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        <title>Frontiers in Genetics | Cytogenomics section | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/genetics/sections/cytogenomics</link>
        <description>RSS Feed for Cytogenomics section in the Frontiers in Genetics journal | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-05-12T23:26:25.839+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1769931</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1769931</link>
        <title><![CDATA[Case Report: Rare triple-line chromosome 9 mosaicism (47,XX,+del(9)(q13)/47,XX,+9/46,XX) associated with severe neurodevelopmental impairment and congenital anomalies]]></title>
        <pubdate>2026-04-07T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Andreja Zagorac</author><author>Mirjana Miksić</author><author>Boris Zagradišnik</author><author>Bojan Korpar</author><author>Nadja Kokalj Vokač</author>
        <description><![CDATA[BackgroundChromosome 9 abnormalities are rare. Full trisomy 9 is mostly incompatible with postnatal survival, whereas mosaic trisomy 9 permits survival with highly variable clinical manifestations. Triple-line mosaicism involving both full trisomy 9 and structural chromosome 9 abnormalities is exceptionally rare.Case PresentationA 1-year-old girl, conceived via IVF, had normal nuchal translucency and NIPT. Prenatal ultrasound showed a single umbilical artery, lower abdominal cyst, borderline ventriculomegaly at 28 weeks, and late polyhydramnios. She was born at 40 weeks, 3,430 g, 49 cm, head circumference 36 cm, Apgar 8/9/9, requiring mild oxygen supplementation. At age 1 year, she exhibited dysmorphic facial features (prominent forehead, hypertelorism, upslanting palpebral fissures, short philtrum, low-set mildly dysplastic ears, retrognathia), bilateral ovarian cysts, minimal clinodactyly of the right fifth finger, palmar and plantar crease abnormalities, hemodynamically significant patent ductus arteriosus (PDA), patent foramen ovale (PFO), previously closed muscular ventricular septal defect (VSD), severe hypotonia, global developmental delay, convergent strabismus, and feeding difficulties requiring gastrostomy. Cranial ultrasound revealed ventriculomegaly, grade II intraventricular hemorrhage, slightly thin corpus callosum, and altered posterior cranial fossa. Postnatal genetic evaluation, including array CGH (comparative genomic hybridization), conventional karyotyping, FISH (fluorescent in situ hybridization), and QF-PCR (Quantitative Fluorescence Polymerase Chain Reaction), identified a complex mosaicism comprising three cell lines: 47,XX,+del(9)(q13)[60%]/47,XX,+9[20%]/46,XX[20%].ConclusionThis case expands the phenotypic spectrum of chromosome 9 mosaicism and highlights the diagnostic value of multimodal genomic analysis for accurate detection and counselling.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1768485</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1768485</link>
        <title><![CDATA[Low-dose X-Ray induced genetic damage in human peripheral blood lymphocytes]]></title>
        <pubdate>2026-02-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Laura Camila Villalba-Rondón</author><author>Laura Vélez-Lemus</author><author>William Jaramillo-Garzón</author><author>Martín Pulido-Medellín</author><author>Nelson Rangel</author><author>Milena Rondón-Lagos</author>
        <description><![CDATA[X-rays (XR) are electromagnetic waves capable of inducing significant biological effects in living organisms. Although widely used in medicine and industry, the impact of low-dose XR exposure on human health remains insufficiently characterized. XR can generate direct and indirect DNA damage such as single- and double-strand breaks, base modifications, and DNA–protein crosslinks, leading to chromosomal alterations that disrupt cellular homeostasis and may contribute to disease development. Although previous studies have reported general increases in cytogenetic damage at low exposures, they seldom provide detailed descriptions of which chromosomes are most affected, which structural or numerical alterations predominate, or how frequently each alteration occurs. This study aimed to characterize the type and frequency of chromosomal alterations and the spectrum of genetic damage, including both clonal and non-clonal alterations, in human lymphocytes exposed in vitro to a low X-ray dose (94.33 mGy), using non-exposed samples as controls. Peripheral blood was collected from 12 healthy donors, and genetic damage was assessed using GTG-banding cytogenetics and the cytokinesis-block micronucleus assay. Irradiated samples exhibited a significantly higher frequency of chromosomal alterations and fragile sites compared with their respective controls (p ≤ 0.0093). Among numerical alterations, monosomies were the most frequent, with chromosomes 8 and 21 being the most commonly affected, detected in 50% of irradiated samples. Structural chromosomal alterations predominantly involved chromosomes 11, 16, and 17, while recurrent deletions included del(15)(q22) and del(16)(q12). Among heterochromatic variants, chtb(9)(q12) was the most frequent, and fra(9)(q12) represented the most prevalent fragile site. MN frequency increased significantly after irradiation (p = 0.0214), and women exhibited higher MN frequencies than men regardless of treatment (p = 0.0224). Overall, these findings indicate that low-dose XR exposure is associated with detectable chromosomal damage and underscore the relevance of biosafety practices and cytogenetic monitoring approaches in contexts involving XR exposure, even at doses traditionally considered safe.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1723599</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1723599</link>
        <title><![CDATA[Pediatric-onset spinocerebellar ataxia type 3 with dual ATXN3 and HTT gene mutations: a case report and literature-informed hypothesis]]></title>
