Table 1.
Copy number differences in 1q21 between the GRCh37 build and the CHM1 assembly
| Gene name | GRCh37/hg19 | CHM1 assembly |
|---|---|---|
| FAM72D | 1 | 2 |
| FCGR1A | 1 | 2 |
| HYDIN | 0 | 1 |
| NBPF16 | 1 | 0 |
| NBPF24 | 1 | 0 |
| NBPF25 | 1 | 0 |
| NBPF26 | 0 | 1 |
| NOTCH2NL | 1 | 3 |
| PDE4DIP | 1 | 3 |
| PDZK1 | 3 | 2 |
| SEC22B | 1 | 3 |
| SRGAP2 | 1 | 2 |
| Total 1q21 DUF1220 | 242 | 238 |
| DUF1220 CON1 | 22 | 17 |
| DUF1220 CON2 | 13 | 11 |
| DUF1220 CON3 | 12 | 11 |
| DUF1220 HLS1 | 60 | 62 |
| DUF1220 HLS2 | 68 | 69 |
| DUF1220 HLS3 | 64 | 66 |
| DUF1220 Triplets | 51 | 59 |
Table 1 describes changes in copy number between the GRCh37 and new CHM1 assemblies. The majority of non-DUF1220 changes were gain in copy, with 8 genes previously under represented in GRCh37. Three NBPF genes are no longer present, although DUF1220 numbers remained close to the same with DUF1220 copies being mostly redistributed among the remaining NBPF genes. This may indicate that the gene loss is an artifact of misassembly rather than true gene copy number differences. Numbers do not include the additional DUF1220 domains and NBPF genes added to the 1p11.2 region as a result of the human-specific 1q21.2 segmental duplication described in the text.