Mapping Tumor-Suppressor Genes with Multipoint Statistics from Copy-Number– Variation Data  Iuliana Ionita, Raoul-Sam Daruwala, Bud Mishra  The American Journal of Human Genetics  Volume 79, Issue 1, Pages 13-22 (July 2006) DOI: 10.1086/504354 Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 1 Prior score as a function of the length of the interval. A priori, shorter intervals receive higher weight than larger intervals. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 2 The tail probability P(Sw⩾k) for different numbers of breakpoints k (0≤k≤20) and different window sizes w. Sw is the maximum number of breakpoints in a window of length w. The total number of breakpoints in the region is N=50. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 3 Depiction of the simulation process described in the text. A single precancerous cell (both copies of the TSG are nonfunctional) starts multiplying indefinitely. Over time, the new progenitor cells also incur other independent damage (i.e., deletions). The tumor sample that we collected comprised different tumor cells and some normal cells. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 4 Box plots of the Jaccard measure of overlap for each of the six models (table 1). Fifty data sets are simulated according to each model, and the distribution of the resulting 50 overlap measures is depicted in each box plot. Average intermarker distance is 10 kb. A, LR. B, Max. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 5 Box plots of the sensitivity measure for each of the six models (table 1). Fifty data sets are simulated according to each model, and the distribution of the resulting 50 sensitivity measures is depicted in each box plot. Average intermarker distance is 10 kb. A, LR. B, Max. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 6 Box plots of the Jaccard measure of overlap for each of the six models (table 1). Fifty data sets are simulated according to each model, and the distribution of the resulting 50 overlap measures is depicted in each box plot. Average intermarker distance is 20 kb. A, LR. B, Max. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 7 Box plots of the sensitivity measure for each of the six models (table 1). Fifty data sets are simulated according to each model, and the distribution of the resulting 50 sensitivity measures is depicted in each box plot. Average intermarker distance is 20 kb. A, LR. B, Max. The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 8 The histogram for the log2 ratio values for all SNPs in all 70 tumors, together with an empirical null density fitted to the histogram: N(μˆ,σˆ2). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 9 Copy-number histogram for individual samples (samples 1–16). Overlaid is the fitted empirical null density N(μˆ0,σˆ02). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 10 Copy-number histogram for individual samples (samples 17–32). Overlaid is the fitted empirical null density N(μˆ0,σˆ02). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 11 Copy-number histogram for individual samples (samples 33–48). Overlaid is the fitted empirical null density N(μˆ0,σˆ02). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 12 Copy-number histogram for individual samples (samples 49–64). Overlaid is the fitted empirical null density N(μˆ0,σˆ02). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 13 Copy-number histogram for individual samples (samples 65–70). Overlaid is the fitted empirical null density N(μˆ0,σˆ02). The American Journal of Human Genetics 2006 79, 13-22DOI: (10.1086/504354) Copyright © 2006 The American Society of Human Genetics Terms and Conditions