Table 3. Results from multiple CNV calling algorithms and qPCR validation of CNVRs on chromosome 6p21.3 and chromosome 11q14.3.
| Cytoband | Risk allele | CNV calling algorithm | CNVR boundaries | Concordance rate with qPCR | Genes overlapped |
|---|---|---|---|---|---|
| Chr 6p21.3 | CN = 1 | PennCNV | Chr6:31468233–31562343 | 99.75% | MICA, HCP5, HCG26 |
| cnvPartition | Chr6:31468233–31571696 | 99.50% | |||
| Chr 11q14.3 | CN = 3 | PennCNV | Chr11:88309000–88433828 | 91.67% | GRM5 |
| cnvPartition | Chr11:88336310–88433828 | 90.15% |
MICA (MHC class I polypeptide-related sequence A); HCP5 (HLA complex 5); HCG26 (HLA complex group 26); GRM5 (Metabotropic glutamate receptor 5)