Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Two amniotic fluid sample performed by affymetrix cytoscan HD

ABSTRACT: The uploaded results of two samples were SNParray results in our research of which fetal CNVs were detected by noninvasive prenatal test (NIPT) and confirmed by microarray results. Sample ZNY162 received prenatal diagnosis because at 17 gestational week the pregnant woman received NIPT showing 23Mb microdeletion in Chr18. Later ultrasound examination showed developmental anomalies of feet and the 13th ribs. The pregnant woman received amniocentesis and SNParray at the 21st gestational week, which confirmed the existence of the microdeletion in Chr18. DNA was extracted from 10ml amniotic fluid and tested by Affymetrix CytoScan HD array to detect CNVs in whole genome, showing arr 18q22.3q23(69,461,933-78,014,123) Ã1. Sample LMQ155 received prenatal diagnosis because of advanced maternal age and NIPT result of a 2.29Mb microduplication in Chr13 at 15 gestational week. Amniocentesis was performed at the 17th gestational week. Affymetrix CytoScan HD array were used to detect fetal CNVs in whole genome, which showed arr 13q21.2(60,399,612-61,730,194) Ã3 that was consistent with NIPT result.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhiyang HU

PROVIDER: E-MTAB-4738 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The contribution of copy number (CN)-altered genes in cervical carcinogenesis is unknown owing to a lack of correlation with gene expression. We mapped CN-altered genes in 31 cervical cancers (CCs), and investigated the expression of 21,000 genes in 55 CCs using microarrays. Biological processes associated with genes deregulated by gene dosage and the relationship between gene dosage and patient survival were investigated. CN-altered genome (CN-AG) percentages varied widely among tumors from 0% to 32.2% (mean = 8.1 ± 8.9). Tumors were classified as low (mean = 0.5 ± 0.6, n = 11), medium (mean = 5.4 ± 2.4, n = 10), or high (mean = 19.2 ± 6.6, n = 10) CN. The highest %CN-AG was found in 3q, which contributed an average of 55% of all CN alterations. Genome-wide, only 5.3% of CN-altered genes were deregulated by gene dosage; by contrast, the rate in fully duplicated 3q was twice as high. Amplification of 3q explained 23.6% of deregulated genes in whole tumors (r2 = 0.236, p = 0.006; analysis of variance), including those in 3q and other chromosomes. A total of 862 genes were deregulated exclusively in high-CN tumors, but only 22.9% were CN altered. This result suggests that the remaining genes are not deregulated directly by gene dosage but by mechanisms induced in trans by CN-altered genes. Anaphase-promoting complex/cyclosome (APC/C)-dependent proteasome proteolysis, glycolysis, and apoptosis were upregulated, whereas cell adhesion and angiogenesis were downregulated exclusively in high-CN tumors. The high %CN-AG and upregulated gene expression profiles of APC/C-proteasome-dependent proteolysis and glycolysis were associated with poor patient survival, although only the first 2 correlations were statistically significant (p < 0.05, log-rank test). The data suggest that inhibitors of APC/C-dependent proteasome proteolysis and glycolysis may be useful treatments in these patients. In this study 31 tumors and 25 reference controls were used for analysis of copy number alterations using the 500K microarray. The results obtained from 500K array analysis were validated in 15 of the 31 tumors with a higher density microarray (Cytoscan HD). For the analysis of gene expression 55 cervical tumors (27 of them belong to the group of 31 tumors analyzed for copy number) and 17 exocervical controls were used. Please note that the sample R397 in the CytoScanHD_Array set corresponds to the R392 sample in the other data sets (due to an error in file name).

Project description:Objective: Chromosomal 1q21.1 deletions and duplications are genomic disorders which are usually diagnosed postnatally. However, the genotype-phenotype correlations of 1q21.1 copy number variants (CNVs) during prenatal period are still not clear. This study aimed to provide a systematical summary of prenatal phenotypes for such genomic disorders. Methods: Twenty-six prenatal amniotic fluid samples diagnosed with 1q21.1 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed for all cases simultaneously. The pregnancy outcomes and health conditions after birth for all cases were followed up. Meanwhile, prenatal cases with 1q21.1 microdeletions or microduplications in the literature were retrospectively collected. Results: Eleven pregnancies (11/8252, 0.13%) with 1q21.1 microdeletions and fifteen (15/8252, 0.18%) with 1q21.1 microduplications were identified. Among these 1q21.1 CNVs, four cases covered thrombocytopenia-absent radius (TAR) region, sixteen cases covered 1q21.1 recurrent microdeletion/microduplication region, and six cases covered all regions mentioned above. The prenatal abnormal ultrasound findings were recorded in four participants with 1q21.1 deletions and seven participants with 1q21.1 duplications. Finally, three cases with 1q21.1 deletions and five with 1q21.1 duplications terminated their pregnancies. Conclusion: 1q21.1 microdeletions were associated with increased nuchal translucency (NT), anomalies of urinary system and cardiovascular abnormalities, and 1q21.1 microduplications were correlated with cardiovascular malformations, nasal bone dysplasia and increased NT in prenatal setting. In addition, cerebral ventriculomegaly might be correlated with 1q21.1 microduplications. Considering the variable expressivity and incomplete penetrance of 1q21.1 CNVs, long term follow up after birth should be carried out for these cases. We identified 26 fetuses carrying the 1q21.1 microdeletions and microduplications using chromosomal microarray analysis. And diverse prenatal phenotypes and the critical genes involved in the deleted/duplicated regions were described in this study.

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Two amniotic fluid sample performed by affymetrix cytoscan HD

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