Molecular Cytogenetics最新文献

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Prenatal diagnosis of 1q21.1 microdeletions and microduplications: a retrospective case series. 1q21.1微缺失和微重复的产前诊断:回顾性病例系列。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-09-30 DOI: 10.1186/s13039-025-00731-6
Ziyang Liu, Song Yi, Manman Li, Nian Liu
{"title":"Prenatal diagnosis of 1q21.1 microdeletions and microduplications: a retrospective case series.","authors":"Ziyang Liu, Song Yi, Manman Li, Nian Liu","doi":"10.1186/s13039-025-00731-6","DOIUrl":"10.1186/s13039-025-00731-6","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to characterize the prenatal features, inheritance patterns, and outcomes of 1q21.1 copy number variations (CNVs) and refine prenatal counseling strategies.</p><p><strong>Methods: </strong>We conducted a retrospective analysis of 20 consecutive prenatal cases diagnosed with 1q21.1 CNVs between 2017 and 2024. Genetic testing included karyotyping, chromosomal microarray analysis (CMA), and copy number variation sequencing (CNV-seq). Phenotypic data, inheritance patterns, and pregnancy outcomes were evaluated.</p><p><strong>Results: </strong>The cohort comprised 12 microdeletions (60%) and 8 microduplications (40%). Ultrasound anomalies were detected in 66.7% (8/12) of microdeletion cases (e.g., fetal growth restriction, cardiac defects) and 37.5% (3/8) of microduplication cases (e.g., nasal bone hypoplasia). No specific prenatal ultrasound markers pathognomonic for 1q21.1 CNVs were identified. Termination of pregnancy (TOP) was elected in 50% (10/20) of cases, predominantly for de novo CNVs (80% of TOP decisions). Among live-born infants (n = 9), no overt abnormalities were detected during postnatal follow-up (3 months to 5 years).</p><p><strong>Conclusion: </strong>Prenatal 1q21.1 CNVs demonstrate incomplete penetrance and variable expressivity, without consistent association with specific prenatal ultrasound markers. The TOP rate for de novo CNVs reflects profound parental anxiety regarding neurodevelopmental outcomes. These findings underscore the critical need for comprehensive prenatal counseling that integrates genomic findings, phenotypic severity, and psychosocial support.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"23"},"PeriodicalIF":1.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isodicentric Y chromosome with SRY duplication in a female with complete gonadal dysgenesis. 完全性腺发育不全的女性中具有SRY重复的等心Y染色体。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-09-30 DOI: 10.1186/s13039-025-00728-1
Arash Salmaninejad, Zahra Yaghoubi, Tahereh Haghzad, Maryam Latifi, Reza Bayat, Somaye Esnaashari, Setila Dalili
{"title":"Isodicentric Y chromosome with SRY duplication in a female with complete gonadal dysgenesis.","authors":"Arash Salmaninejad, Zahra Yaghoubi, Tahereh Haghzad, Maryam Latifi, Reza Bayat, Somaye Esnaashari, Setila Dalili","doi":"10.1186/s13039-025-00728-1","DOIUrl":"10.1186/s13039-025-00728-1","url":null,"abstract":"<p><strong>Background: </strong>Sexual differentiation and development rely upon many genetic and environmental factors and any disruption of these can lead to Differences/Disorders of Sex Development (DSDs). DSDs are a diverse group of heterogeneous rare diseases that can be categorized into three main groups. 46,XY, complete gonadal dysgenesis is a subgroup of 46,XY, DSD that appears as female phenotype and external genitalia characterized by primary amenorrhea at adolescent.</p><p><strong>Case presentation: </strong>Here, we present a 14-year-old female patient with structural rearrangements of the Y chromosome including SRY gene duplication. These chromosomes were characterized by karyotyping, Oligo-array comparative genomic hybridization (CGH), metaphase fluorescence in situ hybridization (FISH), and exome sequencing (ES). The mechanism(s) by which these rearrangements could have occurred is discussed.</p><p><strong>Conclusions: </strong>46,X, idic(Y)(p11.32→q11.22:: q11.22→p11.32)] in this proband led to a large copy-number change including 24.5 Mb gain on the Yp11.32q11.223 region and a 33 Mb loss on the Yq11.223q11.23 region.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"25"},"PeriodicalIF":1.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rare single PML::RARA fusion transcript from insertion on derivative chromosome 17 in acute promyelocytic leukemia. 急性早幼粒细胞白血病衍生染色体17上少见的单PML::RARA融合转录物。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-09-30 DOI: 10.1186/s13039-025-00727-2
