Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1.
Project description:Genome wide DNA methylation profiling of A2780 cells 1) infected with control virus, no H2O2 (Scr_mock), 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2), 3) infected with shTET2 virus, no H2O2 (shTET2_mock), and 4) infected with shTET2 virus, with H2O2 treatment (30 min plus 2.5 h resting) (shTET2_H2O2, two biological replicates). The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs.
Project description:Genome wide DNA methylation profiling of A2780 cells untreated (mock), treated with H2O2 for 30 min (H2O2 30 min), or treated with H2O2 for 30 min with additional 2.5 hour resting ( H2O2 3h) . The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs.
Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 97 complete hydatidiform moles (CHMs) tissues collected throughout Japan.
Project description:Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with = 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. Keywords: Autism spectrum disorder, Affymetrix SNP genotyping, linkage analysis, copy number analysis, chromosomal rearrangements.
