Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosomal microarray analysis for validation of the WGS-based CNV detection results in recurrent miscarriage couples

ABSTRACT: In order to validate of CNV detection from low-coverage whole-genome sequencing in the blood samples from recurrent miscarriage couples, we employed a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach as chromosomal microarray analysis (CMA) in present study for a cohort of 78 DNA samples from blood. CMA results were compared with low-coverage whole-genome sequencing detection results. 100% consistency was obtained in pathogenic or likely pathogenic CNVs detection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE83941 | GEO | 2017/11/01

SECONDARY ACCESSION(S): PRJNA327497

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

aCGH for CNV detection in clinical samples

Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides snp-array, we used a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach for a cohort of clinical samples including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.

2015-10-01 | GSE72891 | GEO

Chromosomal microarray analysis for validation of the NGS-based CNV detection results in clinical samples

Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.

2015-10-01 | GSE73190 | GEO

Genotyping by array of affected sib-pairs with recurrent miscarriage

Project description:siblings of patients with idiopathic recurrent miscarriage have a higher risk of miscarriage. <br>We hypothesized that this in part was conferred by shared genetic factors.<br>We took blood samples from patients with three or more miscarriages and from siblings with two or more miscarriages in order to perform affected sib-pair analysis.

2010-12-01 | E-MEXP-2942 | biostudies-arrayexpress

MicroRNA Predictors of Miscarriage

Project description:MicroRNA Predictors of Miscarriage

| PRJNA877004 | ENA

The Clinical impact of Chromosomal microarray on Paediatric care in Hong Kong (CGX-6)

Project description:Objective: To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong Methods: We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/ developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results: Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n=9, Level 1) or peer-reviewed publications making medical management recommendation (n=10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n=24); diagnostic testing (n=24), surveillance of complications (n=19), interventional procedure (n=7), medication (n=15) or lifestyle modification (n=12).

2014-08-31 | E-MTAB-2883 | biostudies-arrayexpress

The Clinical impact of Chromosomal microarray on Paediatric care in Hong Kong (CGX-12)

2014-09-04 | E-MTAB-2884 | biostudies-arrayexpress

DNA methylation profiling of placental villi from karyotypically normal recurrent miscarriage

Project description:Miscarriage occurs in 15-20% of clinical pregnancies. While chromosomal errors are observed in over 50%, causes of karyotypically normal losses are poorly understood. DNA methylation undergoes reprogramming during development and must be appropriately set to maintain a healthy pregnancy. We hypothesize that aberrant DNA methylation may cause karyotypically normal miscarriage, particularly among women experiencing recurrent miscarriage (RM). DNA methylation in first trimester chorionic villi was assessed in chromosomally normal miscarriages from women with RM (N=33) or isolated miscarriage (M, N=21), and elective terminations (TA, N=16). Differentially methylated candidate loci were identified using the Illumina Infinium HumanMethylation27 BeadChip array by comparing 10 RM to 10 TA samples. Follow up showed a significant increase in methylation in RM and M compared to TA placentae at the CYP1A2 (p=0.002) and AXL (p=0.02) promoters and decrease at the DEFB1 (p=0.008) promoter. Gene function analysis showed an enrichment of imprinted genes (p=9.53E-10) and genes previously associated with RM (p=9.51E-06). DNA methylation was evaluated at 7 imprinted loci using bisulfite pyrosequencing. An increase of outliers at these loci was observed in RM (3.9%) compared to M (0%) and TA (0.9%) (p=0.02), with increased average methylation at the H19/IGF2 ICR1 in M samples (p<0.0001). Altered DNA methylation in the placenta at specific loci, as well as global dysregulation in specific cases, may contribute to or be a consequence of placental insufficiency in karyotypically normal miscarriage. First-trimester placental villi samples from karyotypically normal miscarriages from recurrent miscarriage patients (N, N=10) and chromosomally normal elective terminations (PZET, N=10).

2016-07-04 | E-GEOD-43256 | biostudies-arrayexpress

microRNA-array of human miscarriage chorionic villous tissue and controls

Project description:To identify the significant different gene, which maybe involved in the etiology of early miscarriage

2022-02-07 | E-MTAB-11443 | biostudies-arrayexpress

DNA methylation profiling in recurrent miscarriage

Project description:We used the Illumina Infinium HumanMethylation450 array platform to conduct a genome-wide screening of DNA methylation in decidua samples from the products of conception of women with recurrent miscarriage and to identify novel methylation variable positions (MVPs) and differentially methylated regions (DMRs).

2019-12-03 | GSE141298 | GEO

DNA methylation profiling of placental villi from karyotypically normal recurrent miscarriage

2016-01-02 | GSE43256 | GEO