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single nucleotide polymorphism array analysis for fetuses from balanced translocation carriers at the second trimester

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Heliyon 2024年第20期10卷 e38387页

作者： Wu, Xiaoqing Du, Shengrong Liang, Bin Su, Linjuan Li, Ying Chen, Yuqin Zheng, Lin Lin, Na Huang, Hailong Xu, Liangpu Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics Fujian Medical University Fujian Fuzhou China Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect Fujian Fuzhou China Department of Laboratory Medicine Fujian Medical University Fujian Fuzhou China Key Laboratory of Clinical Laboratory Technology for Precision Medicine (Fujian Medical University) Fujian Province University Fujian Fuzhou China

Prenatal diagnosis is crucial for pregnancies from couples with a carrier of a balanced translocation. We retrospectively reviewed 195 pregnancies from 189 couples with a balanced translocation carrier. Of these, 126 were from natural conception, while 69 were conceived through assisted reproductive technology (ART) with preimplantation genetic diagnosis (PGD). Both single nucleotide polymorphism (SNP) array analysis and conventional karyotyping were conducted on all pregnancies, and karyotype-visible imbalances and pathogenic/likely pathogenic copy number variations (CNVs) were categorized as clinically significant abnormalities. In natural conception group, couples with a female carrier experiencing more than two miscarriages accounted for 30.2 %, significantly higher than the 14.0 % in male carrier couples (p < 0.05). In the PGD group, similar difference was observed between female and male carrier couples (p < 0.05). In the natural pregnancies, SNP array analysis yielded additional 12 cases of CNVs, including two cases of pathogenic (P)/likely pathogenic (LP) aberrations, four variants with uncertain significance (VUS), and six likely benign variants. Only two CNVs were found to be associated with translocation breakpoints, which were finally confirmed to be of parental inheritance. In the PGD pregnancies, two cases of VUS unrelated to the translocation breakpoints were revealed. Taken together, repeated miscarriage was more frequently observed in couples where the carrier was female than male. Conventional SNP array analysis in prenatal diagnosis indicated insufficient evidence to support the notion that balanced translocations increase the likelihood of fetuses having clinically significant CNVs. © 2024

关键词： Balanced translocation Conventional karyotyping Copy number variants single nucleotide polymorphism array Translocation breakpoints

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Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array

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MOLECULAR CYTOGENETICS 2021年第1期14卷 19-19页

作者： Zhou, Lili Zheng, Zhaoke Xu, Yunzhi Lv, Xiaoxiao Xu, Chenyang Xu, Xueqin Wenzhou Cent Hosp Ctr Prenatal Diag Wenzhou 325000 Peoples R China

Background The phenotypes of uniparental disomy (UPD) are variable, which may either have no clinical impact, lead to clinical signs and symptoms. Molecular analysis is essential for making a correct diagnosis. This study involved a retrospective analysis of 4512 prenatal diagnosis samples and explored the molecular characteristics and prenatal phenotypes of UPD using a single nucleotide polymorphism (SNP) array. Results Out of the 4512 samples, a total of seven cases of UPD were detected with an overall frequency of 0.16%. Among the seven cases of UPD, two cases are associated with chromosomal aberrations (2/7), four cases (4/7) had abnormal ultrasonographic findings. One case presented with iso-UPD (14), and two case presented with mixed hetero/iso-UPD (15), which were confirmed by Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as maternal UPD (15) associated with Prader-Willi syndrome (PWS). Four cases had iso-UPD for chromosome 1, 3, 14, and 16, respectively;this is consistent with the monosomy rescue mechanism. Another three cases presented with mixed hetero/isodisomy were consistent with a trisomy rescue mechanism. Conclusion The prenatal phenotypes of UPD are variable and molecular analysis is essential for making a correct diagnosis and genetic counselling of UPD. The SNP array is a useful genetic test in prenatal diagnosis cases with UPD.

关键词： uniparental disomy single nucleotide polymorphism array prenatal diagnosis

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Clinical findings and genetic analysis of patients with copy number variants involving 17p13.3 using a single nucleotide polymorphism array: a single-center experience

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BMC MEDICAL GENOMICS 2022年第1期15卷 268-268页

作者： Liang, Bin Yu, Donghong Zhao, Wantong Wang, Yan Wu, Xiaoqing Chen, Lingji Lin, Na Huang, Hailong Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Med Genet Diag & Therapy CtrFujian Key Lab Prenat Fuzhou 350001 Peoples R China Fujian Obstet & Gynecol Hosp Fuzhou 350011 Fujian Peoples R China Fujian Med Univ Fujian Matern & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Med Res Ctr Fuzhou 350001 Peoples R China

