Molecular Cytogenetics最新文献

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Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer 杂合性缺失影响 CDK12 突变前列腺癌免疫微环境中的 MHC 表达
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-05-04 DOI: 10.1186/s13039-024-00680-6
William Lautert-Dutra, Camila M. Melo, Luiz P. Chaves, Cheryl Crozier, Fabiano P. Saggioro, Rodolfo B. dos Reis, Jane Bayani, Sandro L. Bonatto, Jeremy A. Squire
{"title":"Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer","authors":"William Lautert-Dutra, Camila M. Melo, Luiz P. Chaves, Cheryl Crozier, Fabiano P. Saggioro, Rodolfo B. dos Reis, Jane Bayani, Sandro L. Bonatto, Jeremy A. Squire","doi":"10.1186/s13039-024-00680-6","DOIUrl":"https://doi.org/10.1186/s13039-024-00680-6","url":null,"abstract":"In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into “High” and “Low” expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"107 1 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140829320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Noninvasive prenatal testing for the detection of fetal chromosome 17 microduplication: clinical implications and findings 检测胎儿 17 号染色体微重复的无创产前检测:临床意义和结果
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-04-22 DOI: 10.1186/s13039-024-00674-4
Ye Shi, Fang-xiu Zheng, Jing Wang, Qin Zhou, Ying-ping Chen, Bin Zhang
{"title":"Noninvasive prenatal testing for the detection of fetal chromosome 17 microduplication: clinical implications and findings","authors":"Ye Shi, Fang-xiu Zheng, Jing Wang, Qin Zhou, Ying-ping Chen, Bin Zhang","doi":"10.1186/s13039-024-00674-4","DOIUrl":"https://doi.org/10.1186/s13039-024-00674-4","url":null,"abstract":" Noninvasive prenatal testing (NIPT) is widely used to screen for fetal aneuploidies. However, there are few reports of using NIPT for screening chromosomal microduplications and microdeletions. This study aimed to investigate the application efficiency of NIPT for detecting chromosomal microduplications. Four cases of copy number gains on the long arm of chromosome 17 (17q12) were detected using NIPT and further confirmed using copy number variation (CNV) analysis based on chromosome microarray analysis (CMA). The prenatal diagnosis CMA results of the three cases showed that the microduplications in 17q12 (ranging from 1.5 to 1.9 Mb) were consistent with the NIPT results. The karyotypic analysis excluded other possible unbalanced rearrangements. The positive predictive value of NIPT for detecting chromosomal 17q12 microduplication was 75.0%. NIPT has a good screening effect on 17q12 syndrome through prenatal diagnosis, therefore it could be considered for screening fetal CNV during the second trimester. With the clinical application of NIPT, invasive prenatal diagnoses could be effectively reduced while also improving the detection rate of fetal CNV.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"232 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140634290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium 20 三体综合征全基因组 cfDNA 筛查阳性病例的临床结果:全球扩大的 NIPT 联合会的结果
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-04-16 DOI: 10.1186/s13039-024-00677-1
Erica Soster, Tamara Mossfield, Melody Menezes, Gloudi Agenbag, Marie-Line Dubois, Jean Gekas, Tristan Hardy, Kelly Loggenberg
{"title":"Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium","authors":"Erica Soster, Tamara Mossfield, Melody Menezes, Gloudi Agenbag, Marie-Line Dubois, Jean Gekas, Tristan Hardy, Kelly Loggenberg","doi":"10.1186/s13039-024-00677-1","DOIUrl":"https://doi.org/10.1186/s13039-024-00677-1","url":null,"abstract":"Trisomy 20 has been shown to be one of the most frequent rare autosomal trisomies in patients that undergo genome-wide noninvasive prenatal testing. Here, we describe the clinical outcomes of cases that screened positive for trisomy 20 following prenatal genome-wide cell-free (cf.) DNA screening. These cases are part of a larger cohort of previously published cases. Members of the Global Expanded NIPT Consortium were invited to submit details on their cases with a single rare autosomal aneuploidy following genome-wide cfDNA screening for retrospective analysis. Clinical details including patient demographics, test indications, diagnostic testing, and obstetric pregnancy outcomes were collected. Genome-wide cfDNA screening was conducted following site-specific laboratory