A Trio Based Approach to Epilepsy Methylome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE119684 | GEO | 2018/09/09
REPOSITORIES: GEO
Similar Datasets
Project description:Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. We determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP array. The Affymetrix 500K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosome CNVs in 30 trios. 147 of these CNVs were de novo, but only 33 (22%) of the de novo CNVs were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 pathogenic and 4 possibly pathogenic CNVs for MR. All 11 of these CNVs were detected by both the Agilent and NimbleGen arrays, 9 by the Affymetrix 500K and Illumina beadchips, and 5 by the SMRT BAC array. Two of the 4 pathogenic or possibly pathogenic CNVs present in the trios tested with the Affymetrix 6.0 array were identified. Our findings demonstrate that different results are obtained with different AGH platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls supports the need for validating clinically important findings with a different methodology. 15 trios were analysed consisting of child (proband) and both normal parents. We performed separate hybridizations for the mother, father, and child and then performed pair-wise comparisons of the normalized hybridization intensities for the child to the mother and of the child to the father in silico.
2011-02-17 | E-GEOD-27145 | biostudies-arrayexpress
Project description:In order to study parent-of-origin effects on gene expression, we performed RNAseq analysis (100bp single end reads) of 165 children who formed part of mother/father/child trios where genotype data was available from the HapMap and/or 1000 Genomes Projects. Based on phased genotypes at heterozygous SNP positions, we generated allelic counts for expression of the maternal and paternal alleles in each individual. This analysis reveals significant bias in the expression of the parental alleles for dozens of genes, including both previously known and novel imprinted transcripts.
2018-06-15 | GSE92521 | GEO
Project description:Genome-wide association study of severe malaria in Gambian mother-father-child trios
| EGAS00000000087 | EGA
Project description:Suicidal behavior (SB) has a complex etiology of genes, environment or both. One of the genetic components in SB could be copy number variations (CNVs), since CNVs are implicated in a range of neurodevelopmental disorders. However, a recently published genome-wide and case-control study failed to observe a significant role of CNVs in SB (see E-MTAB-3519). Here we complement those initial observations by conducting a brief CNV-association study, for the first time in a family-based trio-sample with severe suicide attempt (SA) outcome in offspring (n=660 trios; the \GISS\ sample, see http://www.ncbi.nlm.nih.gov/pubmed/23422793 and refs therein). For association testing, we here used the FBAT-CNV methodology (http://www.ncbi.nlm.nih.gov/pubmed/18228561), which allows for CNV association testing directly on the raw intensity values (Illumina \log R ratio\), evaluating any type of CNVs (e.g. de novo or inherited) without reliance on CNV calling algorithms and robust to control selection biases. Here we have deposited these raw logR-values for 88,450 on-chip CNV-loci of the HumanOmni1-Quad_v1 chip, arranged in a standard pedigree format used as input for FBAT-CNV analysis in SVS software (goldenhelix.com): column 1 is the family ID, column 2 is the Subject type (1 = offspring, 2 = mother, 3 = father), column 3 is the father ID (? for missing), column 4 is the mother ID (? for missing), column 5 is the sex (1 = female, 0 = male), column 6 is the affection status (1 = suicide attempt, 0 = not affected) and columns 7 and onward are the logR-values for each CNV-loci as is listed in the header row. We observed experiment-wide significant association (P ≤ 5.6 x 10-7) of two proximal CNVs at chromosome 14 (Illumina markers cnvi0108946 and cnvi0118308, with NCBI 36.3 start positions 22794779 and 22582820). However, these CNV-associations mapped to T-cell receptor regions, and therefore most likely reflect inter-individual variation in somatic rearrangements occurring in white blood cells (as our source of DNA was blood), rather than association with SA. In conclusion, our results did not suggest any major role of CNVs in SA etiology, in line with the results of the recent case-control study (see E-MTAB-3519).
2015-10-30 | E-MTAB-3744 | biostudies-arrayexpress
Project description:We designed a microarray to test at exonic resolution for genomic imbalance for genes representative of all known chromosomal microdeletion/microduplication syndromes, all known causative genes for ID, all known genes encoding glutamate receptors and their known encoding proteins and all known genes encoding proteins with epigenetic regulatory function. We found 36 de novo copy number variants affecting 35 children in this study. 167 trios, each comprising an affected child and both its normal parents were analyzed by conducting two comparative hybridizations; child vs. mother and child vs. father, and only selecting a CNV if it appeared in both hybridizations, i.e., was de novo. De novo CNVs were independantly validated using quantitative PCR.
2012-07-23 | E-GEOD-39533 | biostudies-arrayexpress
Project description:Preterm birth is the major cause of newborn and infant mortality affecting nearly one in every ten live births. This study was designed to develop an epigenetic biomarker for susceptibility of preterm birth using buccal cells from the mother, father, and child (triads). MeDIP-seq was used to identify differential DNA methylation regions (DMRs) using a comparison of control term birth versus preterm birth triads. Epigenetic DMR associations with preterm birth were identified for both the mother and father that were distinct and suggest potential epigenetic contributions from both parents. The mother (165 DMRs) and female child (136 DMRs) at p<1e-04 had the highest number of DMRs and were highly similar suggesting potential epigenetic inheritance of the epimutations. The male child had negligible DMR associations. The DMR associated genes for each group involve previously identified preterm birth associated genes.
2022-03-09 | GSE194227 | GEO
Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ
2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress
Project description:The ketogenic diet (KD) is an anticonvulsant treatment that has been used to manage medically-intractable epilepsies. The KD requires 10-12 days to become maximally effective, suggesting that changes in gene expression are involved in its anticonvulsant action. Using the Affymetrix rat arrays (RAE230A), 6 control samples and 5 KD samples were run. Keywords: other
2004-03-29 | GSE1155 | GEO
Project description:Genome-wide DNA methylation profiling of peripheral blood mononuclear cells from 30 male offspring from the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort and 30 male offspring from the Yucheng' neighborhood referents with similar backgrounds. The Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across appromixmately 480,000 CpGs.
2018-09-21 | GSE120228 | GEO
Project description:Fetal health is dependent upon the epigenetic-based regulation of gene expression in placenta. Genomic imprinting is an epigenetic phenomenon common to placenta and refers to the monoallelic expression of a gene in a parental-specific manner. We aimed to detect novel imprinted genes in human placenta by applying whole transcriptome RNA-sequencing and genotyping of coding variants. Ten family trios with healthy spontaneous single term pregnancy were recruited. Parental and child DNA genotypes were analysed using exome SNP genotyping microarrays, revealing the inheritance of parental alleles. Total RNA was extracted from placental tissue for whole transcriptome analysis. The imprinted genes showed consistent expression from either parental allele as demonstrated by the SNP content of sequenced transcripts. We found seven novel imprinted genes (ABP1, BCLAF1, IFI30, LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed five known imprinted genes (AIM1, PEG10, RHOBTB3, ZFAT and ZFAT-AS1). The main functions of the proteins encoded by the imprinted genes can be grouped as being involved in: i) cellular apoptosis and tissue development; ii) regulating inflammation and modulating the immune system; iii) facilitating metabolic processes and iv) regulating the cell cycle. Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.
2014-09-01 | E-GEOD-56685 | biostudies-arrayexpress