Ping Yang, Daniel Cassidy, Catalina Amador, Sangeetha Venugopal
{"title":"Rare single PML::RARA fusion transcript from insertion on derivative chromosome 17 in acute promyelocytic leukemia.","authors":"Ping Yang, Daniel Cassidy, Catalina Amador, Sangeetha Venugopal","doi":"10.1186/s13039-025-00727-2","DOIUrl":"10.1186/s13039-025-00727-2","url":null,"abstract":"<p><p>Over 90% of patients with acute promyelocytic leukemia (APL) harbor the typical translocation characterized by the dual fusion of PML::RARA and RARA::PML transcripts. Here, we report a case with a single fusion of PML::RARA formed on der(17), without the RARA::PML fusion, and the patient responded well to all-trans-retinoic acid (ATRA) and arsenic trioxide (ATO) therapy. To our knowledge, this represents only the fourth reported case of this type. Our findings indicate that the PML::RARA fusion is the primary driver of APL leukemogenesis and the main therapeutic target for ATRA and ATO, suggesting that the RARA::PML transcript may not be essential for APL development.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"26"},"PeriodicalIF":1.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic analysis of an asymptomatic female with a large Xp deletion revealed insights into the X chromosome inactivation pattern: a case report. 对一个无症状女性的大量Xp缺失的遗传分析揭示了对X染色体失活模式的见解:一个病例报告。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-09-30 DOI: 10.1186/s13039-025-00729-0
Li-Jun Zhang, Wen-Lan Liu, Shu-Yi Shao, Yong Xu, Lu Zhou
{"title":"Genetic analysis of an asymptomatic female with a large Xp deletion revealed insights into the X chromosome inactivation pattern: a case report.","authors":"Li-Jun Zhang, Wen-Lan Liu, Shu-Yi Shao, Yong Xu, Lu Zhou","doi":"10.1186/s13039-025-00729-0","DOIUrl":"10.1186/s13039-025-00729-0","url":null,"abstract":"<p><strong>Background: </strong>X-linked disorders caused by skewed X chromosome inactivation (XCI) result in phenotypic heterogeneity, which is rarely reported. XCI testing is not widely used in clinical cases, making risk assessment for carriers of X-linked unbalanced structural abnormalities challenging.</p><p><strong>Case presentation: </strong>We present genetic data from an asymptomatic female with a de novo 6.31 Mb deletion on Xp11.23-p11.22, identified through CMA-array analysis. The deletion includes 101 OMIM genes, 11 haplo-insufficient (HI) genes, and 4 escape genes. An androgen receptor (AR) methylation assay showed a 100% skewed XCI pattern silencing the abnormal X-chromosome. RNA-seq analysis revealed up-regulation of escape genes within the deletion at the transcriptional level. The absence of a severe clinical phenotype, aside from infertility, in this female was most likely attributed to the extremely skewed XCI and the compensatory up-regulation of XCI escape genes.</p><p><strong>Conclusions: </strong>Our data indicate that XCI can modify the phenotype in female carriers of heterozygous X-linked deletion and provide valuable information about the analysis of XCI pattern in risk assessment of this kind cases, especially precious fetuses.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"24"},"PeriodicalIF":1.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maternal uniparental disomy of chromosome 15 with concurrent paternal non-chromosome 15 marker chromosome: a rare presentation of prader-willi syndrome. 母亲单代15号染色体二体伴父代非15号染色体标记染色体:普莱德-威利综合征的罕见表现。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-08-29 DOI: 10.1186/s13039-025-00726-3
Yang Nannan, Yang Yang, Wang Yan, Wang Hao
{"title":"Maternal uniparental disomy of chromosome 15 with concurrent paternal non-chromosome 15 marker chromosome: a rare presentation of prader-willi syndrome.","authors":"Yang Nannan, Yang Yang, Wang Yan, Wang Hao","doi":"10.1186/s13039-025-00726-3","DOIUrl":"10.1186/s13039-025-00726-3","url":null,"abstract":"<p><strong>Background: </strong>Prader-Willi Syndrome (PWS) is a complicated genetic disorder demonstrating a variety of clinical phenotypes. Using molecular cytogenetics approaches to detect the deletions of the paternal 15q11-q13 region and maternal uniparental disomy of chromosome 15 plays an important role in the prenatal diagnosis of PWS.