procedures. Cases which screened positive for trisomy 20 (n = 10) were reviewed. Clinical outcome information was available for 90% (9/10) of our screen-positive trisomy 20 cases; the case without diagnostic testing ended in a fetal demise. Of the nine cases with outcome information, one was found to have a mosaic partial duplication (duplication at 20p13), rather than a full trisomy 20. Only one case in the study cohort had placental testing; therefore, confined placental mosaicism could not be ruled out in most cases. Adverse pregnancy outcomes were seen in half of the cases, which could suggest the presence of underlying confined placental mosaicism or mosaic/full fetal trisomy 20. Based on our limited series, the likelihood of true fetal aneuploidy is low but pregnancies may be at increased risk for adverse obstetric outcomes and may benefit from additional surveillance.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"1 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mosaic derivative chromosomes at chorionic villi (CV) sampling are expression of genomic instability and precursors of cryptic disease-causing rearrangements: report of further four cases 绒毛取样中的马赛克衍生染色体是基因组不稳定性的表现,也是隐性致病重排的前兆:新增四例病例的报告
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-04-08 DOI: 10.1186/s13039-024-00675-3
Giulia Vitetta, Laura Desiderio, Ilaria Baccolini, Vera Uliana, Giulia Lanzoni, Tullio Ghi, Gianluigi Pilu, Enrico Ambrosini, Patrizia Caggiati, Valeria Barili, Anna Carmela Trotta, Maria Rosaria Liuti, Elisabetta Malpezzi, Maria Carla Pittalis, Antonio Percesepe
{"title":"Mosaic derivative chromosomes at chorionic villi (CV) sampling are expression of genomic instability and precursors of cryptic disease-causing rearrangements: report of further four cases","authors":"Giulia Vitetta, Laura Desiderio, Ilaria Baccolini, Vera Uliana, Giulia Lanzoni, Tullio Ghi, Gianluigi Pilu, Enrico Ambrosini, Patrizia Caggiati, Valeria Barili, Anna Carmela Trotta, Maria Rosaria Liuti, Elisabetta Malpezzi, Maria Carla Pittalis, Antonio Percesepe","doi":"10.1186/s13039-024-00675-3","DOIUrl":"https://doi.org/10.1186/s13039-024-00675-3","url":null,"abstract":"Mosaic chromosomal anomalies arising in the product of conception and the final fetal chromosomal arrangement are expression of complex biological mechanisms. The rescue of unbalanced chromosome with selection of the most viable cell line/s in the embryo and the unfavourable imbalances in placental tissues was documented in our previous paper and in the literature. We report four additional cases with mosaic derivative chromosomes in different feto-placental tissues, further showing the instability of an intermediate gross imbalance as a frequent mechanism of de novo cryptic deletions and duplications. In conclusion we underline how the extensive remodeling of unbalanced chromosomes in placental tissues represents the ‘backstage’ of de novo structural rearrangements, as the early phases of a long selection process that the genome undergo during embryogenesis.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"46 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
X chromosome rearrangement associated with premature ovarian insufficiency as diagnosed by molecular cytogenetic methods: a case report and review of the literature 通过分子细胞遗传学方法诊断的与卵巢早衰相关的X染色体重排:病例报告和文献综述
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-04-03 DOI: 10.1186/s13039-024-00676-2
Zhifang Peng, Renqi Yang, Qing Liu, Binbin Chen, Panpan Long
{"title":"X chromosome rearrangement associated with premature ovarian insufficiency as diagnosed by molecular cytogenetic methods: a case report and review of the literature","authors":"Zhifang Peng, Renqi Yang, Qing Liu, Binbin Chen, Panpan Long","doi":"10.1186/s13039-024-00676-2","DOIUrl":"https://doi.org/10.1186/s13039-024-00676-2","url":null,"abstract":"Premature ovarian insufficiency (POI) is a clinical condition characterized by ovarian dysfunction in women under 40. The etiology of most POI cases remains unidentified and is believed to be multifactorial, including factors such as autoimmunity, metabolism, infection, and genetics. POI exhibits significant genetic heterogeneity, and it can result from chromosomal abnormalities and monogenic defects. The study participant, a 33-year-old woman, presented with a history of irregular menstruation that commenced two