Figure 1. (a) Individual ratios of IPM to IMM (y-axis) plotted against genomic address (x-axis) reveal noise that masks deletions, hindering discovery. (b) The problem of identifying deleted regions is dramatically facilitated by investigating sets of tandem values using the TSTEP algorithm, which yields P values (y-axis) for each ratio. The x-axis is the same portion of the genome as in a. (c) Corrected P values, which account for testing more than 111,000 probe-pair hybridization ratios, are plotted against genomic address. Black bars indicate the regions of sequence-confirmed deletion. Orange bars indicate the regions predicted by a heuristic to assemble putative deletion intervals from P values calculated by TSTEP.

Figure 2. Longer deletions are not a great challenge to identify: Plotted against the genomic address (x-axis) the y-axis values are (a) IPM/IMM, (b) TSTEP-calculated P values, (c) P values corrected for multiple tests. The interval of the deletion is closely predicated by our assembly to be 1695829-1708776 (length 12948). The sequence confirmed interval is 1696017-1708750 (length 12734).

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