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Open Access Research article

Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates

Jeana T DaRe1, Drew P Kouri12, Peter A Zimmerman1* and Peter J Thomas2345*

Author Affiliations

1 Center for Global Health and Disease, Case Western Reserve University School of Medicine, Wolstein Research Building, 4-125, Cleveland, Ohio 44106-7286, USA

2 Department of Mathematics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7058, USA

3 Department of Biology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7058, USA

4 Department of Cognitive Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7058, USA

5 Department of Neuroscience, Oberlin College, 119 Woodland Street, Oberlin, OH, 44074, USA

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BMC Genetics 2010, 11:57  doi:10.1186/1471-2156-11-57

Published: 29 June 2010

Additional files

Additional file 1:

Primers and PCR amplification conditions for additional SNPs. Primers and conditions for PCR amplification of additional SNPs utilized in assessing the sensitivity of the histogram segmentation analysis and for examining the diagnostic threshold variability.

Format: PDF Size: 20KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Plot of chr1SNP fluorescence data with conventional Cartesian thresholds and thresholds generated by the polar coordinate histogram method. Samples (n = 357) were genotyped at Chr1SNP using the LDR-FMA method. Allele calls were then made using both the conventional methods (3× standard deviations above the mean of known negative samples) and by the polar coordinate histogram method. Conventional thresholds are indicated by the red dotted line, and the polar thresholds are indicated by the black solid line with the black dotted line showing the 95% confidence intervals.

Format: PDF Size: 49KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Plot of chr9SNP fluorescence data with conventional Cartesian thresholds and thresholds generated by the polar coordinate histogram method. Samples (n = 357) were genotyped at Chr9SNP using the LDR-FMA method. Allele calls were then made using both the conventional methods (3× standard deviations above the mean of known negative samples) and by the polar coordinate histogram method. Conventional thresholds are indicated by the red dotted line, and the polar thresholds are indicated by the black solid line with the black dotted line showing the 95% confidence intervals.

Format: PDF Size: 47KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Ligation detection reaction primers for genotyping additional SNPs. Primers for the LDR-FMA diagnosis of additional SNPs utilized in assessing the sensitivity of the histogram segmentation analysis and for examining the diagnostic threshold variability.

Format: PDF Size: 20KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data