years ago, progressing to prolonged menstrual episodes and eventual cessation. The participant exhibits a rearrangement of the X chromosome, characterized by heterozygosity duplication on the long arm and heterozygosity deletion on the short arm by whole exome sequencing(WES) combined with cell chromosome detection. This study expands the spectrum of mutations associated with POI resulting from X chromosomal abnormalities. WES-Copy number variation analysis, in conjunction with chromosome karyotype analysis and other detection techniques, can provide a more comprehensive understanding of the genetic landscape underlying complex single or multi-system diseases.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"10 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140602051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Family case of Potocki-Lupski syndrome. 波托基-卢普斯基综合征家庭病例。
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-03-22 DOI: 10.1186/s13039-024-00673-5
L N Kolbasin, T A Dubrovskaya, G B Salnikova, E N Solovieva, M Yu Donnikov, R A Illarionov, A S Glotov, L V Kovalenko, L D Belotserkovtseva
{"title":"Family case of Potocki-Lupski syndrome.","authors":"L N Kolbasin, T A Dubrovskaya, G B Salnikova, E N Solovieva, M Yu Donnikov, R A Illarionov, A S Glotov, L V Kovalenko, L D Belotserkovtseva","doi":"10.1186/s13039-024-00673-5","DOIUrl":"10.1186/s13039-024-00673-5","url":null,"abstract":"<p><strong>Background: </strong>Potocki-Lupski syndrome (PTLS, OMIM # 610883) is a rare genetic developmental disorder resulting from a partial heterozygous microduplication at chromosome 17p11.2. The condition is characterized by a wide variability of clinical expression, which can make its clinical and molecular diagnosis challenging.</p><p><strong>Case presentation: </strong>We report here a family (mother and her two children) diagnosed with PTLS. When examining children, neurological and psychological (neuropsychiatric) manifestations (speech delay, mild mental retardation), motor disorders, craniofacial dysmorphism (microcephaly, dolichocephaly, triangular face, wide bulging forehead, long chin, antimongoloid slant, \"elfin\" ears) were revealed. The suspected clinical diagnosis was confirmed by MLPA and CMA molecular genetic testing which revealed the presence of a segmental aneusomy; microduplication in the 17p11.2 region.</p><p><strong>Conclusions: </strong>Children with PTLS can have a clinically recognizable and specific phenotype: craniofacial dysmorphism, motor and neurological manifestations, which may implicate a possible genetic disease to the attending physician. Moreover, each child with this syndrome is unique and may have a different clinical picture. The management of such patients requires a multidisciplinary team approach, including medical genetic counseling.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"6"},"PeriodicalIF":1.3,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194243","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
11p13 microduplication: a differential diagnosis of Silver-Russell syndrome? 11p13 微重复:银-拉塞尔综合征的鉴别诊断?
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-03-14 DOI: 10.1186/s13039-024-00672-6
Asmaa K Amin, Jeremias Krause, Thomas Eggermann
{"title":"11p13 microduplication: a differential diagnosis of Silver-Russell syndrome?","authors":"Asmaa K Amin, Jeremias Krause, Thomas Eggermann","doi":"10.1186/s13039-024-00672-6","DOIUrl":"10.1186/s13039-024-00672-6","url":null,"abstract":"<p><strong>Background: </strong>Silver-Russel syndrome (SRS) is a congenital disorder which is mainly characterized by intrauterine and postnatal growth retardation, relative macrocephaly, and characteristic (facial) dysmorphisms. The majority of patients shows a hypomethylation of the imprinting center region 1 (IC1) in 11p15 and maternal uniparental disomy of chromosome 7 (upd(7)mat), but in addition a broad spectrum of copy number variations (CNVs) and monogenetic variants (SNVs) has been reported in this cohort. These heterogeneous findings reflect the clinical overlap of SRS with other congenital disorders, but some of the CNVs are recurrent and have therefore been suggested as SRS-associated loci. However, this molecular heterogeneity makes the decision on the diagnostic workup of patients with SRS features challenging.