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Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles

ABSTRACT: Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles

PROVIDER: PRJNA482860 | ENA |

REPOSITORIES: ENA

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Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles

Project description:Heterozygous CHMs have been believed as synonymous with dispermic moles (two sperm origin). The possibility of diploid sperm origin has not been considered. We assessed whether heterozygous CHMs would be of dispermic or diploid sperm origin. In all the cases, centromeric zygosity was random, i.e., mixed status. Theoretically, if the heterozygous CHMs were of diploid sperm origin, the centromeric status will be all homozygous or all heterozygous. Thus, all the analyzed heterozygous CHMs were considered to be of dispermic origin. Three cases showed the trisomy while we did not notice them with STR analysis. Diploid sperm fertilization can be rare during the development of heterozygous androgenetic CHM.

2019-08-31 | GSE117672 | GEO

Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles.

Project description:Hydatidiform moles are abnormal pregnancies, which show trophoblastic hyperplasia. Most often, the nuclear genome in complete hydatidiform moles (CHMs) is composed of only paternal chromosomes. Diploid androgenetic conceptuses can be divided into homozygous and heterozygous CHMs. Heterozygous CHMs originate from two sperms or a diploid sperm, the distinction of which has not been established. Here, we assessed the origin of heterozygous CHMs using single nucleotide polymorphism (SNP) array. Thirteen heterozygous CHMs were analysed using B allele frequency (BAF) plotting to determine the centromeric zygosity status of all chromosomes. One case was from the duplication of a single sperm with an XY chromosome. In the other twelve cases, centromeric zygosity was random, i.e. mixed status. Thus, the twelve heterozygous CHMs were considered to be of dispermic origin but not diploid sperm origin. BAF plotting of SNP array can be a powerful tool to estimate the type of hydatidiform moles.

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Genome-wide DNA methylation analysis of diploid hydatidiform moles with androgenetic or biparental genomic origin

Project description:Only very few studies have investigated methylation patterns of different types of hydatidiform moles (HMs). Methylation patterns of androgenetic HMs (AnHMs) are abnormal due to the fact that the nuclear genome in AnHMs is inherited from the father, only. Diploid biparental HMs (BiHM) have been suggested to display the same methylation patterns of imprinted genes as AnHMs, and the methylation patterns are suspected to be a consequence of a failure to establish maternal methylation at multiple genome-wide loci. We have investigated the methylation patterns of AnHMs, BiHM-like placentas with a chr. 11p15.5 deletion and a BiHM from a woman with NLRP7 mutations and compared these to methylation patterns of normal placentas. Using the Next Generation Sequencing (NGS) technique Reduced Representation Bisulfite Sequencing (RRBS) we instigated the genome-wide CpG methylation of 32 samples, including nine normal placentas, 20 androgenetic diploid HMs (AnHMs), and three diploid biparental HMs/HM-like placentas. This dataset contains RRBS data from 12 samples, including the nine normal placentas and the three diploid biparental HMs/HM-like placentas.The RRBS data from 20 androgenetic diploid HMs (AnHMs) was deposited in GSE65881:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65881

2015-06-01 | GSE67412 | GEO

RNA sequencing data from androgenetic cells

Project description:Androgenetic induced pluripotent stem cells (AgHiPSCs) were generated from androgenetic fibroblasts derived from a complete hydatidiform mole. AgHiPSCs can be used in regenerative medicine, for analysis of genomic imprinting, to study imprinting-related development, and for disease modeling in humans. To investigate the pluripotency state of AgHiPSCs, we analyzed their cellular and molecular characteristics (morphology, RT-PCR, qPCR, immunochemistry, and differentiation capacity in vitro and in vivo). We tested the DNA methylation status of imprinted genes using bisulfite sequencing and demonstrated the androgenetic identity of AgHiPSCs.

2019-12-12 | GSE141906 | GEO

mRNA expression profiles in androgenetic, parthenogenetic and fertilized embryonic stem cells

Project description:In this study, mRNA expression profiles were examined by Illumina microarray in mouse embryonic stem cells (ESCs) derived from androgenetic (aESC), parthenogenetic (pESC) and fertilized (fESC) blastocysts. Results showed that 2394, 87 and 1788 mRNAs were differentially expressed in the aESCs vs. fESCs, pESCs vs. fESCs and aESCs vs. pESCs, respectively. Androgenetic, parthenogenetic and fertilized embryonic stem cell lines were established from androgenetic, parthenogenetically activated and fertilized blasotocyst. mRNA microarrays were repeated three times using passages 6, 7 and 8.

2013-04-04 | E-GEOD-45749 | biostudies-arrayexpress

microRNA expression profiles in androgenetic, parthenogenetically activated and fertilized embryonic stem cells

Project description:In this study, miRNA expression profiles were examined by Illumina microarray in mouse embryonic stem cells (ESCs) derived from androgenetic (aESC), parthenogenetic (pESC) and fertilized (fESC) blastocysts. Results showed that 125, 42 and 99 miRNAs were differentially expressed in the aESCs vs. fESCs, pESCs vs. fESCs and aESCs vs. pESCs, respectively. Androgenetic, parthenogenetically activated and fertilized embryonic stem cell lines were established from androgenetic and fertilized blasotocyst. microRNA microarrays were repeated three times using passages 6, 7 and 8.

2013-04-04 | E-GEOD-45753 | biostudies-arrayexpress

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Project description:Microbiome in the hair follicle of androgenetic alopecia patients

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GSTM3 single nucleotide polymorphism (rs7483) associated with peripheral BMC expression in Alzheimer disease

Project description:Comparisons between the sample groups (normal elderly control (NEC) and Alzheimer disease (AD)) allowed the identification of genes with disease expression patterns associated with the glutathione S-transferase M3 single nucleotide polymorphism rs7483. Keywords: biological repeat

2009-01-12 | GSE4227 | GEO

Genetic predisposition to neuroblastoma mediated by a single nucleotide polymorphism within a LMO1 oncogene super-enhancer element

Project description:A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility in children and oncogenic addiction to LMO1 in the tumor cells1. Here we sought to discover the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding sites. SNP rs2168101 G>T was the most highly associated variant (combined P=7.47x10-29, Odds Ratio 0.65, 95% CI: 0.60-0.70) and resided in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumor formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P=0.028) in neuroblastoma primary tumors and ablates GATA3 binding (P=0.007). We demonstrate monoallelic LMO1 expression from the G-containing strand in tumors heterozygous for this SNP as demonstrated both by RNA sequencing (P<0.0001) and reporter assays (P=0.002). These findings show that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumor cells.

2015-10-18 | GSE65664 | GEO

Microarray expression profile analysis of long non-coding RNA in androgenetic alopecia: a study of Chinese men

Project description:To examined the genome-wide expression levels of lncRNAs in androgenetic alopecia tissues and paired adjacent normal tissues by microarray analysis. We identified numerous lncRNAs that were differentially regulated between androgenetic alopecia and paired normal tissues.

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