</p><p><strong>Case presentation: </strong>A pregnant woman with advanced maternal age underwent amniocentesis. The amniotic fluid was subjected to karyotyping and chromosomal microarray analysis. A marker without autosomal material and loss of heterozygosity (LOH) of 15q14-q23 were found in the fetus. The LOH was consistent with maternal uniparental isodisomy (UPD) and the marker was inherited from the father. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) found increased methylation in the fetal 15q11.2-q13 region and fluorescence in situ hybridization confirmed the marker was not originated from chromosome 15.</p><p><strong>Conclusion: </strong>We presented a rare PWS case showing maternal UPD of chromosome 15 with concurrent paternal marker chromosome in the prenatal setting.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"22"},"PeriodicalIF":1.4,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Potential role of SLC6A3 in neurodevelopmental impairments associated with corpus callosum abnormalities: insights from CNV analysis and clinical phenotyping. SLC6A3在与胼胝体异常相关的神经发育障碍中的潜在作用:来自CNV分析和临床表型的见解
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-08-22 DOI: 10.1186/s13039-025-00725-4
Shan-Yu Liu, Wei Huang, Hui-Lin Ou, Li Wang, Dan-Dan Wang, Wei-He Tan, Qin She
{"title":"Potential role of SLC6A3 in neurodevelopmental impairments associated with corpus callosum abnormalities: insights from CNV analysis and clinical phenotyping.","authors":"Shan-Yu Liu, Wei Huang, Hui-Lin Ou, Li Wang, Dan-Dan Wang, Wei-He Tan, Qin She","doi":"10.1186/s13039-025-00725-4","DOIUrl":"10.1186/s13039-025-00725-4","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to investigate the role of pathogenic copy number variations (CNVs) in neurodevelopmental impairments among children with corpus callosum abnormalities (CCAs). We focused primarily on SLC6A3 associated mechanisms and aimed to delineate genotype-phenotype correlations in our cases.</p><p><strong>Methods: </strong>From January 2021 to July 2023, 13 children with MRI-confirmed CCAs underwent chromosomal microarray analysis (CMA) for CNV detection. We performed bioinformatic analyses (Gene Ontology, STRING network) to identify neurodevelopmental genes within pathogenic CNVs, and clinical follow up assessed neurobehavioral outcomes.</p><p><strong>Results: </strong>We identified pathogenic CNVs in 3/13 cases (23.08%). Specifically, Case 8 harbored a 43.05-Mb duplication (5p15.33p12) encompassing SLC6A3, a dopamine transporter gene linked to synaptic signaling. Interaction network analysis suggested that SLC6A3 was the most interconnected gene, providing evidence of its role in CCAs. Clinically, 84.6% of cases (11/13) exhibited psychomotor delay, while 15.4% of cases (2/13) developed seizure. Notably, we observed hearing impairment and psychomotor developmental delay in Case 8 with a SLC6A3 duplication, further suggesting dopaminergic dysregulation in callosal connectivity.</p><p><strong>Conclusion: </strong>Our study suggests that SLC6A3 may represent a potential contributor to neurodevelopmental impairments in CCAs. Further, CMA-based CNV screening is critical for early intervention in high-risk children. These findings bridge genetic etiology with clinical phenotypes and offer insights into future targeted therapeutic strategies.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"21"},"PeriodicalIF":1.4,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Clarification of the clinical significance of an intron variant in a case of Peutz-Jeghers syndrome with abnormal RNA splicing of STK11. 阐明一个内含子变异在Peutz-Jeghers综合征伴STK11 RNA剪接异常的病例中的临床意义
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-08-20 DOI: 10.1186/s13039-025-00710-x
Aki Ishikawa, Masahiro Gotoh, Mineko Ushiama, Hiromi Sakamoto, Noriko Tanabe, Tomoko Watanabe, Hourin Cho, Masayoshi Yamada, Kokichi Sugano, Kouya Shiraishi, Makoto Hirata, Teruhiko Yoshida, Akihiro Sakurai
{"title":"Clarification of the clinical significance of an intron variant in a case of Peutz-Jeghers syndrome with abnormal RNA splicing of STK11.","authors":"Aki Ishikawa, Masahiro Gotoh, Mineko Ushiama, Hiromi Sakamoto, Noriko Tanabe, Tomoko Watanabe, Hourin Cho, Masayoshi Yamada, Kokichi Sugano, Kouya Shiraishi, Makoto Hirata, Teruhiko Yoshida, Akihiro Sakurai","doi":"10.1186/s13039-025-00710-x","DOIUrl":"10.1186/s13039-025-00710-x","url":null,"abstract":"","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"20"},"PeriodicalIF":1.4,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analysis of chromosomal aberrations in early pregnancy loss using high-throughput ligation-dependent probe amplification and single tandem repeats. 使用高通量结扎依赖探针扩增和单串联重复序列分析早期妊娠丢失的染色体畸变。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-08-13 DOI: 10.1186/s13039-025-00724-5
