Next-generation sequencing (NGS) has emerged as a powerful tool for advancing research in chronic myeloid leukemia (CML) by providing a deeper understanding of its genetic complexity. Beyond detecting the hallmark BCR::ABL1 fusion gene, NGS has enabled the identification of additional mutations associated with disease progression, therapy resistance, and clonal evolution. NGS also facilitates the detection of rare BCR::ABL1 fusion variants and cryptic rearrangements, offering a more refined genetic characterization of the disease. Additionally, it enhances the study of minimal residual disease (MRD) and evolving resistance patterns, which are crucial for developing targeted therapeutic strategies. However, challenges such as data interpretation, standardization, and cost constraints continue to limit the widespread application of NGS in routine research and clinical settings. This review explores the contributions of NGS to CML research, highlighting its role in uncovering novel genetic alterations, tracking clonal evolution, and identifying potential therapeutic targets. As sequencing technologies evolve, NGS is expected to further shape the future of CML research, providing critical insights that may ultimately refine disease management strategies.

Ezrin, encoded by EZR, is a central module of epithelial polarity and links membrane proteins to the actin cytoskeleton directly or indirectly through scaffold proteins in the epithelium. Ezrin knockout mice fail to thrive and do not survive past weaning. We identified a homozygous EZR loss-of-function (LoF) variant, c.356dup, by exome sequencing in an infant with intractable diarrhea and failure to thrive, who died from septicemia at 5 months of age. The variant localized within a homozygous region of 13.2 Mb in the proband, is consistent with inheritance identical-by-descent from the consanguineous parents, and segregated with disease in the proband’s family. EZR transcript analyses in a heterozygous carrier showed that the variant triggers nonsense-mediated mRNA decay. Homozygous EZR LoF variants have not been reported in public databases. In this study, we generated a Caco-2 EZR knockout cell line to investigate the role of ezrin in human intestinal epithelia. Our analyses used electron and immunofluorescence microscopy to assess structural changes in the knockout cells. We observed significant disorganization of the terminal web region, microvillus rarefaction and abnormal branching. Furthermore, the absence of ezrin resulted in the mislocalization of the ezrin-interacting scaffold protein Na+/H + exchanger regulatory factor-1. In conclusion, this represents the first documentation of complete ezrin deficiency in humans, highlighting the essential and non-redundant functions of the protein in maintaining intestinal physiology.

Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods to accurately determine the clinical impact of variants of unknown significance (VUS). Towards this goal, the ARSA Critical Assessment of Genome Interpretation (CAGI) challenge was designed to characterize progress by utilizing 219 experimentally assayed missense VUS in the Arylsulfatase A (ARSA) gene to assess the performance of community-submitted predictions of variant functional effects. The challenge involved 15 teams, and evaluated additional predictions from established and recently released models. Notably, a model developed by participants of a genetics and coding bootcamp, trained with standard machine-learning tools in Python, demonstrated superior performance among submissions. Furthermore, the study observed that state-of-the-art deep learning methods provided small but statistically significant improvement in predictive performance compared to less elaborate techniques. These findings underscore the utility of variant effect prediction, and the potential for models trained with modest resources to accurately classify VUS in genetic and clinical research.

Developmental anomalies of the hearing organ, the cochlea, are diagnosed in approximately one-fourth of individuals with congenital. The majority of patients with cochlear malformations remain etiologically undiagnosed due to insufficient knowledge about underlying genes or the inability to make conclusive interpretations of identified genetic variants. We used exome sequencing for the genetic evaluation of hearing loss associated with cochlear malformations in three probands from unrelated families deafness. We subsequently generated monoclonal induced pluripotent stem cell (iPSC) lines, bearing patient-specific knockins and knockouts using CRISPR/Cas9 to assess pathogenicity of candidate variants. We detected FGF3 (p.Arg165Gly) and GREB1L (p.Cys186Arg), variants of uncertain significance in two recognized genes for deafness, and PBXIP1(p.Trp574*) in a candidate gene. Upon differentiation of iPSCs towards inner ear organoids, we observed developmental aberrations in knockout lines compared to their isogenic controls. Patient-specific single nucleotide variants (SNVs) showed similar abnormalities as the knockout lines, functionally supporting their causality in the observed phenotype. Therefore, we present human inner ear organoids as a potential tool to validate the pathogenicity of DNA variants associated with cochlear malformations.Graphical

