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BMC Neurology Aug 2023Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic...
BACKGROUND
Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis.
METHODS
Between 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods.
RESULTS
Of 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling.
CONCLUSIONS
Our study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.
Topics: Child; Humans; Male; Autism Spectrum Disorder; Exome Sequencing; Pathology, Molecular; Genetic Testing; Microarray Analysis
PubMed: 37543562
DOI: 10.1186/s12883-023-03341-0 -
Clinics in Laboratory Medicine Jun 2022The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront.... (Review)
Review
The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront. In this review, we will discuss the history and utility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) molecular diagnostics and the associated current and future regulatory process in Europe. We will assess the performance characteristics of a range of the most common SARS-CoV-2 molecular tests currently used in Europe with a focus on as rapid molecular platforms, stand-alone RT-PCR kits, the role of low-throughput and high-throughput end-to-end testing platforms, and the rapidly evolving field of SARS-CoV-2 variant of concern identification.
Topics: COVID-19; Europe; Humans; Pandemics; Pathology, Molecular; SARS-CoV-2
PubMed: 35636820
DOI: 10.1016/j.cll.2022.02.005 -
Virchows Archiv : An International... Aug 2019Machine learning techniques, especially deep learning techniques such as convolutional neural networks, have been successfully applied to general image recognitions... (Review)
Review
Machine learning techniques, especially deep learning techniques such as convolutional neural networks, have been successfully applied to general image recognitions since their overwhelming performance at the 2012 ImageNet Large Scale Visual Recognition Challenge. Recently, such techniques have also been applied to various medical, including histopathological, images to assist the process of medical diagnosis. In some cases, deep learning-based algorithms have already outperformed experienced pathologists for recognition of histopathological images. However, pathological images differ from general images in some aspects, and thus, machine learning of histopathological images requires specialized learning methods. Moreover, many pathologists are skeptical about the ability of deep learning technology to accurately recognize histopathological images because what the learned neural network recognizes is often indecipherable to humans. In this review, we first introduce various applications incorporating machine learning developed to assist the process of pathologic diagnosis, and then describe machine learning problems related to histopathological image analysis, and review potential ways to solve these problems.
Topics: Humans; Machine Learning; Pathology, Clinical
PubMed: 31222375
DOI: 10.1007/s00428-019-02594-w -
PLoS Pathogens Aug 2023Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients,...
Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients, unrestricted high-level replication of donor-derived BKPyV in the allograft underlies polyomavirus-associated nephropathy, a condition with massive epithelial cell loss and inflammation causing premature allograft failure. There is limited understanding on how BKPyV disseminates throughout the reno-urinary tract and sometimes causes kidney damage. Tubule epithelial cells are tightly connected and have unique apical and basolateral membrane domains with highly specialized functions but all in vitro BKPyV studies have been performed in non-polarized cells. We therefore generated a polarized cell model of primary renal proximal tubule epithelial cells (RPTECs) and characterized BKPyV entry and release. After 8 days on permeable inserts, RPTECs demonstrated apico-basal polarity. BKPyV entry was most efficient via the apical membrane, that in vivo faces the tubular lumen, and depended on sialic acids. Progeny release started between 48 and 58 hours post-infection (hpi), and was exclusively detected in the apical compartment. From 72 hpi, cell lysis and detachment gradually increased but cells were mainly shed by extrusion and the barrier function was therefore maintained. The decoy-like cells were BKPyV infected and could transmit BKPyV to uninfected cells. By 120 hpi, the epithelial barrier was disrupted by severe cytopathic effects, and BKPyV entered the basolateral compartment mimicking the interstitial space. Addition of BKPyV-specific neutralizing antibodies to this compartment inhibited new infections. Taken together, we propose that during in vivo low-level BKPyV replication, BKPyV disseminates inside the tubular system, thereby causing minimal damage and delaying immune detection. However, in kidney transplant recipients lacking a well-functioning immune system, replication in the allograft will progress and eventually cause denudation of the basement membrane, leading to an increased number of decoy cells, high-level BKPyV-DNAuria and DNAemia, the latter a marker of allograft damage.
Topics: Humans; Cytology; BK Virus; Polyomavirus; Kidney; Epithelial Cells; Polyomavirus Infections
PubMed: 37639485
DOI: 10.1371/journal.ppat.1011622 -
Archives of Pathology & Laboratory... Aug 2019Fatal dermatologic diseases and ones with high morbidity can occur in the inpatient setting. In such cases, prompt and accurate assessment of a bedside skin biopsy is... (Review)
Review
CONTEXT.—
Fatal dermatologic diseases and ones with high morbidity can occur in the inpatient setting. In such cases, prompt and accurate assessment of a bedside skin biopsy is required. This may be challenging for many pathologists who are not familiar with the complexity of skin pathology and skin terminology within the fields of dermatopathology and dermatology.