Rong Wei, Haili Hu, Shenlin Wang, Junxiang Tang, Jingran Li, Keting Tong, Chaohong Wang, Jiansheng Zhu
{"title":"Analysis of chromosomal aberrations in early pregnancy loss using high-throughput ligation-dependent probe amplification and single tandem repeats.","authors":"Rong Wei, Haili Hu, Shenlin Wang, Junxiang Tang, Jingran Li, Keting Tong, Chaohong Wang, Jiansheng Zhu","doi":"10.1186/s13039-025-00724-5","DOIUrl":"10.1186/s13039-025-00724-5","url":null,"abstract":"<p><strong>Introduction: </strong>Embryonic chromosomal abnormalities are the major cause of miscarriage. As a relatively novel genetic screening technology, high-throughput ligation-dependent probe amplification combined with short tandem repeat analysis (HLPA + STR) demonstrates significant clinical advantages, including shorter turnaround time, user-friendly technical workflows, and superior cost-effectiveness. The purpose of this study is to evaluate the frequency and characteristics of fetal chromosomal abnormalities using HLPA + STR in early pregnancy loss (EPL).</p><p><strong>Methods: </strong>A retrospective analysis was conducted on women who experienced EPL and underwent HLPA + STR. Group differences were compared using χ2 or Fisher's exact test, and multivariate logistic regression analysis was performed to examine the correlation between the fetal cytogenetic results and maternal age, gestational age, and history of miscarriage.</p><p><strong>Results: </strong>In total, 820 (61.75%) cases were detected to be chromosomal abnormalities, including 748 (91.22%) had numerical abnormalities, 59 (7.19%) had structural abnormalities, and 13 (1.59%) had chromosome mosaicism. The most frequent chromosomal abnormality was autosomal trisomy, of which trisomy (T) 16 was the most common, followed by sex chromosome monosomy and triploid. The incidence of fetal chromosomal abnormalities was significantly higher advanced maternal age (AMA) than in non-advanced maternal age (non-AMA) (p < 0.001). The AMA had a 1.93 times higher risk of fetal chromosomal abnormalities compared to the non-AMA (odds ratio [OR], 1.93; 95% confidence interval [95% CI], 1.39-2.68; p < 0.001). The risk of fetal chromosomal abnormalities in fetuses with a gestational age > 8 weeks was found to be 1.34 times higher compared to those with a gestational age ≤ 8 weeks (OR, 1.34; 95% CI, 1.07-1.69; p = 0.012). No statistically significant variation in fetal chromosomal abnormalities was observed in the history of miscarriage (p > 0.05).</p><p><strong>Conclusion: </strong>In conclusion, our results show that HLPA + STR is an effective strategy for cytogenetic analysis of EPL. In addition, Multivariate analysis identified advanced maternal age and gestational age are independent risk factors for fetal cytogenetic results in EPL, but not related to the history of miscarriage. Therefore, we recommend HLPA + STR as the first-tier screening tool for genetic evaluation in EPL. However, the results of complex abnormalities need to be combined with other techniques.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"19"},"PeriodicalIF":1.4,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144847920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A homozygous TRIP13 pathogenic variant associated with familiar oocyte arrest and prematurely condensed sperm chromosomes. 一种纯合子TRIP13致病变异,与常见的卵母细胞阻滞和精子染色体过早凝聚有关。
IF 1.4 4区 生物学
Molecular Cytogenetics Pub Date : 2025-07-23 DOI: 10.1186/s13039-025-00722-7
Michal Schweiger, André Reis, Esen Gümüslü, Alice Krebsova, Andreas Raab, Christine Lang, Denise Horn, Karl Sperling, Heidemarie Neitzel