        <pubdate>2026-02-10T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Dedong Wang</author><author>Mengyao Zhou</author><author>Kang Du</author><author>Yue Wang</author><author>Kunzhi Tang</author><author>Yuanfang Duan</author><author>Mengting Shi</author><author>Haohao Wu</author>
        <description><![CDATA[Spinocerebellar ataxia type 3 (SCA3) is an autosomal dominant neurodegenerative disorder caused by CAG repeat expansion in the ATXN3 gene, typically onsetting in adults aged 30–40 years. Pediatric-onset cases are extremely rare, and concurrent CAG repeat expansions in both ATXN3 and huntingtin (HTT) genes are even more exceptional. Herein, we report a 10-year-old female patient who presented with gait instability and dysarthria as initial symptoms. Diagnosis of SCA3 was confirmed by genetic and radiological evaluations. Genetic testing revealed biallelic CAG repeat lengths of 20 (normal) and 77 (expanded) in ATXN3, and 19 (normal) and 38 (expanded) in HTT. Imaging findings included mild cerebellar atrophy and bilateral tibial exostoses, consistent with her clinical phenotype. Integrated analysis of the case and a review of the literature indicated that the extreme CAG expansion in ATXN3 (77 repeats) is the primary determinant of the remarkably early onset in this patient. The concurrent HTT CAG expansion may also influence the phenotype, suggesting a potential complex interaction that warrants further investigation. This case report provides a clinical example of SCA3 complicated with concurrent ATXN3 and HTT mutations, offering preliminary clinical data for future large-sample studies on the correlation between these two mutations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1750362</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1750362</link>
        <title><![CDATA[The value of quantitative fluorescence polymerase chain reaction for the products of conception in the era of copy number variation sequencing]]></title>
        <pubdate>2026-01-09T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Shaozhe Yang</author><author>Hewei Zhang</author><author>Yongli Wang</author><author>Qingwei Zhang</author><author>Yongyong Wu</author><author>Xiuhong Fu</author><author>Rongxiang Li</author>
        <description><![CDATA[PurposeThe purpose of this research was to assess the effectiveness of copy number variation sequencing (CNV-Seq) and quantitative fluorescence polymerase chain reaction (QF-PCR) in detecting chromosomal abnormalities in products of conception of women and to evaluate the pros and cons of three different combined detection strategies, CNV-Seq and QF-PCR.MethodsGenetic testing was conducted on 701 samples using QF-PCR and CNV-Seq. The detection efficiency of the two methods for various chromosomal abnormalities was calculated. The relationships between maternal age, miscarriage gestational age, number of prior miscarriages, and conception method with fetal chromosomal abnormalities were assessed. The detection efficiency and cost of three different combined detection strategies were compared.ResultsMaternal cell contamination was found in 2.57% of samples. The overall occurrence rate of various chromosomal abnormalities was as high as 67.20% (459/683). QF-PCR was effective in detecting maternal cell contamination, triploidy, and common aneuploidies but was not effective in detecting mosaicism. Advanced maternal age, abnormal pregnancy history, early abortion, and naturally conceived products of conception were more likely to detect aneuploidy but were unrelated to triploidy and CNVs.ConclusionQF-PCR can effectively complement the limitations of CNV-Seq. Employing QF-PCR to rule out maternal cell contamination prior to performing CNV-Seq on all samples is the best detection strategy.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1540161</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1540161</link>
        <title><![CDATA[LDLRAD4 is a potential diagnostic and prognostic biomarker correlated with immune infiltration in myelodysplastic syndromes]]></title>
        <pubdate>2025-10-29T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mengjie Xu</author><author>Shihao Wu</author><author>Kaixiang Zhang</author><author>Lirong Nie</author><author>Qinghua Li</author><author>Jihong Zhong</author><author>Yuming Zhang</author><author>Honghua He</author>
        <description><![CDATA[PurposeMyelodysplastic syndromes (MDS) are a group of hematological disorders that remain relatively under-explored, which are characterized by inconspicuous early symptoms and generally poor prognosis. Owing to the complex and variable pathogenesis of MDS, there is a relative paucity of available therapeutic options. Consequently, in-depth investigation into the pathogenesis of MDS and the search for effective targeted therapies have become urgent priorities.MethodsIn this study, we leveraged the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) and conducted functional enrichment analysis. Utilizing three machine learning algorithms—Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine Recursive Feature Elimination (SVM-RFE), and Random Forest (RF)—we pinpointed hub genes. Furthermore, this study explored the relationship between hub gene expression levels and immune infiltration.ResultsOur analysis identified three hub genes: LDLRAD4, FAM43A, and KCNK5, with LDLRAD4 showing a close association with TGF-β and MAPK signaling pathways. Furthermore, this study revealed a positive correlation between LDLRAD4 expression levels and immune infiltration, particularly with natural killer (NK) cells, offering a novel immunological perspective on LDLRAD4. Ultimately, we observed that the overexpression of LDLRAD4 can suppress the proliferative capacity of MDS cells, induce cell cycle arrest, and enhance apoptosis.ConclusionWe conclude that LDLRAD4, FAM43A, and KCNK5 are potential biomarkers for MDS. LDLRAD4’s overexpression in vitro inhibits MDS cell proliferation and promotes apoptosis, suggesting significant potential for immunotherapy research. These findings collectively identify LDLRAD4 as a promising therapeutic target for MDS. However, its clinical applicability warrants further investigation to validate its potential.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1610008</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1610008</link>
