DNA copy numbers and the Circular Binary Segmentation Algorithm

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CBS ASCN Allele Specific Copy Number • Traditional methods measure the sum of copy numbers of the parental chromosomes. • SNP arrays can be used for allele specific copy numbers. • Total copy number of 2 can be from AA, AB or BB. • Data from Molecular Inversion Probes (MIPs) SNP genotyping/copy number technology from Affymetrix. • Intensities for the two alleles converted to copy numbers. 31
CBS MIPs Example ASCN Allele A copy number 0 1 2 3 4 5 6 Allele B copy number 0 1 2 3 4 5 6 0 500 1000 1500 2000 2500 3000 Genomic Position (Mb) 0 500 1000 1500 2000 2500 3000 Genomic Position (Mb) Sum of copy numbers 0 1 2 3 4 5 6 0 500 1000 1500 2000 2500 3000 Genomic Position (Mb) 32
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 and 28: CBS Lung Project Example -./0123" &
Page 29 and 30: CBS Copy Number Variation TCGA 28
Page 31: CBS Multi platform data wCBS Weight
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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