PLoS Comput Biol
November 2024
Autism is a developmental disability. Research demonstrated that children with autism benefit from early diagnosis and early intervention. Genetic factors are considered major contributors to the development of autism.
View Article and Find Full Text PDFMeta-researchers commonly leverage tools that infer gender from first names, especially when studying gender disparities. However, tools vary in their accuracy, ease of use, and cost. The objective of this study was to compare the accuracy and cost of the commercial software Genderize and Gender API, and the open-source gender R package.
View Article and Find Full Text PDFBackground: The variant call format (VCF) file is a structured and comprehensive text file crucial for researchers and clinicians in interpreting and understanding genomic variation data. It contains essential information about variant positions in the genome, along with alleles, genotype calls, and quality scores. Analyzing and visualizing these files, however, poses significant challenges due to the need for diverse resources and robust features for in-depth exploration.
View Article and Find Full Text PDFJMIR Bioinformatics and Biotechnology supports interdisciplinary research and welcomes contributions that push the boundaries of bioinformatics, genomics, artificial intelligence, and pathology informatics.
View Article and Find Full Text PDFMismatch repair (MMR) alterations are important prognostic and predictive biomarkers in a variety of cancer subtypes, including colorectal and endometrial. However, in breast cancer (BC), the distinction and clinical significance of MMR are largely unknown. This may be due in part to the fact that genetic alterations in MMR genes are rare and only seen to occur in around 3% of BCs.
View Article and Find Full Text PDFAdvanced urothelial carcinoma continues to have a dismal prognosis despite several new therapies in the last 5 years. and mutations and fusions, PD-L1 expression, tumor mutational burden, and microsatellite instability are established predictive biomarkers in advanced urothelial carcinoma. Novel biomarkers can optimize the sequencing of available treatments and improve outcomes.
View Article and Find Full Text PDFAutism spectrum disorder (ASD) affects 1 in 44 children. Chromatin regulatory proteins are overrepresented among genes that contain high risk variants in ASD. Disruption of the chromatin environment leads to widespread dysregulation of gene expression, which is traditionally thought of as a mechanism of disease pathogenesis associated with ASD.
View Article and Find Full Text PDFBackground: Gastric cancer is a heterogeneous disease with poorly understood genetic and microenvironmental factors. Mutations in collagen genes are associated with genetic diseases that compromise tissue integrity, but their role in tumor progression has not been extensively reported. Aberrant collagen expression has been long associated with malignant tumor growth, invasion, chemoresistance, and patient outcomes.
View Article and Find Full Text PDFSummary: Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information.
View Article and Find Full Text PDFChristianson syndrome (CS), an X-linked neurological disorder characterized by postnatal attenuation of brain growth (postnatal microcephaly), is caused by mutations in , the gene encoding endosomal Na/H exchanger 6 (NHE6). To hasten treatment development, we established induced pluripotent stem cell (iPSC) lines from patients with CS representing a mutational spectrum, as well as biologically related and isogenic control lines. We demonstrated that pathogenic mutations lead to loss of protein function by a variety of mechanisms: The majority of mutations caused loss of mRNA due to nonsense-mediated mRNA decay; however, a recurrent, missense mutation (the G383D mutation) had both loss-of-function and dominant-negative activities.
View Article and Find Full Text PDFAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface.
View Article and Find Full Text PDFThe objective of this study was to establish a large, densely sampled, U.S. population-based cohort of people with autism spectrum disorder (ASD).
View Article and Find Full Text PDFChristianson syndrome (CS) is an X-linked disorder resulting from loss-of-function mutations in , which encodes the endosomal Na/H exchanger 6 (NHE6). Symptoms include early developmental delay, seizures, intellectual disability, nonverbal status, autistic features, postnatal microcephaly, and progressive ataxia. Neuronal development is impaired in CS, involving defects in neuronal arborization and synaptogenesis, likely underlying diminished brain growth postnatally.
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