        <title><![CDATA[S100A10 knockdown exacerbates phenylephrine-induced cardiomyocyte hypertrophy via modulating mitochondrial oxidative phosphorylation]]></title>
        <pubdate>2025-10-22T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Feixue Xu</author><author>Yajie Chen</author><author>Man Xu</author><author>Dan Li</author><author>Yinshan Lu</author><author>Meng Zhang</author><author>Jiahao Li</author><author>Wanyi Li</author><author>Yingying Guo</author>
        <description><![CDATA[BackgroundMitochondrial dysfunction is a well-established hallmark of pathological cardiac hypertrophy, though its underlying mechanisms are not fully understood. S100A10, a calcium-binding protein, participates in diverse cellular processes, including the regulation of mTOR signaling and mitochondrial function. This study aims to investigate the role and mechanistic basis of S100A10 in phenylephrine (PE)-induced cardiomyocyte hypertrophy.MethodsPrimary neonatal rat cardiomyocytes (NRVMs) were treated with phenylephrine (PE) to induce hypertrophy. S100A10 expression was modulated by siRNA knockdown. The interaction between S100A10 and ANXA2 was confirmed by co-immunoprecipitation. mTOR pathway activation was analyzed by Western blotting. Mitochondrial function was assessed by measuring the expression of electron transport chain complexes, mitochondrial membrane potential using JC-1 staining, and mitochondrial oxidative stress using MitoSOX.ResultsS100A10 expression was significantly upregulated in hypertrophic murine hearts. We further demonstrated that S100A10 interacts with ANXA2 to activate the mTOR/4E-BP signaling pathway. Knockdown of S100A10 in NRVMs suppressed the expression of mitochondrial respiratory chain proteins, impaired oxidative phosphorylation activity, and reduced mitochondrial membrane potential and ATP production.ConclusionThese findings indicate that downregulation of S100A10 exacerbates PE-induced cardiomyocyte hypertrophy and uncover a novel function of S100A10 in modulating mitochondrial respiratory chain protein levels, potentially through the mTOR/4E-BP pathway. This may provide a theoretical basis for future therapeutic strategies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1640775</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1640775</link>
        <title><![CDATA[DLL1 haploinsufficiency in prenatal brain anomalies: a retrospective analysis of 6q terminal deletions]]></title>
        <pubdate>2025-10-20T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Tingting Ge</author><author>Xiaojuan Lin</author><author>Xinyuan Tian</author><author>Xiaoyu Song</author><author>Bingbo Zhou</author><author>Ling Hui</author><author>Xiaozhuan Wang</author><author>Zhiqiang Zhang</author><author>Chuan Zhang</author>
        <description><![CDATA[Objective6q terminal deletion is a rare genetic cause of prenatal brain anomalies. We evaluated five cases of cerebral dysplasia within a familial context for genetic diagnosis. Aims to analyze prenatal brain abnormalities from 6q terminal deletion of DLL1 and support prenatal diagnosis and genetic counseling.MethodsA retrospective analysis was conducted on data from five families with fetal brain structural dysplasia, collected at Gansu Provincial Maternity and Child-care Hospital (Gansu Central Hospital) between January 2017 and April 2024. We applied copy number variation sequencing (CNV-Seq) and when negative, whole-exome sequencing (WES) to define genomic etiologies of prenatal brain anomalies.ResultsA total of 5 fetuses were included in this study. All fetuses exhibited a cerebellar diameter smaller than expected for their gestational age, as determined by US, 4/5 cases underwent MRI. In fetuses 1–4, CNV-Seq analysis identified heterozygous deletions of 1.74 Mb, 2.88 Mb, 0.72 Mb, and 21.99 Mb at the terminal region of chromosome 6q. In fetus 5, WES successfully identified the deletion that CNV-seq had missed, likely terminal coverage drop/binning limit.ConclusionFetuses with reduced transverse cerebellar diameter and ventriculomegaly should be evaluated for 6q terminal deletions involving DLL1; combining CNV-seq with reflex WES reduces missed diagnoses and informs counseling.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1605461</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1605461</link>
        <title><![CDATA[Analysis of complex chromosomal structural variants through optical genome mapping integrated with karyotyping]]></title>
        <pubdate>2025-08-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xiaoxi Zhu</author><author>Huiling Zheng</author><author>Xue Wan</author><author>Hang Duan</author><author>Ying Qi</author><author>Weijia Tang</author><author>Fan Yang</author><author>Limei Yu</author>
        <description><![CDATA[Background and ObjectiveParental chromosomal structural variations (SVs) represent a primary genetic factor contributing to recurrent spontaneous abortion (RSA). Individuals carrying SVs with complex chromosomal rearrangements (CCRs) typically exhibit a normal phenotype but are at an increased risk of miscarriage. Current standard clinical detection methods are insufficient for the identification and interpretation of all SV types, particularly complex and occult SVs, thereby presenting a significant challenge for clinical genetic counseling. Leveraging the high-resolution capabilities of optical genome mapping (OGM) technology, this study aims to rapidly and accurately identify complex SVs in RSA couples. Furthermore, it seeks to conduct an in-depth analysis of the genetic information within the breakpoint regions, thereby providing a more comprehensive scientific foundation for genetic counseling of RSA couples at both the cellular and genetic levels.Material and MethodsThis study involved the selection of nine subjects from two families who