The sequence windows were subsequently filtered by removing windows completely encompassed by other windows, and sequence fragments were trimmed to remove flanking regions corresponding to negative probes.
For population 4 clone 1, we identified 17 split-reads mapping within the 893 bp windows encompassing the left junction and 18 split-reads within the 507 bp window for the right junctions identified by aCGH.
As a control, we also constructed an artificial annotation (Random) comprised of 31,000 randomly selected, 10 Kb genomic windows encompassing ∼10% of the genome.
Next, the z scores of the genomic windows encompassing CNVs shared by OFC patients were calculated.
The variability distributions of windows encompassing deletions and duplications are in both cases slightly shifted towards increased variability.
For two deleted (USP14 and ZMYND11) and four duplicated (RIC8A, PSMD13, SIRT3 and YES1) novel candidates, the variability score was not assessable due to the exclusion of the windows encompassing telomeric sequences.
The windows encompassing assembly gaps (telomeres and short arm of chr13, 14, 15, 21, 22), alternative haplotype sequences (e.g., chr6_ssto_hap7) and random contigs (e.g., chr4_gl000193_random) reported in the UCSC Genome Browser archive (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/) were removed to avoid bias.
For any sequence, the %MinMax output is presented as a series of sliding windows (1 to z, 2 to z+1, etc).. Specific codon positions reported in the text represent the midpoint of the window (for example, "406" represents the window encompassing codons 397 414).
(a) Data acquired in a window centered on the lower photopeak; (b) data acquired in a wide window encompassing both the lower photopeak and the coincidence sum peak; and (c) data acquired in a window including only the coincidence sum peak.
In addition, a coincidence sum peak window (47 to 71 keV) and a wide window encompassing both peaks (16 to 74 keV) were acquired.
