DNA copy numbers and the Circular Binary Segmentation Algorithm

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CBS Lung Project Example • No obvious focal gain or loss stood out • Clusters had weak association with EGFR but not KRAS • Incorporated information from U133 expression arrays • Potentially interesting gene DUSP4 Acknowledgements Marc Ladanyi, William Gerald, Valerie Rusch, Stephen Broderick, Cameron Brennan, Dhananjay Chitale, Bhuvanesh Singh <strong>and</strong> o<strong>the</strong>rs. 27
CBS Copy Number Variation TCGA 28
Page 1 and 2: DNA copy numbers and the Circular B
Page 3 and 4: CBS Background Comparative genomic
Page 5 and 6: CBS Example Lung cancer BAC array w
Page 7 and 8: CBS Analysis Overall plan In sample
Page 9 and 10: CBS Change-points Methods Let Z 1 ,
Page 11 and 12: CBS Binary Segmentation Fails Metho
Page 13 and 14: CBS Circular Binary Segmentation Me
Page 15 and 16: CBS More on CBS Example −2 −1 0
Page 17 and 18: CBS Hybrid p-value Faster CBS Test
Page 19 and 20: CBS Stopping rule Faster CBS • da
Page 21 and 22: CBS Performance gain Faster CBS 100
Page 23 and 24: CBS Lung Project Example 22
Page 25 and 26: CBS Lung Project Example 24
Page 27: CBS Lung Project Example -./0123" &
Page 31 and 32: CBS Multi platform data wCBS Weight
Page 33 and 34: CBS MIPs Example ASCN Allele A copy
Page 35 and 36: CBS Allele A vs B ASCN Homozygotes
Page 37 and 38: CBS Allele A vs B ASCN Step 3: Test
Page 39 and 40: CBS Reconstruction ASCN Allele A co
Page 41 and 42: CBS Equality of parental CN ASCN Ch
Page 43 and 44: CBS References 1. Autio, R. et al.

DNA copy numbers and the Circular Binary Segmentation Algorithm

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