</p><p><strong>Case presentation: </strong>A girl with clinical features of SRS but negatively tested for the IC1 hypomethylation and upd(7)mat was analyzed by whole genome sequencing in order to address both CNVs and SNVs in the same run. We identified a 11p13 microduplication affecting a region overlapping with a variant reported in a previously published patient with clinical features of Silver-Russel syndrome.</p><p><strong>Conclusions: </strong>The identification of a 11p13 microduplication in a patient with SRS features confirms the considerable contribution of CNVs to SRS-related phenotypes, and it strengthens the evidence for a 11p13 microduplication syndrome as a differential diagnosis SRS. Furthermore, we could confirm that WGS is a valuable diagnostic tool in patients with SRS and related disorders, as it allows CNVs and SNV detection in the same run, thereby avoiding a time-consuming diagnostic testing process.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"5"},"PeriodicalIF":1.3,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132104","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
Identification of chromosomal abnormalities in miscarriages by CNV-Seq. 通过 CNV-Seq 鉴定流产中的染色体异常。
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-02-18 DOI: 10.1186/s13039-024-00671-7
Yuqi Shao, Saisai Yang, Lin Cheng, Jie Duan, Jin Li, Jiawei Kang, Fang Wang, Juan Liu, Fang Zheng, Jianhong Ma, Yuanzhen Zhang
{"title":"Identification of chromosomal abnormalities in miscarriages by CNV-Seq.","authors":"Yuqi Shao, Saisai Yang, Lin Cheng, Jie Duan, Jin Li, Jiawei Kang, Fang Wang, Juan Liu, Fang Zheng, Jianhong Ma, Yuanzhen Zhang","doi":"10.1186/s13039-024-00671-7","DOIUrl":"10.1186/s13039-024-00671-7","url":null,"abstract":"<p><strong>Objective: </strong>The primary object of this study is to analyze chromosomal abnormalities in miscarriages detected by copy number variants sequencing (CNV-Seq), establish potential pathways or genes related to miscarriages, and provide guidance for birth health in the following pregnancies.</p><p><strong>Methods: </strong>This study enrolled 580 miscarriage cases with paired clinical information and chromosomal detection results analyzed by CNV-Seq. Further bioinformatic analyses were performed on validated pathogenic CNVs (pCNVs).</p><p><strong>Results: </strong>Of 580 miscarriage cases, three were excluded as maternal cell contamination, 357 cases showed abnormal chromosomal results, and the remaining 220 were normal, with a positive detection rate of 61.87% (357/577). In the 357 miscarriage cases, 470 variants were discovered, of which 65.32% (307/470) were pathogenic. Among all variants detected, 251 were numerical chromosomal abnormalities, and 219 were structural abnormalities. With advanced maternal age, the proportion of numerical abnormalities increased, but the proportion of structural abnormalities decreased. Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology analysis revealed that eleven pathways and 636 biological processes were enriched in pCNVs region genes. Protein-protein interaction analysis of 226 dosage-sensitive genes showed that TP53, CTNNB1, UBE3A, EP300, SOX2, ATM, and MECP2 might be significant in the development of miscarriages.</p><p><strong>Conclusion: </strong>Our study provides evidence that chromosomal abnormalities contribute to miscarriages, and emphasizes the significance of microdeletions or duplications in causing miscarriages apart from numerical abnormalities. Essential genes found in pCNVs regions may account for miscarriages which need further validation.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"4"},"PeriodicalIF":1.3,"publicationDate":"2024-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10875874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900237","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
Chromosomal microarray analysis for prenatal diagnosis of uniparental disomy: a retrospective study 用于单亲裂殖症产前诊断的染色体微阵列分析:一项回顾性研究
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-01-30 DOI: 10.1186/s13039-023-00668-8
Chenxia Xu, Miaoyuan Li, Tiancai Gu, Fenghua Xie, Yanfang Zhang, Degang Wang, Jianming Peng