{"title":"A homozygous TRIP13 pathogenic variant associated with familiar oocyte arrest and prematurely condensed sperm chromosomes.","authors":"Michal Schweiger, André Reis, Esen Gümüslü, Alice Krebsova, Andreas Raab, Christine Lang, Denise Horn, Karl Sperling, Heidemarie Neitzel","doi":"10.1186/s13039-025-00722-7","DOIUrl":"10.1186/s13039-025-00722-7","url":null,"abstract":"<p><p>We report on a consanguineous family with two infertile sisters with oocyte arrest and prematurely condensed sperm chromosomes. A genome-wide linkage scan and exome sequencing revealed a homozygous variant in the gene for the thyroid receptor interacting protein 13 (TRIP13), c.518G˃A (p.Arg173Gln), affecting an evolutionary highly conserved amino acid within an ATP binding motif. Just recently, compound heterozygosity for this variant was described in a Chinese proband as pathogenic, confirming that the homozygous mutation is causative for the oocyte arrest. The TRIP13 gene and the orthologous yeast pch2 gene are, amongst others, involved in a meiotic checkpoint control. This checkpoint defect is obviously responsible for the premature condensation of the sperm chromosomes. TRIP13 and pch2 are involved in meiotic recombination. To exclude that it is involved in reciprocal somatic exchanges, we analyzed the rate of sister chromatid exchanges (SCEs) in the proband´s lymphoblastoid cells. Obviously, TRIP13 is not involved in this type of somatic recombination. Moreover, we tested whether TRIP13 can complement the defect of the yeast pch2 gene. Using a yeast deletion strain lacking pch2, we integrated plasmids containing either the yeast pch2 or the human TRIP13 gene, both harboring the wild-type or the mutant allele and assessed the crossingover rate between marker genes lys2 and leu2 as a measure of complementation. Evidence is presented that the human plasmids, unexpectedly also that with the mutation, could complement the pch2 deficient yeast strain, underlining that the evolutionary conservation at the molecular level obviously extends to the functional level.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"17"},"PeriodicalIF":1.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome. 杂交snp微阵列与纳米孔测序检测人类基因组大拷贝数变异的比较分析。
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2025-07-23 DOI: 10.1186/s13039-025-00721-8
Catarina Silva, José Ferrão, Bárbara Marques, Sónia Pedro, Hildeberto Correia, Ana Valente, António Sebastião Rodrigues, Luís Vieira
{"title":"Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome.","authors":"Catarina Silva, José Ferrão, Bárbara Marques, Sónia Pedro, Hildeberto Correia, Ana Valente, António Sebastião Rodrigues, Luís Vieira","doi":"10.1186/s13039-025-00721-8","DOIUrl":"10.1186/s13039-025-00721-8","url":null,"abstract":"<p><strong>Background: </strong>Nanopore sequencing is a technology that holds great promise for identifying all types of human genome variations, particularly structural variations. In this work, we used nanopore sequencing technology to sequence 2 human cell lines at low depth of coverage to call copy number variations (CNV), and compared the results variant by variant with chromosomal microarray (CMA) results.</p><p><strong>Results: </strong>We analysed sequencing data using CuteSV and Sniffles2 variant callers, compared breakpoints based on hybrid-SNP microarray, nanopore sequencing and Sanger sequencing, and analysed CNV coverage. From a total of 48 high confidence variants (truth set), variant calling detected 79% of the truth set variants, increasing to 86% for interstitial CNV. Simultaneous use of the 2 callers slightly increased variant calling. Both callers performed better when calling CNV losses than gains. Variant sizes from CMA and nanopore sequencing showed an excellent correlation, with breakpoints determined by nanopore sequencing differing by only 20 base pairs on average from Sanger sequencing. Nanopore sequencing also revealed that four variants concealed genomic inversions undetectable by CMA. In the 10 CNV not called in nanopore sequencing, 8 showed coverage evidence of genomic loss or gain, highlighting the need to improve SV calling algorithms performance.</p><p><strong>Conclusions: </strong>Nanopore sequencing offers advantages over CMA for structural variant detection, including the identification of multiple variant types and their breakpoints with increased precision. However, further improvements in variant calling algorithms are still needed for nanopore sequencing to become a highly robust and standardized approach for a comprehensive analysis of genomic structural variation.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"18"},"PeriodicalIF":1.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12288236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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