High resolution X chromosome copy number analysis in fertile and POI females
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ABSTRACT:
PROVIDER: PRJNA524810 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:comparison of copy number profile between health fertile females and women affected by POI
2019-03-01 | GSE127453 | GEO
Project description:Premature Ovarian Insufficiency (POI) refers to the decline and stagnation of ovarian function in women before the age of 40.POI-associated EIF4ENIF1 mutations and the distribution of functional domains in the EIF4ENIF1 protein have been separately described. However, not all the clinically observed EIF4ENIF1 mutations in POI cases fall in clearly defined functional domains of the EIF4ENIF1 protein. Herein, we introduce T&T seq as a new evaluation tool to sensitively measure the translation regulation capacities of EIF4ENIF1 proteins with clinically discovered mutations. The sequencing results showed that POI-associated EIF4ENIF1 mutations impaired its translation repression function to different degrees.
2024-04-09 | GSE240761 | GEO
Project description:Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant.
2014-03-20 | GSE56043 | GEO
Project description:4-vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure leading to POIs, which can seriously affect a woman's physical health and fertility. Investigating its pathogenic mechanisms can help provide guidance for the prevention of ovarian impairment and the treatment of POI. We built a mouse model of POI by intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. Then compared it with the control group at two time points, day 15 and day 30, including the comparison of phenotypic characteristics and differences in the transcriptome. We performed a comprehensive analysis of the differential genes identified and validated some key genes by RT-PCR. The results showed that sex hormone levels, follicle number and estrous cycle of VCD-induced POI mice were significantly affected at both day 15 and day 30. Regarding DEGs and enrichment results, the results obtained at day 15 were not as significant as those at day 30. Our results provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis play an important part in the process by which VCD affects ovarian function. Maybe it was due to impaired follicular development caused by VCD damage to the primordial follicular pool, and with the progression of time, the ovarian damage was aggravated, and it was gradually difficult to perform normal function.
2024-03-27 | GSE249151 | GEO
Project description:Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples. DNA of eight individuals including three affected subjects was used for homozygosity mapping. Genotyping was performed using the Affymetrix Axiom_GW_Hu_SNP array. Briefly, 250 ng genomic DNA was digested with Digestion Master Mix containing 2 µl NE buffer 2 (10X), 0.5 µl BSA (100X; 10 mg/ml) and 1 µl Nsp1. Digested DNA sample was ligated to Nsp1 adaptor using T4 DNA ligase and amplified by 2 µl of TITANIUM Taq DNA polymerase (50X) and 100 µM PCR primer. PCR products were purified on a Clean-Up plate (Clontech Lab, Madison, USA) and eluted by RB buffer. Purified PCR products were fragmented using Fragmentation Reagent (0.05U/µl DNase 1) for 35 minutes at 37°C followed by labeling of fragmented samples with Labeling Master Mix (30 mM GeneChip DNA Labeling Reagent, 30 U/µl Terminal Deoxynucleotidyl Transferase) for 4 hours at 37°C. Labeled samples were hybridized to Axiom_GW_Hu_SNP array by mixing the sample with Hybridization Master Mix, denatured on thermoblock and loaded on to Array. Array was then placed in a hybridization oven (GeneChip Hybridization Oven 640, USA) for 16-18 hours. After hybridization, array was washed and stained on an automated Fluidic Station 450 followed by scanning on GeneChip Scanner 3000 7G using GeneChip Operating Software (GCOS).
2014-03-20 | E-GEOD-56043 | biostudies-arrayexpress
Project description:Chromosome 16 is one of the gene-rich chromosomes; however, approximately 10% of the chromosome 16 sequence is composed of segmental copies, which renders this chromosome instable and predisposes it to rearrangements via frequent nonallelic homologous recombination. Microarray technologies have enabled the analysis of copy number variations (CNV), which may be associated with the risk of developing complex diseases. Through comparative genomic hybridisation in 1,298 patients, we detected 18 cases with chromosome 16 CNV. We identified 2recurrent CNV regions, including 1 at 16p13.11 in 4 patients and another at 16p11.2 in 7 patients. We also detected atypical chromosome 16 rearrangements in 7 patients. Furthermore, we noted an increased frequency of co-occurring genomic changes, supporting the two-hit hypothesis to explain the phenotypic variability in the clinical presentation of CNV syndromes. Our findings can contribute to the creation of a chromosome 16 disease map based on regions that may be associated with disease development.
