some centromeric and telomeric regions are not well mapped, and this can potentially result in CNV-calling errors in these regions (Dr. Kai Wang, personal communication). Also, genomic regions coding for immunoglobulin genes have previously been shown to be potential sites of false-positive PennCNV calls [62]. Our own research has shown that calls in both of these types of region differed significantly depending on the sample type used for DNA extraction (significant difference p<10−10 for deletion and/or duplication frequencies between samples genotyped on DNA extracted from blood or saliva, data not shown). We therefore excluded any CNV that overlapped any of the following regions by 50% or more of its length: chr2: 87.0–92.0, chr14: 18–23.6 Mb, chr14: 104.5–106.5 Mb, chr15: 17.0–21.0, chr16: 31.8–36.0 Mb, chr22: 20.5–21.8 Mb (immunoglobin regions); chr1:0–4 Mb, 240–247 Mb; chr2: 87.0–92.0 Mb; chr4: 0–1.43 Mb, 48.75–49 Mb, 190.7–191.3 Mb; chr7:0–200 kb, 56.5–62.5 Mb; chr8: 39–45 Mb, 145–146.3 Mb; chr9: 44.5–70.1 Mb; 138–140.2 Mb; chr10: 38.5–42 Mb, 134–135.4 Mb; chr11: 0–1.8 Mb; chr14: 18–23.6 Mb, 104.5–106.5 Mb; chr15: 17.0–21.100–100.3 Mb; chr16: 0–2.1 Mb, 31.8–36.0 Mb, 86.6–88.9 Mb; chr17:0–1 Mb, 76.5–78.8 Mb; chr18: 14–16 Mb, 75.5–76 Mb; chr19: 0–2.1 Mb, 25.7–28.3 Mb, 61.5–62.5 Mb; chr20: 25.7–28.3 Mb, 61.5–62.5 Mb;
