ABSTRACT: Optimize SNP genotyping probes and demonstrate a new P. falciparum microarray platform that includes CGH and resequencing probes on the same chip 3D7 common reference; lab samples: HB3, Dd2, SC05, 7C126; field patient samples: M1176, M1069, M1094, M1321, M1064, M1111
Project description:Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits. 91 malaria parasite isolates assayed for single nucleotide polymorphisms across 45K loci
Project description:Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin. comparison of test samples from chordoma families to a reference DNA sample
Project description:Paper abstract: Neural stem cells must strike a balance between self-renewal and multipotency, and differentiation. Identification of the transcriptional networks regulating stem cell division is an essential step in understanding how this balance is achieved. We have shown that the homeodomain transcription factor, Prospero, acts to repress self-renewal and promote differentiation. Amongst its targets are three neural stem cell transcription factors, Asense, Deadpan and Snail, of which Asense and Deadpan are repressed by Prospero. Here we identify the targets of these three factors throughout the genome. We find a large overlap in their target genes, and indeed with the targets of Prospero, with 245 genomic loci bound by all factors. Many of the genes have been implicated in vertebrate stem cell self-renewal, suggesting that this core set of genes is crucial in the switch between self-renewal and differentiation. We also show that multiply bound loci are enriched for genes previously linked to nervous system phenotypes, thereby providing a short-cut to identifying genes important for nervous system development. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed for Prospero (with 2 dye-swaps). For Asense, Deadpan and Snail, two biological replicates were performed.
Project description:This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent. We attempted to validate 9 de novo CNVs in the same number of trios. In 3 cases, paternal DNA was not available leaving a total of 24 distinct samples for hybridization. All samples were hybridized against a previously well-characterized reference (NA15510; see Tuzun et al., Nat Genet 2005).
Project description:This SuperSeries is composed of the following subset Series: GSE23572: Custom array CGH validation of de novo CNVs in asthma samples GSE23575: Custom array CGH validation of de novo CNVs in CEU HapMap samples Refer to individual Series
Project description:Utilizing methylation DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays, we analyzed the methylation profiles of pooled DNA from human cervical carcinoma and normal cervix Cervical carcinoma compaire with normal cervix
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).
Project description:Association of the (histone) deacetylase SIRT1 with promoters was assessed to determine putative SIRT1-regulated genes. Based on the observation that the SIRT1 yeast ortholog Sir2 redistributes across the yeast genome in repsonse to genotoxic stress and double strand breaks (DSBs), we investigated the impact of oxidative stress on the chromatin binding pattern of SIRT1. Oxidative stress causes a major change in SIRT1 binding that is accompanied by an inverse H1K26 acetylation pattern. H1K26 was shown to be a direct target for deacetylation by SIRT1. Keywords: ChIP-chip, stress response ES cells were left untreated or treated with 2 mM H2O2 for 1 hour. Both samples were subjected to ChIP against SIRT1, H1AcK26 or rabbit Ig (one IP per treatment and Ab). Input DNA was labeled with Cy3, IP DNA with Cy5, enrichment over input is reported as 2log.
Project description:Streptococcus suis serotype 2 (SS2), an important zoonotic agent, is notorious for causing contagious porcine diseases and human infection. The two outbreaks in China (in 1998 and in 2005) have caused serious economic losses in the pig industry and posed public health for its new toxin shock symptoms (TSS). However, the molecular mechanism of SS2 pathogenicity is still poorly understood. In order to get insights into pathogenecity of SS2, eighteen SS2 strains of different virulence and sources have been subjected to whole genome comparison by NimbleGen CGS arrays Comparative genomic analysis of 18 SS2 strains with 05ZYH33 as reference
Project description:We profiled the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II following mitogen stimulation. We classified the genes that rapidly coassemble p300 and pol II following mitogen stimulation Comparison the unstimulated to P/I stimulated pol II and p300 enrichment fold in Jurkat