{"title":"Chromosomal microarray analysis for prenatal diagnosis of uniparental disomy: a retrospective study","authors":"Chenxia Xu, Miaoyuan Li, Tiancai Gu, Fenghua Xie, Yanfang Zhang, Degang Wang, Jianming Peng","doi":"10.1186/s13039-023-00668-8","DOIUrl":"https://doi.org/10.1186/s13039-023-00668-8","url":null,"abstract":"Chromosomal microarray analysis (CMA) is a valuable tool in prenatal diagnosis for the detection of chromosome uniparental disomy (UPD). This retrospective study examines fetuses undergoing invasive prenatal diagnosis through Affymetrix CytoScan 750 K array analysis. We evaluated both chromosome G-banding karyotyping data and CMA results from 2007 cases subjected to amniocentesis. The detection rate of regions of homozygosity (ROH) ≥ 10 Mb was 1.8% (33/2007), with chromosome 11 being the most frequently implicated (17.1%, 6/33). There were three cases where UPD predicted an abnormal phenotype based on imprinted gene expression. The integration of UPD detection by CMA offers a more precise approach to prenatal genetic diagnosis. CMA proves effective in identifying ROH and preventing the birth of children affected by imprinting diseases.","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"334 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Contribution of genetic variants to congenital heart defects in both singleton and twin fetuses: a Chinese cohort study. 遗传变异对单胎和双胎先天性心脏缺陷的影响:一项中国队列研究。
IF 1.3 4区 生物学
Molecular Cytogenetics Pub Date : 2024-01-04 DOI: 10.1186/s13039-023-00664-y
Shaobin Lin, Shanshan Shi, Jian Lu, Zhiming He, Danlun Li, Linhuan Huang, Xuan Huang, Yi Zhou, Yanmin Luo
{"title":"Contribution of genetic variants to congenital heart defects in both singleton and twin fetuses: a Chinese cohort study.","authors":"Shaobin Lin, Shanshan Shi, Jian Lu, Zhiming He, Danlun Li, Linhuan Huang, Xuan Huang, Yi Zhou, Yanmin Luo","doi":"10.1186/s13039-023-00664-y","DOIUrl":"10.1186/s13039-023-00664-y","url":null,"abstract":"<p><strong>Background: </strong>The contribution of genetic variants to congenital heart defects (CHDs) has been investigated in many postnatal cohorts but described in few prenatal fetus cohorts. Overall, specific genetic variants especially copy number variants (CNVs) leading to CHDs are somewhat diverse among different prenatal cohort studies. In this study, a total of 1118 fetuses with confirmed CHDs were recruited from three units over a 5-year period, composing 961 of singleton pregnancies and 157 of twin pregnancies. We performed chromosomal microarray analysis on all cases to detect numerical chromosomal abnormalities (NCAs) and pathogenic/likely pathogenic CNVs (P/LP CNVs) and employed whole-exome sequencing for some cases without NCAs and P/LP CNVs to detect P/LP sequence variants (P/LP SVs).</p><p><strong>Results: </strong>Overall, NCAs and P/LP CNVs were identified in 17.6% (197/1118) of cases, with NCA accounting for 9.1% (102/1118) and P/LP CNV for 8.5% (95/1118). Nonisolated CHDs showed a significantly higher frequency of NCA than isolated CHD (27.3% vs. 4.4%, p < 0.001), but there was no significant difference in the frequency of P/LP CNVs between isolated and nonisolated CHD (11.7% vs. 7.7%). A total of 109 P/LP CNVs were identified in 95 fetuses, consisting of 97 (89.0%) de novo, 6 (5.5%) parental inherited and 6 (5.5%) with unavailable parental information. The 16p11.2 proximal BP4-BP5 deletion was detected in 0.9% (10/1118) of all cases, second only to the most common 22q11.21 proximal A-D deletion (2.1%, 23/1118). Most of the 16p11.2 deletions (8/10) detected were de novo, and were enriched in CHD cases compared with a control cohort from a previous study. Additionally, SV was identified in 12.9% (8/62) of cases without NCA and P/LP CNV, most of which were de novo with autosomal dominant inheritance.</p><p><strong>Conclusions: </strong>Our cohort study provides a deep profile of the contribution of genetic variants to CHDs in both singleton and twin fetuses; NCA and P/LP CNV contribute to 9.1% and 8.5% of CHD in fetuses, respectively. We confirmed the 16p11.2 deletion as a CHD-associated hotspot CNV, second only to the 22q11.21 deletion in frequency. Most 16p11.2 deletions detected were de novo. Additionally, P/LP SV was identified in 12.9% (8/62) of fetuses without NCA or P/LP CNV.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"2"},"PeriodicalIF":1.3,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10768341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139098341","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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