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Omics score: 1003

Albert Einstein College of Medicine

ABSTRACT: Organisation EGAO00000000223

PROVIDER: EGAO00000000223 | EGA |

REPOSITORIES: EGA

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Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.

Carmi Shai S Hui Ken Y KY Kochav Ethan E Liu Xinmin X Xue James J Grady Fillan F Guha Saurav S Upadhyay Kinnari K Ben-Avraham Dan D Mukherjee Semanti S Bowen B Monica BM Thomas Tinu T Vijai Joseph J Cruts Marc M Froyen Guy G Lambrechts Diether D Plaisance Stéphane S Van Broeckhoven Christine C Van Damme Philip P Van Marck Herwig H Barzilai Nir N Darvasi Ariel A Offit Kenneth K Bressman Susan S Ozelius Laurie J LJ Peter Inga I Cho Judy H JH Ostrer Harry H Atzmon Gil G Clark Lorraine N LN Lencz Todd T Pe'er Itsik I

Nature communications 20140909

The Ashkenazi Jewish (AJ) population is a genetic isolate close to European and Middle Eastern groups, with genetic diversity patterns conducive to disease mapping. Here we report high-depth sequencing of 128 complete genomes of AJ controls. Compared with European samples, our AJ panel has 47% more novel variants per genome and is eightfold more effective at filtering benign variants out of AJ clinical genomes. Our panel improves imputation accuracy for AJ SNP arrays by 28%, and covers at least ...[more]

PMID: 25203624

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Human embryonic stem cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

Project description:Background: To perform epigenome-wide association studies in human disease, assays need to be comprehensive and quantitative while remaining cost-effective. We explored how the strengths of prior tag-based cytosine methylation assays based on massively-parallel sequencing can be maximised analytically. Results: We find that the use of the EcoP15I restriction enzyme to generate long tags and the normalisation of methylation-sensitive by methylation-insensitive restriction enzyme representations greatly improve assay performance. When exploring sources of bias, we find that the length of the restriction fragment has moderate effects on EcoP15I digestion, while base composition exerts minimal effects. We detail the analytical workflow that maximises the quantitative capabilities of this modified assay. Also revealed are polymorphic sequences in the genome that could confound microarray, bisulphite sequencing or mass spectrometry-based assays, and a position effect causing hypomethylation of transposable elements near gene promoters. Conclusions: The new combined assay, referred to as HELP-tagging, interrogates over 1.8 million loci in the human genome quantitatively with a single lane of Illumina sequencing. When the goal is to study not only CG-dense sequence but also the CG-depleted majority of the genome, this assay system should be suitable.

2010-04-12 | GSE19937 | GEO

Hematopoietic stem/progenitor cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

Project description:Extreme fetal growth is associated with adult disease through a cellular memory of unknown mechanism. We tested whether heritable epigenetic processes in long-lived CD34+ hematopoietic stem/progenitor cells (HSPCs) showed evidence for re-programming associated with the extremes of fetal growth. Here we show that both extremes of fetal growth are associated with global shifts towards DNA hypermethylation, targeting cis-regulatory elements in proximity to genes involved in glucose homeostasis and stem cell function. A sexually dimorphic response was found, intrauterine growth restriction (IUGR) associated with greater epigenetic dysregulation in males but large for gestational age (LGA) growth affecting females to a greater extent. The findings are consistent with extreme fetal growth interacting with variable fetal susceptibility to influence cellular aging characteristics through epigenetic mechanisms, with the potential for identifying infants at higher risk for chronic disease later in life.

2014-07-01 | GSE53177 | GEO

Peripheral blood mononuclear cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

Project description:Obesity-associated asthma is recognized as a distinct entity with non-atopic T-helper 1 polarized systemic inflammation. DNA methylation is linked with T helper cell maturation and is associated with inflammatory patterns in asthma and obesity. However, it is unknown whether pathologic dysregulation of DNA methylation patterns occurs in obesity-associated asthma. Using HELP-tagging, we studied epigenome wide DNA methylation in peripheral blood mononuclear cells in 8 urban minority obese asthmatic pre-adolescent children and compared it to methylation in groups of 8 children with asthma alone, obesity alone and healthy controls. Ingenuity Pathway Analysis was used to identify biological pathways that were differentially targeted by methylation dysregulation. We found that obese asthmatics had distinct epigenome wide methylation patterns associated with decreased promoter methylation of a subset of genes, including RANTES, IL-12R and TBX21 and increased promoter methylation of CD23, a low affinity receptor for IgE and of TGFβ, inhibitor of Th cell activation. T cell signaling and macrophage activation were the two primary pathways that were selectively hypomethylated in obese asthmatics. These methylation patterns suggest that methylation is associated with non-atopic inflammation observed in obese asthmatic children compared to children with asthma alone and obesity alone. Our findings suggest a role of DNA methylation in the observed inflammatory patterns in pediatric obesity-associated asthma in minorities.

2014-04-14 | GSE43705 | GEO

Human embryonic stem cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

2010-04-12 | E-GEOD-19937 | biostudies-arrayexpress

Peripheral blood mononuclear cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

Project description:Obesity-associated asthma is recognized as a distinct entity with non-atopic T-helper 1 polarized systemic inflammation. DNA methylation is linked with T helper cell maturation and is associated with inflammatory patterns in asthma and obesity. However, it is unknown whether pathologic dysregulation of DNA methylation patterns occurs in obesity-associated asthma. Using HELP-tagging, we studied epigenome wide DNA methylation in peripheral blood mononuclear cells in 8 urban minority obese asthmatic pre-adolescent children and compared it to methylation in groups of 8 children with asthma alone, obesity alone and healthy controls. Ingenuity Pathway Analysis was used to identify biological pathways that were differentially targeted by methylation dysregulation. We found that obese asthmatics had distinct epigenome wide methylation patterns associated with decreased promoter methylation of a subset of genes, including RANTES, IL-12R and TBX21 and increased promoter methylation of CD23, a low affinity receptor for IgE and of TGFM-NM-2, inhibitor of Th cell activation. T cell signaling and macrophage activation were the two primary pathways that were selectively hypomethylated in obese asthmatics. These methylation patterns suggest that methylation is associated with non-atopic inflammation observed in obese asthmatic children compared to children with asthma alone and obesity alone. Our findings suggest a role of DNA methylation in the observed inflammatory patterns in pediatric obesity-associated asthma in minorities. 32 HpaII test

2014-04-14 | E-GEOD-43705 | biostudies-arrayexpress

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