File S1 - Genome-Wide Identification of Somatic Aberrations from Paired Normal-Tumor Samples

File S1 contains the following files. Text S1. Detailed description of statistical methods in GIANT. Figure S1. Comparison of BAF signals in two normal replicates on different chromosomes. Figure S2. Visualized genomic aberrations for replicate pairs. Figure S3. Comparison of estimated normal cell contamination levels and tumor average copy number for simulated tumor SNP arrays. Figure S4. Comparison of specificity for identifying normal regions in simulated tumor samples. Figure S5 Sensitivities for distinguishing aberrations from normal regions by five different methods. Figure S6. Theoretical and real mean values of LRR/BAF in different scenarios. Figure S7. Aberrations in chromosome 6 of breast cancer cell line CRL-2324. Figure S8. Aberrations in chromosome 13 of breast cancer cell line CRL-2324. Figure S9. Comparison of results for breast cancer cell line CRL-2324 by different methods. Figure S10. Comparison of self-consistency for GIANT and GPHMM using dilution series data. Figure S11. Visualized results of GIANT for replicate breast cancer sample. Figure S12. Detection of germline homozygous deletion of ADAM3A gene in diluted breast tumor sample 7207. Figure S13. Comparison of the results for chromosome 8 of breast tumor 7207 by different methods. Figure S14. Significance test of genome-wide somatic amplification and LOH for urothelial cancer samples. Figure S15. Significance test of genome-wide somatic deletion for urothelial cancer samples. Figure S16. Box plots of summarized results for 112 breast cancer samples. Figure S17. Distinct patterns of genome-wide copy number profiles identified in two groups of tumors. Figure S18. Genome-wide CNA profiles of breast cancer samples. Figure S19. Frequency plot of genomic-wide CNA for 112 breast cancer samples. Figure S20. Frequency plot of genomic-wide LOH for 112 breast cancer samples. Table S1. Detailed information of hidden states in PSHMM. Table S2. Parameters estimated by GIANT on replicate SNP arrays. Table S3. Details of estimated parameters from paired methods. Table S4. Genomic regions used for illustrating real distributions of LRR/BAF mean values. This file contains a supplementary table with detailed information of 12 genomic regions, including chromosome number, start and end position, aberration type, copy number and mean values of LRR/BAF signal in dilution series. Table S5. Genomic aberrations in known abnormal regions implicated in urothelial cancer. Table S6. Detailed results for significance test of genome-wide aberration in 112 breast cancer samples. This table contains detailed information of significant aberrant regions identified by GIANT.
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