Contents 1 CBC Copy Number Variation Project 2 General Information 3 Analysis Tools 4 Papers 5 Links

[edit] CBC Copy Number Variation Project

[edit] General Information

This wiki page will contain information pertaining to research in DNA copy number variation performed by the Computational Biology Lab (CBC).

[edit] Analysis Tools

MATLAB Bioinformatics Toolbox

Using the MATLAB bioinformatics toolkit to detect DNA copy number variation

[edit] Papers

For now, here are links to recommended papers and articles for learning more about DNA copy number variation.

• Daruwala et al., "A versatile statistical analysis algorithm to detect genome copy number variation."

• Shah et al., "Integrating copy number polymorphisms into array CGH analysis using a robust HMM."

mentioned another dataset MCL with ground truth(32K clones cover the whole genome. at http://www.bccrc.ca/images/cg/wanlam_mcl_sd.txt, the original paper by de Leeuw et al http://hmg.oxfordjournals.org/cgi/content/full/13/17/1827). By looking at the figure 3 in Shah et al, all the methods have some significant false positives. the results are bad in terms of breakpoint detection.

• Wang et al., "PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data."

• Ventrakaman et al., "A faster circular binary segmentation algorithm for the analysis of array CGH data."

• Olshen et al., "Circular binary segmentation for the analysis of array-based DNA copy number data."

• Willenbrock et al., "A comparison study: applying segmentation to array CGH data for downstream analyses."

• "Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes." This paper talks about CNV probes.

[edit] Links

• The Copy Number Variation (CNV) Project at Sanger, including raw and preprocessed HapMap samples