Background: 17p13.3 microdeletions or microduplications (collectively known as copy number variants or CNVs) have been described in individuals with neurodevelopmental disorders. However, 17p13.3 CNVs were rarely reported in fetuses. This study aims to investigate the clinical significance of 17p13.3 CNVs with varied sizes and gene content in prenatal and postnatal samples. Methods: Eight cases with 17p13.3 CNVs out of 8806 samples that had been subjected to single nucleotide polymorphism array analysis were retrospectively analyzed, along with karyotyping, clinical features, and follow-up. Results: Eight cases with 17p13.3 CNVs consisted of five fetuses, one aborted embryo and two probands manifested severe congenital defects. The indications of prenatal testing varied considerably for the five fetuses, including ultrasound abnormalities (n = 3), segmental deletions indicated by non-invasive prenatal testing (n = 1), and intellectual disability in the mother of one fetus (n = 1). Of them, two and six harbored copy number gains and losses involving 17p13.3, respectively. The size of the detected 17p13.3 CNVs ranged from 576 kb to 5.7 Mb. Case 1 was diagnosed with 17p13.3 duplication syndrome, and cases 4, 6, and 7 with Miller-Dieker syndrome (MDS). Microdeletions of the 17p13.3 region in two cases (cases 5 and 8) involving YWHAE and CRK, sparing PAFAH1B1, were classified as pathogenic. Case 2 harbored a 576 kb microduplication, encompassing YWHAE and CRK but not PAFAH1B1, which was of maternal origin and considered a variant of uncertain significance. Case 3 carried one 74.2 Mb mosaic duplication of approximately 3.5 on chromosome 17p13.2q25.3, and two deletions at 17p13.3p13.2 and 17q25.3. The karyotype of case 3 was 46,XY,r(17)(p13q25). For five fetuses, only case 2 continued gestation and showed normal development at the age of 15 months;the others were subjected to termination of pregnancy. Conclusion: The clinical findings of 17p13.3 microdeletions or microdupl

关键词： Miller-Dieker syndrome 17p13.3 Duplication syndrome CNV involving 17p13.3 single nucleotide polymorphism array Genetic analysis

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Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array

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MOLECULAR CYTOGENETICS 2020年第1期13卷 19-19页

作者： Zhou, Lili Zheng, Zhaoke Wu, Lianpeng Xu, Chenyang Wu, Hao Xu, Xueqin Tang, Shaohua Wenzhou Cent Hosp Ctr Prenatal Diag Wenzhou 325000 Peoples R China Wenzhou Med Univ Sch Lab Med & Life Sci Key Lab Med Genet Wenzhou 325000 Peoples R China

Background Defining the phenotype-genotype correlation of small supernumerary marker chromosomes (sSMCs) remains a challenge in prenatal diagnosis. We karyotyped 20,481 amniotic fluid samples from pregnant women and explored the molecular characteristics of sSMCs using a single nucleotide polymorphism (SNP) array. Results Out of the 20,481 samples, 15 abnormal karyotypes with sSMC were detected (frequency: 0.073%) and the chromosomal origin was successfully identified by SNP array in 14 of them. The origin of sSMCs were mainly acrocentric-derived chromosomes and the Y chromosome. Two cases of sSMC combined with uniparental disomy (UPD) were detected, UPD(1) and UPD(22). More than half of the cases of sSMC involved mosaicism (8/15) and pathogenicity (9/15) in prenatal diagnosis. A higher prevalence of mosaicism for non-acrocentric chromosomes than acrocentric chromosomes was also revealed. One sSMC derived from chromosome 3 with a neocentromere revealed a 24.99-Mb pathogenic gain of the 3q26.31q29 region on the SNP array, which presented as an abnormal ultrasound indicating nasal bone hypoplasia. Conclusion The clinical phenotypes of sSMCs are variable and so further genetic testing and parental karyotype analysis are needed to confirm the characteristics of sSMCs. The SNP array used here allows a detailed characterisation of the sSMC and establishes a stronger genotype-phenotype correlation, thus allowing detailed genetic counselling for prenatal diagnosis.

