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Implications for health and disease in the genetic signature of the Ashkenazi Jewish population

Saurav Guha1, Jeffrey A Rosenfeld1, Anil K Malhotra12345, Annette T Lee6, Peter K Gregersen56, John M Kane12345, Itsik Pe'er7, Ariel Darvasi8 and Todd Lencz12345*

Author Affiliations

1 Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore - Long Island Jewish Health System, 75-59, 263rd St Glen Oaks, NY 11004, USA

2 Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA

3 Department of Psychiatry and Behavioral Science, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Ave, Bronx, NY 10461, USA

4 Department of Psychiatry, Hofstra University School of Medicine, Hempstead, NY 11549, USA

5 Department of Molecular Medicine, Hofstra University School of Medicine, Hempstead, NY 11549, USA

6 Robert S Boas Center for Human Genetics and Genomics, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA

7 Department of Computer Science, Columbia University, 500 W 120th St New York, NY 10027, USA

8 Department of Genetics The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904, Israel

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Genome Biology 2012, 13:R2  doi:10.1186/gb-2012-13-1-r2

Published: 25 January 2012

Additional files

Additional file 1:

K = 1 to 15 with corresponding cross validation (CV) score and standard error for 1,312 AJ individuals and HGDP individuals. Europeans (n = 159), Middle Easterners (n = 163), and Central/South Asians (n = 177).

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Additional file 2:

List and annotation of 13,841 significant (P < 10-6) SNPs on Ashkenazi-specific principal component, 1,357 SNPs that were used in the initial ancestry informative marker (AIM) analysis, 103 AJ specific AIMs, 417 coding variants from 13,841 SNPs, Genetic Association Database (GAD) annotation.

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Additional file 3:

ADMIXTURE analysis for ancestry estimation of Ashkenazi Jewish (AJ) population with seven global population groups derived from the HGDP at K = 2 through K = 14. Each individual is represented by a thin vertical line, which is partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters. Black lines separate individuals of different population groups based on geography and ethnicity. Geographical population groups are labeled below the figure.

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Additional file 4:

Principal component analysis (PC1 versus PC2) of 1,312 Ashkenazi Jewish (AJ) subjects combined with Europeans (EU), Middle Easterners (ME), and Central/South Asians (CSA). The x-axis represents the eigenvalue for principal component 1 (PC1) and the y-axis represents the eigenvalue for principal component 2 (PC2). Blue represents AJ, green represents EU, orange represents ME and black represents CSA.

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Additional file 5:

Intra-population principal component analysis of Ashkenazi Jewish (AJ) individuals with cluster 3 (C3) scores > 0.475 derived from ADMIXTURE analysis. The x-axis represents the eigenvalue for principal component 1 (PC1) and the y-axis represents the eigenvalue for principal component 2 (PC2). Different colors represent different geographical origin of Ashkenazi Jewish (AJ) individuals.

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Additional file 6:

Manhattan plot for quantitative genome wide association for Ashkenazi Jewish (AJ) individuals based on cluster 3 (C3) scores derived from ADMIXTURE analysis. The x-axis represents the chromosomes and the y-axis represents -log10 P-values of significance.

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Additional file 7:

Manhattan plot for quantitative genome wide association for Ashkenazi Jewish (AJ) individuals based on principal component 1 (PC1) of intra-population principal component analysis with cluster 3 (C3) scores > 0.475 derived from ADMIXTURE analysis. The x-axis represents the chromosomes and the y-axis represents -log10 P-values of significance.

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Additional file 8:

Principal component analysis of Need et al. [21]cohort with designed Ashkenazi Jewish (AJ) specific ancestry informative markers. The numbers and the corresponding colors represent the degree of self-reported Ashkenazi admixture.

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Additional file 9:

Principal component analysis of all 1,312 AJ individuals with European HGDP individuals for 89 ancestry informative markers. Red indicates AJ individuals with C3 admixture score > 0.475, blue indicates AJ individuals with C3 admixture score < 0.475 and green indicates HGDP European individuals.

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