Inherited mutations in the DNA mismatch repair genes (MMR) can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI) is the defining molecular signature of MMR deficiency. The clinica...
Glutaric aciduria type 1 (GA-1) is a rare but treatable autosomal-recessive neurometabolic disorder of lysin metabolism caused by biallelic pathogenic variants in glutaryl-CoA dehydrogenase gene (GCDH) that lead to deficiency of GCDH protein. Without...
Constitutional haploinsufficiency of the RB1 gene causes heritable retinoblastoma, a tumor predisposition syndrome. Patients with heritable retinoblastoma develop multiple retinoblastomas early in childhood and other extraocular tumors later in life....
The outbreak of the novel coronavirus disease COVID-19 (SARS-CoV-2) has developed into a global epidemic. Due to the pathogenic virus’s high transmission rate, accurate identification and early prediction are required for subsequent therapy. Mo...
Background: Patients with a frontotemporal lobar degeneration (FTLD) usually manifest with behavioral variant frontotemporal dementia (bvFTD). Alzheimer’s disease (AD) may also manifest with a predominant behavioral-dysexecutive syndrome, simil...
Germline pathogenic variants in the DNA mismatch repair (MMR) genes (Lynch syndrome) predispose to colorectal (CRC) and endometrial (EC) cancer. Lynch syndrome specific tumor features were evaluated for their ability to support the ACMG/InSiGHT frame...
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory...
The rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper,...
Remote sensing technologies have been widely used in the contexts of land cover and land use. The image classification algorithms used in remote sensing are of paramount importance since the reliability of the result from remote sensing depends heavi...
Novel coronavirus, known as COVID-19, is a very dangerous virus. Initially detected in China, it has since spread all over the world causing many deaths. There are several variants of COVID-19, which have been categorized into two major groups. These...
In most diagnostic laboratories, targeted next-generation sequencing (NGS) is currently the default assay for the detection of somatic variants in solid as well as haematological tumours. Independent of the method, the final outcome is a list of vari...
Variant annotation is an important step in deciphering the functional impact of genomic variants and their association with diseases. In this study, we analyzed 80 pan-cancer cases that underwent comprehensive genomic testing and compared the auto-cl...
Music genre classification has a significant role in information retrieval for the organization of growing collections of music. It is challenging to classify music with reliable accuracy. Many methods have utilized handcrafted features to identify u...
Acute myeloid leukemia (AML) represents a heterogeneous disease entity that is continuously moving to a more genetically defined classification. The classification of AML with recurrent chromosomal translocations, including those involving core bindi...
Background/Objectives: CDH1 gene is widely studied, as pathogenic variants are involved in diffuse gastric cancers and lobular breast cancers. CDH1 genotype contributes to the management of clinical practice recommendations for cancer prevention...
Binary function analysis is fundamental in understanding the behavior and genealogy of malware. The detection, classification, and analysis of Linux IoT malware and its variants present significant challenges due to the wide range of architectures su...
Background: Practices in somatic variant interpretation and classification vary between Canadian clinical molecular diagnostic laboratories, and understanding of current practices and perspectives is limited. To define gaps and future directions, inc...
For disorders with X-linked inheritance, variants may be transmitted through multiple generations of carrier females before an affected male is ascertained. Pathogenic RS1 variants exclusively cause X-linked retinoschisis (XLRS). While RS1 is constra...
Genetic testing allows for the identification of germline DNA variations, which are associated with a significant increase in the risk of developing breast cancer (BC) and ovarian cancer (OC). Detection of a BRCA1 or BRCA2 pathogenic variant triggers...
The history of gravitational classification started in 1977. Over the years, the gravitational approaches have reached many extensions, which were adapted into different classification problems. This article is the next stage of the research concerni...
Lynch syndrome (LS) is one of the most common hereditary cancer predisposition syndromes worldwide. Individuals with LS have a high risk of developing colorectal or endometrial cancer, as well as several other cancers. LS is caused by autosomal domin...
Accurate interpretation of missense variants in cancer-associated genes remains a critical challenge in precision oncology, as most sequence-based predictors lack mechanistic explanations. Receptor tyrosine kinases like FGFR2 exemplify this problem:...
The identification of a pathogenic variant (PV) in one of the mismatch repair (MMR) genes confirms the diagnosis of Lynch syndrome (LS). Hence, the correct classification of MMR gene variants is of utmost importance for appropriate counselling, surve...
It is estimated that up to one-third of all variants causing inherited diseases affect splicing; however, their deleterious effects and roles in disease pathogenesis are often not fully characterized. Given their prevalence and the development of var...
Osteogenesis imperfecta (OI) is a heritable connective tissue disorder that causes bone fragility due to pathogenic variants in genes responsible for the synthesis of type I collagen. Efforts to classify the high clinical variability in OI led to the...
Mucopolysaccharidoses (MPS) comprise a group of 12 metabolic disorders where defects in specific enzyme activities lead to the accumulation of glycosaminoglycans (GAGs) within lysosomes. This classification expands to 13 when considering MPS IIIE. Th...
