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Open AccessHighly AccessResearch article

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

Adam B Olshen1 email, Bert Gold6 email, Kirk E Lohmueller8 email, Jeffery P Struewing7 email, Jaya Satagopan1 email, Stefan A Stefanov6 email, Eleazar Eskin9 email, Tomas Kirchhoff3 email, James A Lautenberger6 email, Robert J Klein4 email, Eitan Friedman10 email, Larry Norton3 email, Nathan A Ellis11 email, Agnes Viale5 email, Catherine S Lee2 email, Patrick I Borgen2 email, Andrew G Clark8 email, Kenneth Offit3 email and Jeff Boyd2,3 email

1Departments of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

2Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

3Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

4Programs in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

5Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

6Laboratories of Genomic Diversity, National Cancer Institute, Bethesda, MD, USA

7Population Genetics, National Cancer Institute, Bethesda, MD, USA

8Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

9Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA

10Chaim Sheba Medical Center, Tel-Hashomer, and Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel

11Department of Medicine, University of Chicago, Chicago, IL, USA

author email corresponding author email

BMC Genetics 2008, 9:14doi:10.1186/1471-2156-9-14

Published: 5 February 2008

Additional files

Additional File 1:

Table S1. Distribution of SNPs on each chromosome arm

Format: EPS Size: 267KB Download file

Additional File 2:

Figure S1.Percentage of No Calls per SNP by array type

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Additional File 3:

Figure S2. Percentage of No Calls per SNP by array type for SNPS with completion rate of greater than 99.6%

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Additional File 4:

Figure S3. Percentage of No Calls per SNP by array type in CEU

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Additional File 5:

Figure S4. Percentage of No Calls per SNP by array type in CEU

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Additional File 6:

Figure S5. Analysis of Hardy-Weinberg Departures

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Additional File 7:

Figure S6. A sliding window plot of average r2 values across chromosome 22. For this analysis, 1.7 Mb windows with a 1.6 Mb overlap were utilized.

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Additional File 8:

Figure S7. The proportion of SNPs with D' = 1 as a function of distance between SNPs, with data drawn from chromosome 1.

Format: EPS Size: 227KB Download file


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