underwent genetic counseling at our hospital. Family 1 comprised a couple with the wife as a SVs carrier, and both her parents and brother were simultaneously analyzed for chromosomal karyotype. Family 2 included a couple with the husband as the SVs carrier, with his parents also undergoing chromosomal karyotype analysis. For SVs carriers whose karyotype analysis did not elucidate the recombination pattern, optical genome mapping (OGM) technology was utilized for further investigation, followed by Sanger sequencing to validate the OGM findings.ResultsIn Family 1, only the wife was identified as an SVs carrier. Initial chromosomal karyotype analysis suggested a karyotype of 46,XX,t (5; 6;8; 13; 15) (?). However, OGM analysis ultimately confirmed the karyotype as 46,XY,der (5)t (5; 13) (q35.2; q21.32), der (6)t (6; 8) (q25.3; q13.1)ins (6; 13) (q25.3; q21.32q21.33),der (8)t (6; 8) (q26; q13.1)ins (8; 13) (q13.1; q21.33q22.1),der (13)t (13; 15) (q21.32; q26.1)ins (13; 6) (q21.32; q25.3q26), der (15)t (5; 15) (q35.2; q26.1). Furthermore, OGM identified a novel translocation variant of the KIF7 gene that is associated with recurrent miscarriage. In Family 2, both the husband and his maternal parent were identified as SVs carriers. Nuclear type analysis revealed a karyotype of 46,XY,?t (1; 6) (q42; p21) (husband) and 46,XX,?t (1; 2) (p31.1; q24.1),?t (1; 6) (q42; p21) (mother). Through OGM detection and analysis, the final karyotype was determined to be 46,XY,ins (1; 6) (q42.2; p22.3p11.3) (husband) and 46,XX,der (1)t (1; 2) (p31.1; q24.1)ins (1; 6) (q42.2; p22.3p11.3), der (2) t (1; 2), der (6)ins (1; 6) (mother).ConclusionOGM technology facilitates the rapid and precise identification of complex chromosomal structural variations, effectively overcoming the limitations associated with traditional karyotype G-banding techniques in detecting intricate and cryptic SVs. This advancement substantially enhances the diagnostic rates of genetic etiology in patients experiencing RSA. The present study elucidates the specific manifestations of complex SVs using OGM technology, accurately pinpointing breakpoints and interpreting affected gene information. This provides novel reference approaches and evidence for disease assessment and genetic counseling in RSA patients. However, it is important to acknowledge certain limitations of this research: the study’s inclusion of only two RSA family cohorts (comprising nine participants) may limit the generalizability of its conclusions due to the small sample size, necessitating further validation through large-scale studies. Additionally, the causal relationship between KIF7 gene dysfunction and recurrent miscarriage remains to be experimentally verified in subsequent research.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1615268</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1615268</link>
        <title><![CDATA[Identification of key genes associated with infertile endometriosis based on bioinformatic analysis]]></title>
        <pubdate>2025-07-23T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Linlin Chang</author><author>Hongjuan Ye</author><author>Min Hou</author><author>Xin Xie</author><author>Yang Wang</author><author>Jie Cheng</author><author>Rongxiang Wang</author><author>Xiaocong Chen</author><author>Xinxin Quan</author><author>Lihua Sun</author><author>Songguo Xue</author><author>Liya Shi</author>
        <description><![CDATA[BackgroundEndometriosis is a common disease among women of childbearing age. However, the molecular mechanism behind it is still unknown. Therefore, new biomarkers and therapeutic targets are needed to improve the diagnosis and treatment of infertile women.MethodsMicroarray datasets GSE7305, GSE7307, and GSE51981 were downloaded from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) between control and endometriosis. The STRING database and Cytoscape software constructed protein-protein interaction and hub gene networks. At the same time, the three data sets were screened for co-differentially expressed genes related to mitosis. Subsequently, we identified mitosis-related hub genes (MRHGs) associated with both mitosis-related genes and hub genes. Next, enrichment analysis for target genes was performed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the mRNA-miRNA network was constructed. Finally, GSE25628 and GSE6364 were used to verify the expression of MRHGs individually, while GSE120103 was employed to ascertain the influence of mitosis-related genes on female fertility.ResultsA total of 93 DEGs were identified in the endometriosis datasets. Then, we placed 11 potential mitosis-related downregulated hub genes, among which eight showed good diagnostic properties of endometriosis, and two showed good diagnostic properties of infertile endometriosis. The main enriched GO functions revealed that the cell cycle mitotic pathway may be the critical pathway in endometriosis. Meanwhile, mRNA-miRNA interaction networks were constructed by choosing co-expressed mRNAs and miRNAs. Furthermore, cordycepin showed high drug-targeting relevance in infertile endometriosis.ConclusionWe identified eight mitosis-related hub genes as potential biomarkers for diagnosing and treating endometriosis. CENPE and CCNA2 might be associated with infertile endometriosis by affecting the endometrial secretory phase transition. In addition, cordycepin may be a potential clinical treatment for people with infertility-related endometriosis.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1611388</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1611388</link>
        <title><![CDATA[Application of chromosome microarray analysis and karyotyping in fetal cardiac abnormalities]]></title>
        <pubdate>2025-06-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yun Guo</author><author>Xiaoqin Xin</author><author>Linju Zhou</author><author>Jungao Huang</author>
