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Open Access Highly Accessed Research article

Copy number variation in African Americans

Joseph P McElroy1, Matthew R Nelson2, Stacy J Caillier1 and Jorge R Oksenberg1*

Author Affiliations

1 Department of Neurology, University of California, San Francisco, CA, USA

2 GlaxoSmithKline, Research Triangle Park, NC, 27709, USA

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BMC Genetics 2009, 10:15  doi:10.1186/1471-2156-10-15

Published: 24 March 2009

Additional files

Additional file 1:

qPCR supplemental methods. Additional information on the qPCR methods used in this manuscript.

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Open Data

Additional file 2:

Replication of CNV analysis in a single individual. A. CNV calls in replicate individual. A green bar above the line for an individual indicates a duplication at that region in the genome, and a red bar below indicates a deletion at that region in the genome. B. Log R ratios for SNPs on chromosome 21. Arrows indicate the region designated as deleted in the first replicate, but not in the second replicate.

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Open Data

Additional file 3:

Distribution of the numbers of CNV calls per individual before (A) and after (B) removing outliers. The upper panels of each figure are box and whiskers plots of the data. Each box indicates the interquartile range, each line across the boxes indicates the median, the diamonds indicate the means and 95% confidence intervals, and the whiskers indicate the upper quartile + 1.5 × interquartile range (right side of boxes) and the lower quartile – 1.5 × interquartile range (left side of boxes).

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Additional file 4:

CNVs identified in more than a single individual. Location, types of CNV events, and within population frequencies of CNVs identified in two or more individuals. Events (relative to reference population): HDel = two copies decrease, Del = one copy decrease, Dup = one copy increase, HDup = two or more copy increase.

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Additional file 5:

qPCR of chr. 14 replicates (red cell line, blue whole blood). Bar chart of delta Cts for ten individuals with both whole blood and cell line derived DNAs for the chromosome 14q11 cell line associated CNV. Red bars are cell line DNAs, blue bars are whole blood DNAs. In every individual, the cell line DNAs have a lower delta Ct. Primer sequence for chromosome 14 qPCR: forward-5' CAC TGG CAT TTG GTA TCG T 3', reverse-5' CCC AAA GTG AAA CGT ATT 3'.

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Open Data