25 September 2023
Machine learning (ML) has been used in different ways in the fight against COVID-19 disease. ML models have been developed, e.g., for diagnostic or prognostic purposes and using various modalities of data (e.g., textual, visual, or structured). Due t...
Circulating tumor DNA (ctDNA) is a promising cancer biomarker, but accurately detecting tumor mutations in cell-free DNA (cfDNA) is challenging due to their low frequency and sequencing errors. Our study benchmarked Mutect2, VarScan2, shearwater, and...
Background/objectives: Obtaining a genetic diagnosis for patients with inherited retinal diseases has become even more important since gene-specific therapies have become available. When genetic screening reveals variants of uncertain significance (V...
CFTR variant spectra vary across populations, potentially limiting the transferability of reference classifications. We compared CFTR2 and CFTR-France with a single-centre Turkish cystic fibrosis referral cohort of 418 individuals tested between 2016...
Usher syndrome is an autosomal recessive disorder characterized by congenital hearing loss combined with retinitis pigmentosa, and in some cases, vestibular areflexia. Three clinical subtypes are distinguished, and MYO7A and USH2A represent the two m...
Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are spora...
Background: Endometrial carcinoma (EC) is one of the most common gynaecological malignancies, with a steadily increasing incidence worldwide. In 2013, a novel molecular classification of ECs enabled patient stratification into four groups with import...
Banking malware are malicious programs that attempt to steal confidential information, such as banking authentication credentials, from users. Zeus is one of the most widespread banking malware variants ever discovered. Since the Zeus source code was...
App reviews provide crucial feedback for software maintenance and evolution, but manually extracting useful reviews from vast volumes is time-consuming and challenging. This study investigates the effectiveness of six Naïve Bayes variants for au...
Background: With the advent of next-generation sequencing in genetic testing, predicting the pathogenicity of missense variants represents a major challenge potentially leading to misdiagnoses in the clinical setting. In neurofibromatosis type 1 (NF1...
Understanding germline genetic variation is essential for improving human cancer care. Cancer predisposition genetic testing has become a part of the landscape of healthcare. Clinical guidelines have been established to identify individuals with mono...
Bicuspid aortic valve (BAV) is the most common congenital heart anomaly, affecting an estimated 0.5% to 0.77% of the general population. This condition occurs when the aortic valve has only two cusps instead of the usual three, disrupting normal valv...
Several gene-based tests, such as the sequence kernel association test, have been developed to assess associations between rare single nucleotide variants (SNVs) and disease traits. However, these aggregate methods do not distinguish potentially caus...
We have developed MAGI-ACMG, a classification algorithm that allows the classification of sequencing variants (single nucleotide or small indels) according to the recommendations of the American College of Medical Genetics (ACMG) and the Association...
Background: Gain of function (GOF) mutations of PCSK9 cause autosomal dominant familial hypercholesterolemia as they reduce the abundance of LDL receptor (LDLR) more efficiently than wild-type PCSK9. In contrast, PCSK9 loss of function (LOF) variants...
Background/Objectives: Preoperative differentiation among benign thyroid nodules, follicular variant papillary thyroid carcinoma (FV-PTC), and classical papillary thyroid carcinoma (C-PTC) remains clinically challenging. FV-PTC is particularly diffic...
Implementation of next-generation sequencing (NGS) for the genetic analysis of hereditary diseases has resulted in a vast number of genetic variants identified daily, leading to inadequate variant interpretation and, consequently, a lack of useful cl...
Background: The plantaris muscle (PM) shows substantial variability in its proximal belly attachments. Although often deemed vestigial, specific variants may narrow or reshape the popliteal corridor and contribute to vascular (popliteal artery entrap...
TAR DNA binding protein (TARDBP) is one of the major causative genes of amyotrophic lateral sclerosis (ALS), which drives disease progression through both gain-of-toxicity (GOT) and loss-of-function (LOF) mechanisms. The mutant TDP-43 exhibits aberra...
Primary ciliary dyskinesia (PCD) is a disease caused by impaired function of motile cilia. PCD mainly affects the lungs and reproductive organs. Inheritance is autosomal recessive and X-linked. PCD patients have diverse clinical manifestations, thus...
The development of high-throughput sequencing technologies and screening of big patient cohorts with familial and sporadic amyotrophic lateral sclerosis (ALS) led to the identification of a significant number of genetic variants, which are sometimes...
Pathogenic germline variants in the ATM gene are associated with a 20–30% lifetime risk of breast cancer. Crucially, a relevant fraction of loss-of-function variants in breast cancer susceptibility genes disrupts pre-mRNA splicing. We aimed to...
An unintended consequence of cystic fibrosis (CF) newborn screening (NBS) is the identification of infants with a positive NBS who do not meet the diagnostic criteria for CF (two CF-causing variants and/or sweat chloride > 60 mmol/L). This indeter...
In the present study, the histological characteristics of squamous cell carcinomas (SCCs) and basal cell carcinomas (BCCs) obtained from 22 squamate and 13 chelonian species were retrospectively evaluated. While the examined tissues were originally d...
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