        <description><![CDATA[ObjectiveChromosome microarray analysis (CMA) and karyotyping are two important genetic testing techniques used in prenatal diagnosis. This study aims to evaluate the value of chromosome microarray analysis and karyotyping in the diagnosis of fetal cardiac abnormalities, with particular focus on the detection of genomic copy number variations (CNVs).MethodsA retrospective analysis was conducted on 98 pregnant women diagnosed with fetal cardiac abnormalities through ultrasound between January 2022 and June 2024. Amniotic fluid samples from all participants were subjected to the analysis of karyotyping and Chromosome microarray analysis. The detection rates of both techniques in different types of fetal cardiac abnormalities were compared, and the outcomes of positive cases were followed up.ResultsOf the 98 fetuses with cardiac abnormalities, 12 cases showed abnormal genetic results, with a detection rate of 12.24%. Karyotyping identified 5 cases of abnormalities (5.10%), while the chromosome microarray analysis detected 11 cases (11.22%). In the group with isolated cardiac abnormalities (76 cases) and the group with cardiac abnormalities combined with other ultrasound abnormalities (22 cases), karyotyping detected 3.95% (3/76) and 9.09% (2/22) of abnormalities, with no significant statistical difference (P > 0.05). Chromosome microarray analysis detected abnormalities in 6.58% (5/76) of the isolated cardiac abnormalities group and 27.27% (6/22) in the group with combined abnormalities, showing a significant statistical difference (P < 0.05). Of the 12 positive cases, four were live births, eight were terminations, and postpartum cardiac abnormalities were found in two live births during follow-up.ConclusionChromosome microarray analysis has a higher detection rate in fetuses with cardiac abnormalities than traditional chromosome karyotyping, especially when fetal cardiac abnormalities are combined with other ultrasound abnormalities. It is recommended for clinical use to improve the detection of genetic alterations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1539902</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1539902</link>
        <title><![CDATA[Uncovering genetic contributors to developmental delay and intellectual disability: a focus on CNVs in pediatric patients]]></title>
        <pubdate>2025-06-23T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yilun Tao</author><author>Hongzhi Guo</author><author>Dong Han</author><author>Miao Yang</author><author>Ting Lun</author><author>Lihong Wang</author><author>Wenxia Song</author><author>Haiwei Wang</author><author>Xiaoze Li</author>
        <description><![CDATA[BackgroundDevelopmental delay (DD) and intellectual disability (ID) are prevalent in children and often have genetic causes, particularly copy number variations (CNVs). Chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) are key diagnostic tools for identifying genetic contributions to these disorders. This study assesses the prevalence and clinical impact of CNVs in pediatric DD and ID patients.MethodsNinety-nine pediatric patients with DD or ID underwent CMA or WES. Of these, 82 received SNP array analysis, while 17 had WES. CNV pathogenicity was assessed using established databases and ACMG guidelines, with inheritance patterns determined where possible.ResultsAcross the 99 patients, 43 CNVs were identified in 40 individuals, with 32 classified as clinically significant, resulting in a diagnostic rate of 30.3%. These findings included 24 deletions (75%), 7 duplications (22%), and 1 instance of loss of heterozygosity (3%). Of the CNVs with known inheritance, 65.2% were de novo. Recurrent CNVs made up 36.4% of the total, especially in regions 15q11.2-q13.1, 16p11.2, and 22q11.2. Additionally, 11 CNVs were categorized as variants of uncertain significance (VOUS).ConclusionThis study supports CMA as an effective diagnostic tool for DD and ID, highlighting the importance of family-based CNV testing for genetic counseling. The findings emphasize the need for comprehensive genetic testing to improve diagnostic accuracy, with future multi-omics approaches potentially clarifying VOUS mechanisms and CNV variability in neurodevelopmental disorders.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1604822</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1604822</link>
        <title><![CDATA[Directional genomic hybridization (dGH™) identifies small inverted duplications in situ]]></title>
        <pubdate>2025-06-23T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Thomas Liehr</author><author>Erin Cross</author><author>Stefanie Kankel</author>
        <description><![CDATA[Although fluorescence in situ hybridization (FISH) is a standard approach for characterizing the chromosomal structure involving a region of interest, FISH targeting single chromatids is not routinely performed. However, this latter approach seems principally well-suited to distinguish small, tandem inverted duplications from direct duplications in clinical cases. A commercially available single-chromatid FISH approach, called “directional genomic hybridization” (dGH™), was applied in this study to nine cases of small supernumerary marker chromosomes (sSMCs) known to contain inverted duplications. Successful detection of small inverted duplications has been demonstrated for the first time in this study using a custom Kromatid dGH™ InSite Assay. In all five euchromatic sSMC cases, inversions were detected using the dGH single-chromatid molecular cytogenetic assay. Thus, the dGH method of FISH is a readily applicable, straightforward approach for identifying small inverted duplications that are undetectable by conventional (molecular) cytogenetic methods. This technique may be used to identify the presence of small inversions within regions presenting a copy number gain as detected by chromosome microarray. Distinguishing small inverted duplications from direct duplications may have an impact on topologically associating domains (TADs) and, thus, on clinical outcome.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1502538</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1502538</link>