OBJECTIVE.—
To provide the pathologist with a practical, up-to-date, and "must-know" reference guide on dermatologic urgencies and emergencies from a real-world perspective, highlighting diagnostic pearls, diagnostic pitfalls, and commonly encountered practice gaps. This review will focus on key diseases with which every pathologist should be familiar, including angioinvasive fungal infections, Stevens-Johnson syndrome/toxic epidermal necrolysis, staph-scalded-skin syndrome, acute graft-versus-host disease, bullous pemphigoid, calciphylaxis, Sweet syndrome and its histiocytoid variant, pyoderma gangrenosum, and leukocytoclastic vasculitis, as well as those in their clinical and histopathologic differential.
DATA SOURCES.—
This review is based on peer-reviewed literature and our personal experiences with these diseases at major academic institutions, including one where a large number of stem cell transplants are performed. This review is unique as it represents collaborative expert opinion from both a dermatopathology and a dermatology standpoint.
CONCLUSIONS.—
This review outlines the critical role that the pathologist plays in the outcomes of patients with dermatologic urgencies and emergencies. Improved patient care will result from prompt and accurate histopathologic diagnoses as well as an open line of communication with the dermatologist.
Topics: Acute Disease; Biopsy; Dermatology; Graft vs Host Disease; Hematopoietic Stem Cell Transplantation; Humans; Pathologists; Pathology, Clinical; Skin; Skin Diseases
PubMed: 30785787
DOI: 10.5858/arpa.2018-0239-RA -
Archives of Pathology & Laboratory... Aug 2019Cutaneous metastases from a distant malignancy are a diagnostic challenge for pathologists. Secondary involvement of the skin by a metastatic process portends a much... (Review)
Review
CONTEXT.—
Cutaneous metastases from a distant malignancy are a diagnostic challenge for pathologists. Secondary involvement of the skin by a metastatic process portends a much worse clinical prognosis than any primary cutaneous malignant mimickers. Immunohistochemical staining methods continue to evolve and are of paramount importance in diagnosis.
OBJECTIVE.—
To review the clinical, histopathologic, and immunohistochemical staining patterns for commonly encountered entities and discuss potential pitfalls in diagnosis. A practical guide useful in approaching cutaneous metastases of unknown primary is outlined.
DATA SOURCES.—
An extensive search and review of literature in PubMed was performed, processed, and condensed.
CONCLUSIONS.—
Cutaneous metastases have broad histopathologic patterns. They are nearly always dermal based, with an overall foreign appearance. They can be single papules/nodules or multiple in number, mimicking an inflammatory or infectious process. Ultimately, immunohistochemistry remains an essential diagnostic tool, and clinical correlation is paramount in the workup of these entities.
Topics: Biomarkers, Tumor; Diagnosis, Differential; Humans; Immunohistochemistry; Neoplasms, Unknown Primary; Pathology, Clinical; Practice Guidelines as Topic; Skin; Skin Neoplasms
PubMed: 30605024
DOI: 10.5858/arpa.2018-0051-RA -
Analytical Chemistry May 2021CRISPR-diagnostic assays have gained significant interest in the last few years. This interest has grown rapidly during the current COVID-19 pandemic, where...
CRISPR-diagnostic assays have gained significant interest in the last few years. This interest has grown rapidly during the current COVID-19 pandemic, where CRISPR-diagnostics have been frontline contenders for rapid testing solutions. This surge in CRISPR-diagnostic research prompts the following question: what exactly are the achievable limits of detection and associated assay times enabled by the kinetics of enzymes such as Cas12 and Cas13? To explore this question, we here present a model based on Michaelis-Menten enzyme kinetics theory applied to CRISPR enzymes. We use the model to develop analytical solutions for reaction kinetics and develop back-of-the-envelope criteria to validate and check for consistency in reported enzyme kinetic parameters. We applied our analyses to all studies known to us, which report Michaelis-Menten-type kinetic data for CRISPR-associated enzymes. These studies include all subtypes of Cas12 and Cas13 and orthologs. We found all but one study clearly violate at least two of our three rules and therefore present data that violate basic physical limits. We performed an experimental study of reaction kinetics of LbCas12a with both ssDNA and dsDNA activators and use these data to validate our model and its predicted scaling. The validated model is used to explore CRISPR reaction time scales and the degree of reaction completion for practically relevant target concentrations applicable to CRISPR-diagnostic assays. The results have broad implications for achievable limits of detection and assay times of emerging, amplification-free CRISPR-detection methods.