| S-EPMC9149555 | biostudies-literature
Project description:The nematode Auanema rhodensis is trioecious (co-occurrence of males, females and self-fertile hermaphrodites). To better understand its sex determination system, we have compared the transcriptomic profiles of early (L2) females, hermaphrodites and converted females (hermaphrodite-fated larvae induced to develop as females). Additionally, we sequenced the transcriptome of adult males and individuals from various stages and sexes (mixed stages samples) to compare global gene expression profiles along the assembled draft chromosomes of A. rhodensis (BioProject PRJEB29492). The RNA-seq data was also used to predict genes in the assembled genome. We generated three biological replicates for each RNA-seq condition (L2 females, L2 converted females, L2 hermaphrodites, males and mixed stages). Comparisons of the expression profiles of the L2 conditions was performed to identify genes potentially involved in the sexual differentiation process, using a standard RNA-seq comparison approach. Briefly, the cleaned reads were aligned to the genome using STAR, the abundance and identification of differentially expressed genes were assessed using FeatureCounts and DEseq2 (using as thresholds an absolute log2(Fold Change) >= 2 and an FDR <0.01).
2019-02-11 | E-MTAB-7667 | biostudies-arrayexpress
Project description:Among the diseases with X-linked inheritance and intellectual disability, duplication of the Xp11.23p11.22 region is indeed a rare phenomenon, with less than 90 cases known in the literature. Most of them have been recognized with the routine application of array techniques, as these copy number variations (CNVs) are highly variable in size, occurring in recurrent and non-recurrent forms. Its pathogenic role is not debated anymore, but the information available about the pathomechanism, especially in affected females, is still very limited. It has been observed that the phenotype in females varies from normal to severe, which does not correlate with the size of the duplication or the genes involved, and which makes it very difficult to give an individual prognosis. Among the patients studied by the authors because of intellectual disability, epilepsy, and minor anomalies, overlapping duplications affecting the Xp11.23p11.22 region were detected in three females. Based on our detailed phenotype analysis, we concluded that Xp11.23p11.22 duplication is a neurodevelopmental disorder.
| S-EPMC8080037 | biostudies-literature
Project description:BackgroundOverall, HER2-amplified female breast cancer (FBC) is associated with a high grade, an aggressive phenotype and a poor prognosis. In male breast cancer (MBC) amplification of HER2, located on chromosome 17, occurs at a lower frequency than in FBC, where it is part of complex rearrangements. So far, only few studies have addressed the occurrence of chromosome 17 alterations in small MBC cohorts.MethodsMultiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) were used to detect and characterize copy number changes on chromosome 17 in a cohort of 139 MBC. The results obtained were compared to those in FBC, and were correlated with clinicopathological features and patient outcome data.ResultsWe observed a lower frequency of chromosome 17 copy number changes with less complex rearrangement patterns in MBC compared to FBC. Chromosome 17 changes in MBC included gains of 17q and losses of 17p. Whole chromosome 17 polyploidies were not encountered. Two recurrent chromosome 17 amplicons were detected: on 17q12 (encompassing the NEUROD2, HER2, GRB7 and IKZF3 gens) and on 17q23.1 (encompassing the MIR21 and RPS6KB1 genes). Whole arm copy number gains of 17q were associated with decreased 5 year survival rates (p = 0.010). Amplification of HER2 was associated with a high tumor grade, but did not predict patient survival. Although copy number gains of HER2 and NEUROD2 were associated with a high tumor grade, a high mitotic count and a decreased 5 year survival rate (p = 0.015), only tumor size and NEUROD2 copy number gains emerged as independent prognostic factors.ConclusionsIn MBC chromosome 17 shows less complex rearrangements and fewer copy number changes compared to FBC. Frequent gains of 17q, encompassing two distinct amplicons, and losses of 17p were observed, but no whole chromosome 17 polyploidies. Only NEUROD2 gains seem to have an independent prognostic impact. These results suggest different roles of chromosome 17 aberrations in male versus female breast carcinogenesis.
| S-EPMC4445249 | biostudies-literature