        <title><![CDATA[Exome sequencing and prenatal skeletal abnormalities: comprehensive review and meta-analysis and way forward]]></title>
        <pubdate>2025-06-11T00:00:00Z</pubdate>
        <category>Systematic Review</category>
        <author>Mengting Jiang</author><author>Bin Zhang</author><author>Jing Wang</author><author>Cui Wei</author><author>Xiuzhen Mao</author><author>Bin Yu</author>
        <description><![CDATA[ObjectiveTo assess the detection rate of exome sequencing (ES) in fetuses diagnosed as skeletal abnormalities (SKA) with normal karyotype or chromosomal microarray analysis (CMA) results.MethodsWe conducted electronic searches in four databases, focusing on studies involving ES in fetuses with SKA. Additional detection rate of ES compared to karyotype/CMA was calculated, followed by a meta-analysis. Subgroup analyses explored the influence of fetal phenotype on diagnostic outcomes.ResultsFrom 2,393 studies, 21 reports covering 476 fetuses were analyzed. Key findings include: (1) an additional detection rate of ES of 63.2% (Risk Difference (RD), 0.68 [95% CI, 0.60–0.76], p < 0.00001); (2) identification of 76 genes across 304 types of variants, with FGFR3, COL1A1, COL1A2, and COL2A1 being prevalent; (3) lower detection rates in fetuses with isolated short long bones compared to non-isolated conditions, though not significantly different (p = 0.35); (4) higher detection rates in subgroups with abnormal ossification, small chest, suspected long bone fractures or angulations, and skull abnormalities.ConclusionThe meta-analysis indicates that genetic variation significantly contributes to fetal SKA, primarily due to single-gene variants. Consequently, ES should be used in the prenatal diagnosis of SKA fetuses in clinical practice.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1569308</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1569308</link>
        <title><![CDATA[Hapten-labeled DNA probes can be stored and used in fluorescence in situ hybridization for decades]]></title>
        <pubdate>2025-05-30T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Thomas Liehr</author><author>Niklas Padutsch</author><author>Stefanie Kankel</author>
        <description><![CDATA[In molecular cytogenetics, fluorescence in situ hybridization (FISH) is the main technique used. In both research and diagnostics, FISH depends on well-defined and mapped DNA probes that produce brilliant signals with minimal background, visible in metaphases and/or interphases. Such probes are either ready-to-use and commercially available or provided as unlabeled DNA. The latter can be obtained by flow sorting, microdissection, or by cloning DNA segments into appropriate bacterial vectors. Labeling can be done with either nonfluorescent or fluorescent haptens. According to international guidelines, such FISH probes must have a minimum shelf life, which is only between 2 and 3 years in human genetic diagnostics. The Molecular Cytogenetics Laboratory reporting here has been purchasing, producing, using, and storing FISH probes since the 1990s. For this study, the available stock of approximately 25,000 labeled probes was screened. A total of 581 FISH probes, labeled and approved 1–30 years before reuse, were selected for this study; of these, 75 were commercially available probes labeled 1–20 years ago. All of these probes, stored in the dark at −20°C, worked perfectly well in the FISH method. Although only slight to no differences in exposure times were observed over the years for self-labeled homemade probes, commercial probes labeled with SpectrumOrange had shorter exposure times and maintained them over the years. DNA probes labeled with SpectrumAqua/diethylaminocoumarin showed bright labeling for the first 3 years and then faded. Accordingly, it can be assumed that self-labeled homemade and commercial FISH probes can be stored stably in the dark and at −20°C for at least 30 years or longer. There is no need to test approved probes on a slide after the official expiry date. In practice, this suggests that a FISH probe tube that has been approved can be used in diagnostics until it is empty; there is no need to dispose of these expensive probes at any point due to their age.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1555485</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1555485</link>
        <title><![CDATA[Case Report: Optical genome mapping enables identification of complex balanced chromosomal rearrangements]]></title>
        <pubdate>2025-05-22T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Xiaohang Hu</author><author>Jing Guo</author><author>Haiyang Sang</author><author>Jinyan Yan</author><author>Hong Chang</author><author>Ting Liu</author><author>Haixin Dong</author><author>Min Kong</author><author>Yanjun Tian</author><author>Liqing Jiang</author>
        <description><![CDATA[IntroductionIndividuals with balanced chromosomal rearrangements are at an increased risk for infertility, recurrent miscarriages, and the birth of infants with congenital malformations. Traditional cytogenetic techniques are limited by their low resolution, whereas optical genome mapping offers enhanced capabilities for detecting chromosomal rearrangements and determining genomic localization and orientation. This study sought to evaluate the efficacy of optical genome mapping in identifying complex balanced chromosomal rearrangements that may contribute to fertility challenges.Case presentationA 21-year-old Asian female patient with a history of recurrent abortions was included in the study. Peripheral blood samples were collected for high-resolution karyotyping, chromosomal microarray analysis, and optical genome mapping. The high-resolution karyotype analysis identified complex chromosomal abnormalities. Optical genome mapping has revealed additional cryptic chromosomal aberrations, such as ins (2; 12) (p16.1; q12q12), inv (6) (q21q21), and inv (12) (q12q12), offering a novel perspective on this case. Notably, the disrupted genes, including CRIM1, MUC19, and PRDM1, have not been classified as pathogenic by existing databases.ConclusionThis study underscores the capability of optical genome mapping to deliver comprehensive and precise information. It is anticipated that optical genome mapping will emerge as a valuable cytogenetic tool within clinical genetic methodologies, providing new references and insights for clinical practice in the future.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1546579</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1546579</link>
