1. 1 Example of HMMs: copy number data

2. 2 DNA copy number is the number of copies of a genomic segment present in the cell. Copy numbers are measured in high-throughput fashion using microarray techniques. Test and reference (assumed to have copy number 2) samples are labeled differently and hybridized together. Under ideal circumstances, the intensity of an array element is linearly proportional to the abundance of the corresponding DNA sequence. Log2 ratios of test and reference intensities reflect the relative copy number in the test sample compared to that in the reference sample. Data often modeled by HMMs.

3. 3 Males have only one copy of the X-chromosome. 1 2 3 4 5 6 7 8 ……. X Log 2 -ratio’s plotted against the genomic order of clones.

4. 4 Deletion on 5p

5. 5 Copy number of each genomic segment unknown.

6. 6 After smoothing (de-noising) copy numbers still unknown.