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Omics score: 5

Whole-Genome Sequencing of 128 Ashkenazi Jewish individuals

ABSTRACT: We sequenced 128 individuals of Ashkenazi Jewish ancestry. All individuals were controls in other studies: (1) Longevity (Gil Atzmon's lab; Albert Einstein College of Medicine), n=74. (2) Parkinson's disease (Lorraine Clark's lab; Columbia University Medical Center), n=54. Whole-genome, high-coverage (50x) sequencing was performed by Complete Genomics in 2012 and 2013.

PROVIDER: EGAS00001000664 | 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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Population genetic structure of the Ashkenazi Jewish population

Project description:The Ashkenazi Jewish population has long been considered a genetic isolate and presumed to have the genetic signatures of founder effects and isolation. We genotyped a large cohort of Ashkenazi Jews and analyzed their genetic structure compared to other worldwide populations. We genotyped 471 normal control Ashkenazi Jewish individuals with the Affymetrix 6.0 array and analyzed their genetic structure relative to other Europe and worldwide populations. We measured heterozygosity, linkage disequilibrium, identity-by-descent and used extended haplotype tests of positive selection.

2010-08-16 | E-GEOD-23636 | biostudies-arrayexpress

Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

Project description:In this study, we employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity. With data from 26.7 million reads comprising 9.4x108 bp from 3 centenarian and 3 control individuals, we discovered a total of 276 known miRNAs and 8 unknown miRNAs ranging several orders of magnitude in expression levels. A total of 22 miRNAs were found to be significantly upregulated, with only 2 miRNAs downregulated, in centenarians as compared to controls. Examination of miRNA profile of two different ages

2012-06-01 | E-GEOD-32493 | biostudies-arrayexpress

Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

2012-06-01 | GSE32493 | GEO

ena-DATASET-TAGC-18-03-2014-13:20:29:283-320 - samples

Project description:Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls

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Population genetic structure of the Ashkenazi Jewish population

2010-08-16 | GSE23636 | GEO

A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A

Project description:Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in the regulation of aging and metabolism. Targeted sequencing identified a SIRT6 allele containing two linked substitutions (N308K/A313S) as enriched in Ashkenazi Jewish (AJ) centenarians as compared to AJ control individuals. Characterization of this SIRT6 (centSIRT6) allele demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double strand break repair, and more robust cancer cell killing compared to the wild type. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.

2022-10-21 | PXD035689 | Pride

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Project description:Population genetic structure of the Ashkenazi Jewish population

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Genetics of Mammographic Density in Ashkenazi Jewish Women

Project description:Genetics of Mammographic Density in Ashkenazi Jewish Women

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Genetics of Mammographic Density in Ashkenazi Jewish Women

Project description:Genetics of Mammographic Density in Ashkenazi Jewish Women

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Expression mRNA data from mouse blood samples measured using the NanoString nCounter platform

Project description:Background: The diagnosis of Parkinson’s disease (PD) is usually not established until advanced neurodegeneration leads to clinically detectable symptoms. Previous blood PD transcriptome studies show low concordance, possibly due to the use of microarray technology, which has high measurement variation. The Leucine-rich repeat kinase 2 (LRRK2) G2019S mutation predisposes to PD. Using preclinical and clinical studies, we sought to develop a novel statistically motivated transcriptomic-based approach to identify a molecular signature in the blood of Ashkenazi Jewish PD patients including LRRK2 mutation carriers. Methods: Using a digital gene expression platform to quantify 175 mRNA markers with low coefficients of variation (CV), we first compared whole blood transcript levels in mouse models 1) over-expressing wild-type (WT) LRRK2, 2) overexpressing G2019S LRRK2, 3) lacking LRRK2 (knockout), 4) and in WT controls. We then studied an Ashkenazi Jewish cohort of 34 symptomatic PD patients (both WT LRRK2 and G2019S LRRK2) and 32 asymptomatic controls. Results: The expression profiles distinguished the 4 mouse groups with different genetic background. In patients, we detected significant differences in blood transcript levels both between individuals differing in LRRK2 genotype and between PD patients and controls. Discriminatory PD markers included genes associated with innate and adaptive immunity and inflammatory disease. Notably, gene expression patterns in L-DOPA-treated PD patients were significantly closer to those of healthy controls in a dose-dependent manner. Conclusions: We identify whole blood low CV mRNA signatures correlating with LRRK2 genotype and with PD disease state. This approach may provide insight into pathogenesis and a route to early disease detection.

2015-10-17 | GSE62470 | GEO

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