        <title><![CDATA[Case Report: A prenatal case with sex discordance between non-invasive prenatal testing and fetal genetic testings due to maternal rare chromosome karyotype]]></title>
        <pubdate>2025-05-06T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Guoxing Zhong</author><author>Jiajia Wu</author><author>Zeyan Zhong</author><author>Dina Chen</author><author>Zhiyang Guan</author><author>Shaohui Huang</author><author>Jianhong Chen</author>
        <description><![CDATA[BackgroundNon-invasive prenatal testing (NIPT), which made use of cell-free DNA (cffDNA) in maternal blood, was currently being applied all over the world for the detection of common chromosome abnormalities. It had relatively high sensitivity and specificity. Nevertheless, studies demonstrated that false positive results happened in 0.3% of the cases due to several factors. These factors included confined placental mosaicism, maternal mosaicism, maternal transfusions, maternal malignancy, vanishing twins and maternal chromosomal abnormalities.Case reportWe presented a case of a 27-year-old healthy woman, who had a high risk of trisomy 21 syndrome in first-trimester serum screening at 12 gestational weeks. The result of NIPT indicated a high risk of klinefelter syndrome (47, XXY) at 15 weeks gestation. Subsequently, amniocentesis revealed a normal female fetus karyotype (46, XX) at 18 weeks gestation. Discordant sex chromosome results emerged. Eventually, it was discovered that there was a rare maternal karyotype 46,X,der(X)t (X; Y) (p22.3; q11.2), which led to the sex discrepancy between the NIPT and the fetal prenatal diagnostic results.ConclusionWe presented a case in which there was a sex discrepancy between NIPT and fetal genetic testing due to a rare chromosome karyotype in the mother. NIPT was merely a prenatal screening test. Consequently, patients who had a screen-positive result for a chromosomal anomaly following NIPT ought to be properly counselled and advised to undergo an invasive diagnostic procedure for confirmation.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1544087</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1544087</link>
        <title><![CDATA[Karyotype and genome size analyses for two spiders of the lycosidae family]]></title>
        <pubdate>2025-03-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yuxuan Zhang</author><author>Mengying Zhang</author><author>Liang Leng</author><author>Ya Wu</author><author>Hanting Yang</author><author>Liangting Wang</author><author>Baimei Liu</author><author>Shuai Yang</author><author>Zizhong Yang</author><author>Shilin Chen</author><author>Chi Song</author>
        <description><![CDATA[BackgroundKaryotype and genome size are critical genetic characteristics with significant value for cytogenetics, taxonomy, phylogenetics, evolution, and molecular biology. The Lycosidae family, known for its diverse spiders with varying ecological habits and behavioral traits, has seen limited exploration of its karyotype and genome size.MethodsWe utilized an improved tissue drop technique to prepare chromosome slides and compare the features of male and female karyotypes for two wolf spiders with different habits of Lycosidae. Furthermore, we predicted their genome sizes using flow cytometry (FCM) and K-mer analysis.ResultsThe karyotypes of female and male Hippasa lycosina were 2n♀ = 26 = 14 m + 12 sm and 2n♂ = 24 = 10 m + 14 sm, respectively, and were composed of metacentric (m) and submetacentric (sm) chromosomes. In contrast, the karyotypes of Lycosa grahami consisted of telocentric (t) and subtelocentric (st) chromosomes (2n♀ = 20 = 20th and 2n♂ = 18 = 12th + 6t, for females and males). The sex chromosomes were both X1X2O. The estimated sizes of the H. lycosina and L. grahami genomes were 1966.54–2099.89 Mb and 3692.81–4012.56 Mb, respectively. Flow cytometry yielded slightly smaller estimates for genome size compared to k-mer analysis. K-mer analysis revealed a genome heterozygosity of 0.42% for H. lycosina and 0.80% for L. grahami, along with duplication ratios of 21.39% and 54.91%, respectively.ConclusionThis study describes the first analysis of the genome sizes and karyotypes of two spiders from the Lycosidae that exhibit differential habits and provides essential data for future phylogenetic, cytogenetic, and genomic studies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1544565</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1544565</link>
        <title><![CDATA[Lessons from a phenotypically normal infant with uniparental isodisomy of chromosome 21: a Case Report and review]]></title>
        <pubdate>2025-03-05T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Yuying Zhu</author><author>Ke Wu</author><author>Cuicui Jiang</author><author>Qiumin Zhu</author>
        <description><![CDATA[Uniparental disomy (UPD) occurs when both homologous chromosomes are inherited from a single parent. To date, the UPD of all autosomes and the X chromosome has been recorded. A few cases of UPD of chromosome 21 have been documented. At 15 weeks of gestation, a 25-year-old pregnant woman’s non-invasive prenatal screening revealed a high risk of trisomy 21. Although no anomalies were detected in the fetal ultrasonography, amniocentesis was performed, and the fetal karyotype analysis was found normal. A single-nucleotide polymorphism (SNP) array revealed that the fetus had the copy-neutral region of homozygosity (ROH) in the long arm of chromosome 21. Subsequently, single whole-exome sequencing was performed due to the risk of recessive gene variants in ROH, and no homozygous like pathogenic or pathogenic variants were found on the long arm of chromosome 21. After genetic counseling, the parents decided to continue this pregnancy. At 37 weeks of gestation, a live male infant was delivered by Cesarean section. Copy number variation sequencing showed that the placental tissue was mosaic for trisomy 21. At the final follow-up evaluation, the 6-month-old boy had a normal phenotype.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1517270</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1517270</link>