Topics: COVID-19; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Humans; Kinetics; Pandemics; Pathology, Molecular; SARS-CoV-2
PubMed: 33979119
DOI: 10.1021/acs.analchem.1c00525 -
Der Pathologe Dec 2019Besides the classical histopathological examination, molecular characterization approaches are moving more and more into the center of clinical pathology. The... (Review)
Review
BACKGROUND
Besides the classical histopathological examination, molecular characterization approaches are moving more and more into the center of clinical pathology. The association of tumors with distinct morphological features with specific molecular alterations can either help to underline a certain histologic diagnosis or to identify alterations that may serve as potential molecular targets.
OBJECTIVES
The aim of the presented studies was the morphomolecular characterization of colorectal neoplasias with either a distinct morphology or in specific clinical settings.
MATERIALS AND METHODS
Targeted massive parallel sequencing (MPS) of various colorectal neoplasias was performed in all of the presented studies.
RESULTS
Our studies showed the clinical utility of MPS for routine molecular diagnostics of colorectal carcinoma (CRC) in different clinical settings. In addition, we were able to demonstrate a close genetic relationship of colorectal adenoneuroendocrine carcinomas with classical CRC as well as a distinct genetic profile for appendiceal goblet cell neoplasias.
CONCLUSIONS
Morphomolecular characterization approaches not only enable the identification of potentially therapeutically relevant alterations, but also allow for the specific identification of morphologically distinct subtypes of colorectal neoplasias, which may be of diagnostic usefulness.
Topics: Colorectal Neoplasms; Humans; Pathology, Molecular
PubMed: 31705232
DOI: 10.1007/s00292-019-00694-7 -
Journal of Forensic and Legal Medicine Jul 2023The time since death is an important aspect of forensic medicine; however, there is not an accurate single method to determine this data. Therefore, this research aimed...
The time since death is an important aspect of forensic medicine; however, there is not an accurate single method to determine this data. Therefore, this research aimed to evaluate parameters and procedures based on the morphological analysis of cells and tissues to determine the time since death, using animal models. Pigs were chosen in this research because of their similarities with human anatomy, physiology, and pathophysiology. We identified the cells and tissue alterations in the viscera of pig cadavers according to the time since death, also describing the changes in the temperature of the organs and the bodies. The environmental temperature during the sample collection was also registered. The viscera analysis was performed for 24 h, with a 2-h variation period. After the sample collection, microscope slides were prepared for optical microscopy analysis. Through this 24-h analysis, we observed that the pancreas, small intestine, and large intestine presented more cellular alterations than the other organs. The alterations observed in the other viscera have significance when analyzed in combination. The meninges presented higher stability and few changes in 24 h, which could be relevant in an investigation of the time since death in a period greater than 24 h. Our results showed that histological evaluation is an excellent method to determine the time since death.
Topics: Swine; Models, Animal; Death; Time Factors; Forensic Pathology; Postmortem Changes; Viscera; Microscopy; Specimen Handling; Animals
PubMed: 37393848
DOI: 10.1016/j.jflm.2023.102554 -
Turk Patoloji Dergisi 2024This review which aims to examine the recent and current status of pathology education in medical schools, and covers the publications related to undergraduate pathology... (Review)
Review
OBJECTIVE
This review which aims to examine the recent and current status of pathology education in medical schools, and covers the publications related to undergraduate pathology education published between 2010 January and June 2023.
MATERIAL AND METHOD
A search was performed through PubMed, Google Scholar, Semantic Scholar, and Ulakbim search engines for the Science Citation Index, Science Citation Index Expanded, Emerging Sources Citation Index, Directory of Open Access Journals, Scopus, PubMed as well as TR Dizin indexed articles. The findings are categorized into two periods as 2010 January - 2020 April (pre-COVID-19 pandemic) and May 2020 - 2023 June. A total of 24 reviews/editorials/letters to the editor and 63 research articles in the pre-pandemic period and 11 reviews/ editorials/ letters to the editor and 35 research articles between 2020 May and 2023 June are included in the analysis.
RESULTS
Currently, medical education generally depends on core education programs with defined learning objectives and outcomes. Moreover, problem-based, case-based, and team-based interactive learning are being used along with traditional didactic courses. Additionally, digital/ web-based/remote education methods have gained prominence after the COVID-19 pandemic. The virtual or augmented reality and 3D drawing applications are offered as a solution for the autopsy and macroscopy courses. A scarce number of publications are found on measuring and evaluating the effectiveness of learning.
CONCLUSION
Artificial intelligence in pathology education is a topic that looks likely to become important in the near future. National and international comprehensive standardization is a necessity. A joint effort and collective intelligence are needed to achieve the desired goals in undergraduate pathology education.
Topics: Humans; COVID-19; Education, Medical, Undergraduate; Pathology; Pandemics; SARS-CoV-2; Coronavirus Infections; Pneumonia, Viral; Curriculum; Betacoronavirus
PubMed: 38265100
DOI: 10.5146/tjpath.2023.13048