Chromosomal microarray analysis for validation of the WGS-based CNV detection results in recurrent miscarriage couples
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE83941 | GEO | 2017/11/01
SECONDARY ACCESSION(S): PRJNA327497
REPOSITORIES: GEO
Similar Datasets
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
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
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
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
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).
2014-09-04 | E-MTAB-2884 | biostudies-arrayexpress
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
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
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
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.
2016-01-02 | GSE43256 | GEO
Project description:Genome wide DNA methylation profiling of chorionic villi and decidua from recurrent miscarriage patients and artificial abortion controls. Infinium HumanMethylation450 BeadChip was used.
2022-04-24 | GSE198700 | GEO