Malak Abedalthagafi
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View article: Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology Open
Background Retinoblastoma is the most common intraocular malignancy of childhood, yet its genomic landscape remains incompletely defined, particularly in understudied populations. Beyond RB1 loss, the contribution of additional somatic and…
View article: BIOM-94. MULTIMODAL EXPLAINABLE AI FOR MOLECULAR SUBTYPING OF GLIOMAS USING RADIOLOGY AND PATHOLOGY INTEGRATION
BIOM-94. MULTIMODAL EXPLAINABLE AI FOR MOLECULAR SUBTYPING OF GLIOMAS USING RADIOLOGY AND PATHOLOGY INTEGRATION Open
Accurate molecular subtyping of gliomas is essential for guiding integrated diagnosis, predicting prognosis, and informing clinical decision-making in neuro-oncology. While imaging and pathology each provide valuable perspectives, unimodal…
View article: IMG-139. AI-Powered Classification of Tissue Sub-Compartments in Glioblastoma: Toward Quantitative Assessment of Tumor Heterogeneity
IMG-139. AI-Powered Classification of Tissue Sub-Compartments in Glioblastoma: Toward Quantitative Assessment of Tumor Heterogeneity Open
BACKGROUND Tumor assessment from routinely available clinical whole slide images (WSIs) of Glioblastoma (GBM) significantly impacts prognosis and treatment response but remains challenging due to heterogeneity. Since current manual assessm…
View article: The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository Open
These findings highlight significant gaps in metadata sharing, underscoring the need for standardized practices to improve metadata availability. Enhanced metadata reporting would foster data reusability, support better-informed decision-m…
View article: Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies Open
Metadata, or "data about data," is essential for organizing, understanding, and managing large-scale omics datasets. It enhances data discovery, integration, and interpretation, enabling reproducibility, reusability, and secondary analysis…
View article: Progress in personalized immunotherapy for patients with brain metastasis
Progress in personalized immunotherapy for patients with brain metastasis Open
Brain metastasis leads to poor outcomes and CNS injury, significantly reducing quality of life and survival rates. Advances in understanding the tumor immune microenvironment have revealed the promise of immunotherapies, which, alongside s…
View article: Patterns of population structure and genetic variation within the Saudi Arabian population
Patterns of population structure and genetic variation within the Saudi Arabian population Open
The Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, w…
View article: Development of Noninvasive Autosomal Recessive Disease Testing in the Saudi Arabian Population
Development of Noninvasive Autosomal Recessive Disease Testing in the Saudi Arabian Population Open
Early diagnosis of prenatal complications, particularly genetic disorders, can enable early intervention and improve outcomes for both mother and infant. However, the current gold-standard testing approaches, including amniocentesis and ch…
View article: Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia Open
The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple in…
View article: EPCO-05. GENOMIC AND CLINICAL INSIGHTS FROM A LARGE-SCALE STUDY OF 172 RETINOBLASTOMAS
EPCO-05. GENOMIC AND CLINICAL INSIGHTS FROM A LARGE-SCALE STUDY OF 172 RETINOBLASTOMAS Open
Retinoblastoma, a pediatric ocular cancer, is the only central nervous system tumor visible without specialized tools, readily detectable with the naked eye. This rare childhood cancer is mainly driven by mutations in RB1 or MYCN amplifica…
View article: CffDNA screening for Niemann–pick disease, type C1: a case series
CffDNA screening for Niemann–pick disease, type C1: a case series Open
Cell-free fetal DNA (cffDNA) screening is a valuable tool in clinical practice for detecting chromosomal abnormalities and autosomal dominant (AD) conditions. This study introduces a novel proof-of-concept assay designed for autosomal rece…
View article: Analytical code sharing practices in biomedical research
Analytical code sharing practices in biomedical research Open
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code an…
View article: LMIC-01. SURVIVAL AND PROGNOSTIC FACTORS IN CHILDHOOD MEDULLOBLASTOMA SINGLE TERTIARY CENTER EXPERIENCE FROM KING FAHAD MEDICAL CITY KFMC SAUDI ARABIA
LMIC-01. SURVIVAL AND PROGNOSTIC FACTORS IN CHILDHOOD MEDULLOBLASTOMA SINGLE TERTIARY CENTER EXPERIENCE FROM KING FAHAD MEDICAL CITY KFMC SAUDI ARABIA Open
BACKGROUND Medulloblastoma (MB) is the most common childhood malignant brain tumor treated with intensive multimodalities therapy including Surgery, Craniospinal Radiation, and chemotherapy. Our study aims to document the clinical courses,…
