Open Access Research article

Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

Liran I Shlush1, Sivan Bercovici2, Walter G Wasser3, Guennady Yudkovsky1, Alan Templeton4, Dan Geiger2 and Karl Skorecki1*

Author Affiliations

1 Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology and Rambam Medical Center, Haifa 31096, Israel

2 Faculty of Computer Science, Technion - Israel Institute of Technology, Haifa 32000, Israel

3 Cabrini Medical Center New York, N.Y., USA

4 Department of Biology, Washington University, St. Louis, Mo, USA

For all author emails, please log on.

BMC Medical Genomics 2010, 3:47  doi:10.1186/1755-8794-3-47

Published: 18 October 2010

Additional files

Additional file 1:

Expected Mutual Information (EMI) ancestry informative markers screening panel. The AIMs were chosen according to EMI enrichment algorithm. 2016 markers were chosen.

Format: TXT Size: 45KB Download file

Open Data

Additional file 2:

Directed enriched panel chromosome 22. Enrichment of the screening panel was applied to chromosome 22. All additional AIMs were chosen according to EMI algorithm. 39 additional AIMs were added. For the sub-analysis of the effect of ancestral LD markers which were 50 kB apart from each other or less were omitted from the analysis. In the status column 1 = AIMs from screening panel 2 = AIMs from directed enriched panel. 3 = AIMs from directed enriched panel which were omiited due to a distance of less than 50 kB from other markers.

Format: TXT Size: 2KB Download file

Open Data

Additional file 3:

Distribution of Fisher Information Content (FIC) along the genome for the 2016 markers of the screening panel. For each chromosome the mean FIC (2 red circles), two standard deviations of the FIC value (dashed line) and outliers of AIMs with high FIC (red plus) are presented.

Format: DOC Size: 41KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Distribution of expected mutual information (EMI) score along the genome for the 2016 markers of the screening panel. The Y axis for each chromosome represents the EMI score (the information of a set of markers regarding the ancestry of a chromosomal position, the X axis represents the genetic position of all AIMs in the screening panel in Cm according to the Marshfield genetic map.

Format: DOC Size: 192KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Differences in the distribution of FIC values between chromosome 22 and other chromosomes. For each chromosome the mean FIC (circles) and the range of FIC (horizontal lines) are displayed. P values represent differences in the distribution of FIC as was calculated by pairwise Kolmogorov-Smirnov test.

Format: DOC Size: 110KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Chromosome 15 LGS and - LOG (P) scores of the screening panel by ANCESTRYMAP and ADMIXMAP respectively. LGS and - LOG (P) are provided by ANCESTRYMAP and ADMIXMAP respectivly for AIMs along chromosome 15. Using the screening panel a total of 576 ESKD AA patients (Red line) were genotyped of whom 299 ESKD patients did not have diabetes mellitus (NonDM) (Blue line).

Format: DOC Size: 143KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data