        <title><![CDATA[Improving prenatal diagnosis with combined karyotyping, CNV-seq and QF-PCR: a comprehensive analysis of chromosomal abnormalities in high-risk pregnancies]]></title>
        <pubdate>2025-01-13T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Jia-pei Liu</author><author>Shan-Bing Wang</author><author>Li Luo</author><author>Ya-mei Guo</author>
        <description><![CDATA[ObjectiveThis study aims to assess the diagnostic efficacy of a combined approach integrating chromosomal karyotyping, copy number variation sequencing (CNV-seq), and quantitative fluorescence polymerase chain reaction (QF-PCR) in detecting chromosomal abnormalities in high-risk pregnancies.MethodsThis retrospective study analyzed 617 high-risk pregnancies undergoing prenatal diagnosis from February 2023 to August 2024, with amniotic fluid samples concurrently analyzed using karyotyping, CNV-seq, and QF-PCR. We evaluated clinical characteristics, diagnostic yields, and inter-method concordance rates. Longitudinal follow-up assessed pregnancy outcomes and neonatal phenotypes, with particular emphasis on cases demonstrating diagnostic discrepancies or variants of uncertain clinical significance.ResultsThe integrated approach detected chromosomal abnormalities in 12.5% (77/617) of cases, significantly higher than the rates achieved by karyotyping alone (9.7%) and CNV-seq/QF-PCR alone (8.3%) (p < 0.05). Karyotyping showed full concordance with CNV-seq and QF-PCR in detecting major chromosomal aneuploidies, identifying 21 cases of trisomy 21 and 4 cases of trisomy 18. CNV-seq uniquely identified additional pathogenic copy number variations in 2.1% of cases and variants of uncertain significance (VUS) in 3.2% of cases, both undetectable by conventional karyotyping. Subjects with high-risk non-invasive prenatal testing (NIPT) results had the highest abnormality detection rate (57.6%, p < 0.05). Follow-up data revealed pregnancy termination in 44 of 97 cases with chromosomal abnormalities. Notably, neonates carrying pathogenic CNVs inherited from asymptomatic parents demonstrated normal phenotypes.ConclusionThe integration of karyotyping, CNV-seq, and QF-PCR provides superior diagnostic yield compared to individual testing strategies in high-risk pregnancies. Although karyotyping remains the gold standard for detecting major chromosomal aberrations, CNV-seq and QF-PCR enhance diagnostic precision through detection of submicroscopic variations. Multi-center studies with larger cohorts are needed to confirm these findings and clarify the clinical significance of uncertain variants.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1486974</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1486974</link>
        <title><![CDATA[Prenatal diagnosis and postnatal follow-up of 15 fetuses with 16p13.11 microduplication syndrome]]></title>
        <pubdate>2024-10-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yan Zhao</author><author>Lina Song</author><author>Shuxia Zhang</author><author>Fei Hou</author><author>Shan Shan</author><author>Hua Jin</author>
        <description><![CDATA[BackgroundThe clinical phenotypes of 16p13.11 microduplication syndrome have been extensively reported in previous studies, mostly about adults and children, with limited information available on fetal cases. This study aims to explore the genotype-phenotype correlation of fetuses with 16p13.11 microduplication syndrome and analyze the characteristics of prenatal diagnosis indications and provide clinical information for prenatal and postnatal genetic counseling.MethodsWe conducted a retrospective analysis of 3,451 pregnant women who underwent invasive prenatal diagnosis for SNP array between January 2018 and December 2022 at the Jinan Maternal and Child Health Hospital. Descriptive statistical analysis was performed on the prenatal diagnosis indications, pedigree analysis, pregnancy outcomes and postnatal follow-up of 15 fetuses with 16p13.11 microduplication syndrome.ResultsSNP array revealed that 15 fetuses had duplications in the 16p13.11 region with varying prenatal diagnosis indications. Among the cases, 6/15 exhibited ultrasound abnormalities, 5/15 had abnormal chromosomal copy number variations as indicated by non-invasive prenatal testing (NIPT), one case involved advanced maternal age, and 3/15 had other abnormalities. 16p13.11 microduplication syndrome was closely related to ultrasound abnormalities, especially structural abnormalities and soft marker anomalies (abnormal ultrasonic soft indicators), while the indication of NIPT could improve the detection rate of copy number variations (CNVs) in this region. Only 7/15 fetuses underwent pedigree verification, with one case of de novo 16p13.11 microduplication, and the others inherited from one parent. Pregnancy was terminated in 2/15 cases and the outcome of one case is unknown due to loss to follow-up. Among the remaining cases, only one case exhibited a ventricular septal defect, while another presented with omphalocele. No other obvious abnormalities were reported postnatally.ConclusionThe prenatal phenotypes of fetuses with 16p13.11 microduplication were highly associated with ultrasound abnormalities but lacked specificity. Comprehensive genetic tracing, outcome analysis, and follow-up are essential for providing accurate prenatal and postnatal genetic counseling.]]></description>
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