View article: Extracavitary primary effusion lymphoma presenting as a solitary brain mass
Extracavitary primary effusion lymphoma presenting as a solitary brain mass Open
Primary effusion lymphoma (PEL) is an uncommon B-cell lymphoma associated with human herpesvirus 8 and comprises 3-4% of all HIV-related lymphomas. It traditionally presents as a pleural, pericardial, and/or peritoneal effusion, though it …
View article: <i>Mycobacterium tuberculosis</i> Myositis Without Concurrent Pulmonary Symptoms in a Patient With Immunosuppression
<i>Mycobacterium tuberculosis</i> Myositis Without Concurrent Pulmonary Symptoms in a Patient With Immunosuppression Open
We describe a rare presentation of extrapulmonary tuberculosis in a patient with type 1 diabetes mellitus and dermatomyositis on immunosuppressive therapy. This case highlights important diagnostic considerations in particular patient popu…
View article: Artificial intelligence in neuro-oncology: advances and challenges in brain tumor diagnosis, prognosis, and precision treatment
Artificial intelligence in neuro-oncology: advances and challenges in brain tumor diagnosis, prognosis, and precision treatment Open
This review delves into the most recent advancements in applying artificial intelligence (AI) within neuro-oncology, specifically emphasizing work on gliomas, a class of brain tumors that represent a significant global health issue. AI has…
View article: Non-invasive prenatal testing: a revolutionary journey in prenatal testing
Non-invasive prenatal testing: a revolutionary journey in prenatal testing Open
Non-invasive prenatal testing (NIPT) is a pioneering technique that has consistently advanced the field of prenatal testing to detect genetic abnormalities and conditions with the aim of decreasing the incidence and prevalence of inherited…
View article: Ameloblastic Fibrosarcoma of the Jaw: Case Report, Genetic Profiling, and Literature Review
Ameloblastic Fibrosarcoma of the Jaw: Case Report, Genetic Profiling, and Literature Review Open
Ameloblastic fibrosarcoma (AFS) is considered a malignant progression resulting from dysplastic changes in an ameloblastic fibroma (AF). Both tumors are extremely rare, with only a few cases reported in the scientific literature. Notably, …
View article: The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel
The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel Open
Purpose: Next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. Patients and Methods: We analyzed the mutation frequencies of common actionable …
View article: Fusing Peptide Epitopes for Advanced Multiplex Serological Testing for SARS-CoV-2 Antibody Detection
Fusing Peptide Epitopes for Advanced Multiplex Serological Testing for SARS-CoV-2 Antibody Detection Open
The tragic COVID-19 pandemic, which has seen a total of 655 million cases worldwide and a death toll of over 6.6 million seems finally tailing off. Even so, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) conti…
View article: Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study Open
Background and aims Hepatocellular carcinoma (HCC) is the third most prevalent cancer in Saudi Arabia. HCC poses a significant clinical challenge due to the presence of resistance among certain patients to the standard therapeutic agent so…
View article: Analytical code sharing practices in biomedical research
Analytical code sharing practices in biomedical research Open
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code an…
View article: Investigating the prevalence of pathogenic variants in Saudi Arabian patients with familial cancer using a multigene next generation sequencing panel
Investigating the prevalence of pathogenic variants in Saudi Arabian patients with familial cancer using a multigene next generation sequencing panel Open
Family history is an important factor in determining hereditary cancer risk for many cancer types. The emergence of next-generation sequencing (NGS) has expedited the discovery of many hereditary cancer susceptibility genes and the develop…
View article: Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing Open
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumo…
View article: Data from Landscape of Genomic Alterations in Pituitary Adenomas
Data from Landscape of Genomic Alterations in Pituitary Adenomas Open
Purpose: Pituitary adenomas are the second most common primary brain tumor, yet their genetic profiles are incompletely understood.Experimental Design: We performed whole-exome sequencing of 42 pituitary macroadenomas and matched normal DN…
View article: Supplementary Materials Legend from Landscape of Genomic Alterations in Pituitary Adenomas
Supplementary Materials Legend from Landscape of Genomic Alterations in Pituitary Adenomas Open
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