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Open Access Methodology article

Reconstructing DNA copy number by joint segmentation of multiple sequences

Zhongyang Zhang1, Kenneth Lange2 and Chiara Sabatti3*

Author Affiliations

1 Department of Statistics, University of California, Los Angeles, CA, USA

2 Department of Human Genetics, Biomathematics and Statistics, University of California, Los Angeles, CA, USA

3 Department of Health Research and Policy and Statistics, Stanford University, Stanford, CA, USA

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BMC Bioinformatics 2012, 13:205  doi:10.1186/1471-2105-13-205

Published: 16 August 2012

Additional files

Additional file 1:

Supplementary Text. Specification of surrogate function, justification of choice of tuning parameters, details of calling procedure.

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Additional file 2:

Table S1. Regions of allelic imbalance imputed to the HapMap sample NA06991.

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Additional file 3:

Table S2. Speed comparison of three methods: GFL, BAFsegmentation and PSCN.

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Additional file 4:

Table S3. Sample information and reference CNV regions summarized for each sample by their types and sizes.

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Additional file 5:

Table S4. Summary of results for four real samples under different CNV analyses.

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Additional file 6:

Figure S1. Visualization of pedigree-wise CNV analysis results of Chromosome 8 data in the bipolar disorder study. In the main body of the plot, CNVs estimated for each individual are marked by small segments with color code: CN= 0 in blue, CN=1 in light blue, CN=3 in red and CN=4 in brown. Each subject is a row, each SNP a column. Subjects belonging to the same pedigree are stacked together. The pedigree names are indicated on the left-hand side with the number of pedigree members included in parentheses. On the right-hand side, the barplot represents the number of CNVs detected per subject. Two shades of green are switched alternately to indicate the pedigree to which the subject belongs. At the bottom, the gray histogram shows the GC content along the chromosome. Coordinated with the representation of CNVs in the main body, the green histogram counts the frequency of CNVs among the subjects represented. Vertical dotted line marks the centromere.

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