关键词： Small supernumerary marker chromosome single nucleotide polymorphism array Prenatal diagnosis

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Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array

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FUTURE SCIENCE OA 2022年第1期8卷 FSO766页

作者： Shioi, Yoshihiro Osakabe, Mitsumasa Yanagawa, Naoki Nitta, Hiroyuki Sasaki, Akira Sugai, Tamotsu Iwate Med Univ Sch Med Dept Mol Diagnost Pathol 2-1-1 Shiwagun Yahaba Iwate 0283695 Japan Iwate Med Univ Sch Med Dept Surg 2-1-1 Shiwagun Yahaba Iwate 0283695 Japan

Lay abstract Biliary tract carcinoma, including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic (single nucleotide polymorphism-array) profiling plays important roles in evaluation of the carcinogenesis of biliary tract carcinoma. In the hierarchical cluster analysis, two clusters were identified (subgroup 1 with low somatic copy number alterations [SCNAs] and subgroup 2 with high SCNAs);GBC was found to be predominant in subgroup 1, whereas BDC was predominant in subgroup 2. These findings suggested that GBC and BDC had different genetic backgrounds in terms of SCNAs. Aim: Biliary tract carcinoma (BTC), including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic profiling has important roles in evaluation of the carcinogenesis of BTC. Materials & methods: We examined somatic copy number alterations (SCNAs) using a single nucleotide polymorphism array system to analyze 36 BTC samples (11 GBCs and 25 BDCs). Results: In hierarchical cluster analysis, two clusters were identified (subgroup 1 with low SCNAs and subgroup 2 with high SCNAs). GBC was predominant in subgroup 1, whereas BDC was predominant in subgroup 2, suggesting that GBC and BDC had different genetic backgrounds in terms of SCNAs. Conclusion: These findings could be helpful for establishing the molecular carcinogenesis of BTCs.

关键词： bile duct cancer biliary tract carcinoma carcinogenesis cluster analysis crypt isolation method gall bladder cancer molecular alteration prognosis single nucleotide polymorphism array somatic copy number alteration

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Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

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ANIMAL GENETICS 2016年第5期47卷 560-569页

作者： Kader, Adiljan Liu, Xuexue Dong, Kunzhe Song, Shen Pan, Jianfei Yang, Min Chen, Xiaofei He, Xiaohong Jiang, Lin Ma, Yuehui Chinese Acad Agr Sci Key Lab Farm Anim Genet Resources & Utilizat Minist Agr China Inst Anim Sci 2 Yuanmingyuan West Rd Beijing 100193 Peoples R China Xinjiang Acad Anim Sci Urumqi 83000 Xinjiang Peoples R China ARS USDA Avian Dis & Oncol Lab E Lansing MI 48823 USA China Agr Univ Dept Anim Genet & Breeding Coll Anim Sci & Technol Beijing 100094 Peoples R China

Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.

关键词： copy number variation region Debao pony growth single nucleotide polymorphism array

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A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

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BMC BIOINFORMATICS 2007年第1期8卷 1-11页

作者： Yu, Tianwei Ye, Hui Sun, Wei Li, Ker-Chau Chen, Zugen Jacobs, Sharoni Bailey, Dione K. Wong, David T. Zhou, Xiaofeng Univ Illinois Coll Dent Ctr Mol Biol Oral Dis Chicago IL 60680 USA Univ Illinois Rollins Sch Publ Hlth Dept Biostat Chicago IL 60680 USA Shanghai Jiao Tong Univ Shanghai Childrens Med Ctr Shanghai Peoples R China Univ Calif Los Angeles Dept Stat Los Angeles CA 90024 USA Univ Calif Los Angeles Dept Human Genet & Microarray Core Los Angeles CA 90024 USA Affymetrix Inc Santa Clara CA USA Univ Calif Los Angeles Dent Res Inst Sch Dent David Geffen Sch Med Los Angeles CA 90024 USA Univ Calif Los Angeles Henry Samueli Sch Engn Los Angeles CA 90024 USA Univ Calif Los Angeles Jonsson Comprehens Canc Ctr Los Angeles CA 90024 USA Sun Yat Sen Univ Guanghua Sch Guangzhou Peoples R China Sun Yat Sen Univ Res Inst Stomatol Guangzhou Peoples R China

Background: DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required. Results: We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step. Conclusion: Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.

关键词： single nucleotide polymorphism Marker Copy Number Change single nucleotide polymorphism array Copy Number Aberration True Edge

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A response to Yu et al.: "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145

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BMC BIOINFORMATICS 2007年第1期8卷 1-9页

作者： Rueda, Oscar M. Diaz-Uriarte, Ramon Spanish Nat Canc Ctr CNIO Stat Comp Team Struct Biol & Biocomp Programme Madrid 28029 Spain

Background: Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state. Methods: We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints. Results: The reanalysis shows that the performance of our method is comparable to that of the other methods analyzed. In addition, we can provide probabilities of a given spot being a breakpoint, something unique among the methods examined. Conclusion: Markov Chain Monte Carlo methods require using a sufficient number of iterations before they can be assumed to yield samples from the distribution of interest. Running our method with too small a number of iterations cannot be representative of its performance. Moreover, our analysis shows how our original approach can be easily adapted to answer specific additional questions (e. g., identify edges).