Consanguineous marriages are common in many worldwide human populations, and the biological consequences for offspring can be relevant at the biomedical level. The current genomic revolution displayed through genome-wide studies is challenging the paradigm in the analysis of consanguinity. Here, we analyzed genomic inbreeding patterns in human populations located at the western edge of the Mediterranean region (Iberia and Morocco). Runs of Homozygosity (ROH) (autozygosity fragments) were identified in 139 autochthonous individuals originating from southern Iberia and Morocco via microarray data. All individuals analyzed carried at least one ROH in their genomes. The genomic inbreeding coefficient (FROH) and the presence of ROH islands (ROHi) revealed interesting patterns in the target populations as well as in the rest of the Mediterranean basin. Moroccan Berbers presented signals of recent inbreeding, relying on high coverage of long ROH (> 5 Mb) and FROH. The location and structure of ROHi among people in the western Mediterranean could be interpreted as a signature of common genetic links across the Strait of Gibraltar. We found a significant enrichment of some relevant biological functions in the estimated ROHi hotspots associated with the immune system and chemosensation. Genomic inbreeding approaches allow us to understand past population histories and can be used as a proxy to scan the genome in search of selection signals.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00439-025-02747-9.

Monogenic liver disorders constitute a major disease burden in pediatric patients presenting with manifestations of liver disease. This is particularly significant in countries with high rates of consanguinity as in Egypt. We recruited 228 infants and children suffering from various forms of liver disease with suspected monogenic background and no conclusive biochemical diagnosis. They presented to the Pediatric Hepatology Unit at Cairo-University-Children’s-Hospital, Egypt, over the period April 2017-June 2023 and were referred for genetic diagnosis by various next-generation-sequencing technologies. One-hundred and eighty-five children (81.1%) had a significant genetic finding. Those included 88 children with a main presentation of organomegaly, 83 with cholestasis, 8 with acute liver failure and 6 with hyperbilirubinemic syndromes. One-hundred seventy-five disease-causing variants (51 pathogenic, 86 likely-pathogenic and 38 of uncertain-significance) in 72 different genes were detected in our cohort, including 85 novel variants in 49 different genes. Variants in AGL (Glycogen storage disease type-III; GSD3), ABCB4 (Progressive familial intrahepatic cholestasis type-III; PFIC3) and ABCB11 (PFIC2) genes were the most common affecting 19, 14 and 13 children, respectively. This study is the first to provide the landscape of pediatric monogenic liver diseases in a homogenous population from the Middle East and Africa, an area notoriously known to be poorly represented in genetic database and literature. Furthermore, our presented data are extremely important for genetic counseling and prenatal diagnosis and will further guide national health care policy makers to prevent or mitigate the effects of such disorders in the future.

This scoping review aims to identify and evaluate the landscape of Polygenic Risk Score (PRS)-based methods for genomic prediction from 2013 to 2023, highlighting their advancements, key concepts, and existing gaps in knowledge, research, and technology. Over the past decade, various PRS-based methods have emerged, each employing different statistical frameworks aimed at enhancing prediction accuracy, processing speed and memory efficiency. Despite notable advancements, challenges persist, including unrealistic assumptions regarding sample sizes and the polygenicity of traits necessary for accurate predictions, as well as limitations in exploring hyper-parameter spaces and considering environmental interactions. We included studies focusing on PRS-based methods for risk prediction that underwent methodological evaluations using valid approaches and released computational tools/software. Additionally, we restricted our selection to studies involving human participants that were published in English language. This review followed the standard protocol recommended by Joanna Briggs Institute Reviewer's Manual, systematically searching Ovid MEDLINE, Ovid Embase, Scopus and Web of Science databases. Additionally, searches included grey literature sources like pre-print servers such as bioRxiv, and articles recommended by experts to ensure comprehensive and diverse coverage of relevant records. This study identified 34 studies detailing 37 genomic prediction methods, the majority of which rely on linkage disequilibrium (LD) information and necessitate hyper-parameter tuning. Nine methods integrate functional/gene annotation, while 12 are suitable for cross-ancestry genomic prediction, with only one considering gene-environment (GxE) interaction. While some methods require individual-level data, most leverage summary statistics, offering flexibility. Despite progress, challenges remain. These include computational complexity and the need for large sample sizes for high prediction accuracy. Furthermore, recent methods exhibit varying effectiveness across traits, with absolute accuracies often falling short of clinical utility. Transferability across ancestries varies, influenced by trait heritability and diversity of training data, while handling admixed populations remains challenging. Additionally, the absence of standard error measurements for individual PRSs, crucial in clinical settings, underscores a critical gap. Another issue is the lack of customizable graphical visualization tools among current software packages. While genomic prediction methods have advanced significantly, there is still room for improvement. Addressing current challenges and embracing future research directions will lead to the development of more universally applicable, robust, and clinically relevant genomic prediction tools.

