, PTEN, RET, CDH1, MEN1, and VHL). Among the different types of pathogenic variants detected, a significant percentage (6.52%) represented copy number variation (CNV). With WES analysis, the following findings were detected: CTC1: c.880C>T, p.(Gln294*); MLH3: c.405del, p.(Asp136Metfs*2), PPM1D: c.1426_1430del, p.(Glu476Leufs*3), and SDHB: c.395A>G, p.(His132Arg). Conclusion: Comprehensive multigene genetic testing is necessary for appropriate clinical management of pathogenic variants’ carriers. Additionally, the information obtained is important for determining the risk of malignancy development in family members of the examined individuals. [ABSTRACT FROM AUTHOR]

Introduction: Primary liver cancer is a major health problem being the sixth most frequent cancer in the world and the third cause of cancer-related death in the world. The most common histological type of liver cancer is hepatocellular carcinoma (HCC, 75–80%). Areas covered: Based on primary literature, this review provides an updated analysis of studies of genetic characterization of HCC at the level of gene mutation profiling, copy number alterations, and gene expression, with the definition of molecular subgroups and the identification of some molecular biomarkers and therapeutic targets. Recent therapeutic developments are also highlighted. Expert opinion: Deepening the understanding of the molecular complexity of HCC is progressively paving the way for the development of more personalized treatment approaches. Two important strategies involve the definition and validation of molecularly defined therapeutic targets in a subset of HCC patients and the identification of suitable biomarkers for approved systematic therapies (multikinase inhibitors and immunotherapies). The extensive molecular characterization of patients at the genomic and transcriptomic levels and the inclusion of detailed and relevant translational studies in clinical trials will represent a fundamental tool for improving the benefit of systemic therapies in HCC. [ABSTRACT FROM AUTHOR]

Aplastic anaemia (AA) is a rare hypocellular bone marrow disease with a large number of mutations in the telomerase reverse transcriptase gene (TERT), leading to bone marrow failure. We used our benchmarked whole exome sequencing (WES) pipeline to identify variants in adult Indian subjects with apparently acquired AA. For 36 affected individuals, we sequenced coding regions to a mean coverage of 100× and a sufficient depth was achieved. Downstream validation and filtering to call mutations in patients treated with Cyclosporin A (CsA) identified variants associated with AA. We report four mutations across the genes associated with the AA, TERT and CYP3A5, in addition to other genes, viz., IFNG, PIGA, NBS/NBN, and MPL. We demonstrate the application of WES to discover the variants associated with CsA responders and non-responders in an Indian cohort. [ABSTRACT FROM AUTHOR]

Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies. [ABSTRACT FROM AUTHOR]

Abstract Objective To investigate the genetic mutations in patients with papillary thyroid carcinoma (PTC) and their clinicopathological features by next generation sequencing (NGS). Methods NGS technology was used to detect genetic mutations in PTC patients, and clinicopathological features were collected. Results ①Among 855 PTC patients, 810 patients had genetic mutations, and 45 patients had no genetic mutation. ②BRAF mutation was associated with tumor diameter (P

Abstract Background Autosomal recessive polycystic kidney disease (ARPKD) is a genetically inherited pediatric disorder. It is caused by a mutation in the PKHD1 gene located on chromosome 6. The predominant phenotype is characterized by early-onset bilateral enlarged kidneys, as well as fibrocystic changes in the kidney and liver. Fetuses or infants usually present with Potter syndrome, and they are more likely to develop severe renal insufficiency. Generally, patients die perinatally or in infancy. Liver involvement has been reported in adults with ARPKD who have survived the neonatal period and childhood. However, renal involvement is rarely expected in adulthood. The case is being presented for its clinical rarity, in addition to emphasize the critical role of NGS approaches in diagnosis. Case presentation We hereby describe a 33-year-old female with adult-onset proteinuria and nephromegaly. She had a rare homozygous missense mutation of the PKHD1 gene with autosomal recessive inheritance. The proband has consanguineous heterozygote parents. The mutation was identified by whole-exome sequencing, and the results were confirmed by segregation analysis. Conclusion Here, we reported a thorough literature review of late-onset autosomal recessive polycystic kidney disease. Furthermore, we explored the importance of genetic work-up in families with genetic disorders and consanguineous marriages, particularly in underdeveloped countries.

The evolving landscape of precision oncology underscores the pivotal shift from morphological diagnosis to treatment decisions driven by molecular profiling. Recent guidelines from the European Society for Medical Oncology recomend the use of next-generation sequencing (NGS) across a broader range of cancers, reflecting its superior efficiency and clinical value. NGS not only updates oncology testing by offering quicker, sample-friendly, and sensitive analysis but also reduces the need for multiple individual tests. Cytology samples, often obtained through less invasive methods, can yield high-quality genetic material suitable for molecular analysis. This article focuses on optimizing the use of cytology samples in NGS, and outlines their potential benefits in identifying actionable molecular alterations for targeted therapies across various solid tumors. It also addresses the need for validation studies and the strategies to incorporate or combine different types of samples into routine clinical practice. Integrating cytological and liquid biopsies into routine clinical practice, alongside conventional tissue biopsies, offers a comprehensive approach to tumor genotyping, early disease detection, and monitoring of therapeutic responses across various solid tumor types. For comprehensive biomarker characterization, all patient specimens, although limited, is always valuable.

Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be clearly identified or characterized by traditional karyotyping. They can appear in a variety of forms, including rings, centric fragments, and other structural abnormalities, and are often detected during prenatal diagnosis. sSMCs occur in approximately 0.075 % of unselected prenatal cases and can be associated with a wide range of phenotypic presentations, from normal development to severe congenital malformations and syndromes. Understanding and interpreting the clinical significance of sSMCs remains challenging in genetic counseling due to their high heterogeneity and potential impact on fetal phenotype. Advances in the field of molecular cytogenetics, including techniques such as fluorescence in situ hybridization (FISH), as well as microarray comparative genomic hybridization (aCGH) and next-generation sequencing (NGS), have significantly improved the ability to accurately characterize sSMCs. These methods can determine their origin, size and genetic content, which is critical for risk assessment and decision-making during pregnancy. Thus, modern molecular cytogenetics techniques play a key role in the identification and characterization of sSMC, allowing for more accurate genetic counseling and helping to make informed pregnancy decisions. However, despite technological advances, sSMCs continue to pose a challenge for prenatal diagnosis due to their complexity and potential impact on fetal development. In this article, we aim to provide a general overview of sSMCs and of their impact on prenatal diagnosis, as well as consider the clinical significance and potential impact of sSMCs on pregnancy outcome.