关键词： Markov Chain Monte Carlo Hide State Markov Chain Monte Carlo Algorithm Viterbi Algorithm single nucleotide polymorphism array

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Endometriosis does not impact aneuploidy rates of products of conception in IVF population

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SCIENTIFIC REPORTS 2025年第1期15卷 1-9页

作者： Kong, Huijuan Fan, Wenqian Ye, Tian Du, Linqing Zhengzhou Univ Ctr Reprod Med Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Henan Key Lab Reprod & Genet Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Clin Res Ctr Henan Prov Obstetr & Gynaecol Dis Reprod Med Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Affiliated Hosp 1 Henan Engn Lab Preimplantat Genet Diag & Screening Zhengzhou 450052 Peoples R China Zhengzhou Univ Dept Oncol Affiliated Hosp 1 1 Jianshe East Rd Zhengzhou 450000 Peoples R China

It has been debated whether endometriosis (EMS) adversely affects oocyte quality, potentially leading to a higher incidence of genetically unbalanced embryos or other egg factors that affect the developmental potential. In this study, we explored the effects of endometriosis on risk of chromosomally aberrant in miscarried products of conception (POC) after assisted reproductive treatment (ART), including fresh and frozen cycles. Miscarried POCs were collected from EMS patients (N = 102) and non-EMS patients (N = 441). single nucleotide polymorphism (SNP) array analysis was conducted on all collected samples. Propensity score matching (PSM, ratio of 1:4) based on maternal age was applied in data analysis. Logistic regression analysis was performed to identify risk factors for chromosomal aberration-induced miscarriage between the two cohorts. A total of 228 (41.99% of 543) conceptuses were identified as having chromosomal aberrations. The results showed that women with EMS had a significantly lower antral follicle count (AFC) (10 +/- 5 vs. 14 +/- 7, P < 0.01) compared to the control group. Additionally, the EMS group had a relatively lower anti-Mullerian hormone (AMH), higher basal follicle stimulating hormone (FSH) and fewer oocytes, (P > 0.05). There was no significant difference in the chromosomal aberration rate of POCs between EMS and non-EMS groups (35.29% vs. 43.54%;odds ratio (OR) = 1.03, 95% confidence intervals (CIs) 0.79-1.35). This is the first study to show that EMS maybe associated with decreased ovarian reserve, but not related to chromosomal abnormalities in POCs. These results suggest that chromosomal abnormalities may not be the only cause of miscarriage in EMS patients.

关键词： Endometriosis single nucleotide polymorphism array Miscarriage Chromosomal abnormality ART

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Genome-wide analysis for loss of heterozygosity in primary and recurrent phyllodes tumor and fibroadenoma of breast using single nucleotide polymorphism arrays

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BREAST CANCER RESEARCH AND TREATMENT 2006年第3期97卷 301-309页

作者： Wang, Zhigang Charles Buraimoh, Ayodele Iglehart, James Dirk Richardson, Andrea Lynn Brigham & Womens Hosp Dept Pathol Boston MA 02115 USA Dana Farber Canc Inst Dept Canc Biol Boston MA USA Brigham & Womens Hosp Dept Surg Boston MA 02115 USA

Phyllodes tumors of the breast are biphasic stromal and epithelial tumors histologically similar to benign fibroadenomas, but with a neoplastic stromal component. In contrast to fibroadenoma, phyllodes tumors can recur and be locally aggressive or be malignant. This study uses SNP array analysis to present a genome-wide map of loss of heterozygosity (LOH) in a cohort of phyllodes tumors and fibroadenomas. LOH is frequent and sometimes extensive in phyllodes tumors, but is rarely seen in fibroadenomas. There is heterogeneity between phyllodes tumors of different patients and no one LOH marker identifies a majority of these lesions. However, a subset of LOH loci occur in multiple cases of phyllodes tumors and are not found in fibroadenomas. Primary phyllodes tumors and paired recurrences from the same patient share common regions of LOH. In contrast, metachronous fibroadenomas from the same patient have different LOH patterns with no indication of a shared origin. Specific LOH loci may be associated with pathologic progression in recurrent phyllodes tumors. In a single case of phyllodes tumor containing a malignant epithelial component the malignant epithelium and stroma partially share an LOH genotype, suggesting a common precursor cell for the biphasic malignant components.

关键词： fibroadenoma loss of heterozygosity phyllodes tumor single nucleotide polymorphism array stem or precursor cell

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