Known risk loci for endometrial cancer explain approximately one third of familial endometrial cancer. However, the association of germline copy number variants (CNVs) with endometrial cancer risk remains relatively unknown. We conducted a genome-wide analysis of rare CNVs overlapping gene regions in 4115 endometrial cancer cases and 17,818 controls to identify functionally relevant variants associated with disease. We identified a 1.22-fold greater number of CNVs in DNA samples from cases compared to DNA samples from controls (p = 4.4 × 10–63). Under three models of putative CNV impact (deletion, duplication, and loss of function), genome-wide association studies identified 141 candidate gene loci associated (p < 0.01) with endometrial cancer risk. Pathway analysis of the candidate loci revealed an enrichment of genes involved in the 16p11.2 proximal deletion syndrome, driven by a large recurrent deletion (chr16:29,595,483-30,159,693) identified in 0.15% of endometrial cancer cases and 0.02% of control participants. Together, these data provide evidence that rare copy number variants have a role in endometrial cancer susceptibility and that the proximal 16p11.2 BP4-BP5 region contains 25 candidate risk gene(s) that warrant further analysis to better understand their role in human disease.

Genome-wide association studies have identified dozens of genomic loci for obesity. However, functional genes and their detailed genetic mechanisms underlying these loci are mainly unknown. In this study, we conducted an integrative study to prioritize plausibly functional genes by combining information from genome-, transcriptome- and proteome-wide association analyses. We first conducted proteome-wide association analyses and transcriptome-wide association analyses for the six obesity-related traits. We then performed colocalization analysis on the identified loci shared between the proteome- and transcriptome-association analyses. Finally, we validated the identified genes with other plasma/blood reference panels. The highlighted genes were assessed for expression of other tissues, single-cell and tissue specificity, and druggability. We prioritized 4 high-confidence genes (FASN, ICAM1, PDCD6IP, and YWHAB) by proteome-wide association studies, transcriptome-wide association studies, and colocalization analyses, which consistently influenced the variation of obesity traits at both mRNA and protein levels. These 4 genes were successfully validated using other plasma/blood reference panels. These 4 genes shared regulatory structures in obesity-related tissues. Single-cell and tissue-specific analyses showed that FASN and ICAM1 were explicitly expressed in metabolism- and immunity-related tissues and cells. Furthermore, FASN and ICAM1 had been developed as drug targets. Our study provided novel promising protein targets for further mechanistic and therapeutic studies of obesity.

Tooth agenesis (TA) occurs when tooth development is disrupted at the initiation stage. It can be classified into non-syndromic and syndromic forms (named NSTA and STA), depending on whether it is accompanied by abnormalities of other organs and systems. Genetic factors play a predominant role in the pathogenesis of tooth agenesis, with dozens of genes implicated in both forms. Several genes have been identified, mutations in which can lead to both forms of TA. Among these, WNT10A and EDA are frequently mutated genes in this context, representing extensively researched and documented genes in human non-syndromic selective agenesis of permanent teeth and their association with ectodermal dysplasia syndromes. In this review, we present an overview of the current knowledge regarding genes associated with NSTA and STA, focusing on the distribution and nature of WNT10A and EDA gene mutations. We also explore how these mutations relate to the condition's both forms, including their association with the number of missing permanent teeth.