Table 1. Detection in 17 patients suggestive of LFS of 21 germline CNVs not recorded in the DGV.
| Cytoband | CNV coordinates (hg18)a | CNV type | Protein-coding genes and microRNAs involvedb | CNV size (kb) | Patient ID | |
|---|---|---|---|---|---|---|
| 1 | p36.12 | chr1:23244421–23562102 | del | KDM1A (part), LUZP1, HTR1D, HNRNPR, ZNF436 (part) | 318 | 53 |
| 1 | q41 | chr1:218356562–218359749 | del | IARS2 (part), MIR215, MIR194-1 | 4 | 16, 57 |
| 2 | p21 | chr2:42591803–42763199 | dup | MTA3 (part) | 172 | 33 |
| 2 | p15 | chr2:61978338–62094667 | del | COMMD1 (part) | 116 | 14 |
| 3 | p14.1 | chr3:65642102–65889226 | del | MAGI1 (part) | 248 | 53 |
| 3 | q13.13 | chr3:110094154–110495138 | dup | GUCA1C, MORC1, DPPA2 (part) | 401 | 53 |
| 3 | q29 | chr3:198768821–198969885 | dup | BDH1 (part), KIAA0226, MIR922, FYTTD1 (part) | 201 | 6 |
| 4 | q32.2 | chr4:162313725–162948651 | dup | FSTL5 (part) | 635 | 17 |
| 5 | p13.3 | chr5:34024123–34126697 | del | AMACR, C1QTNF3 | 103 | 2 |
| 5 | q13.2 | chr5:68405282–68519258 | del | SLC30A5, CCNB1 | 114 | 38 |
| 5 | q14.1 | chr5:79525024–79740886 | dup | SERINC5 (part), SPZ1, ZFYVE16 (part) | 216 | 38 |
| 6 | p21.31 | chr6:34977196–35058894 | del | ANKS1A (part) | 82 | 60 |
| 6 | p12.3 | chr6:47509689–47664601 | del | CD2AP (part) | 155 | 27 |
| 6 | q14.1 | chr6:80910016–81553302 | dup | BCKDHB (part) | 642 | 5 |
| 7 | q22.1 | chr7:98286465–98454581 | dup | TMEM130 (part), TRRAP | 169 | 63 |
| 9 | q22.32 | chr9:96591859–96705414 | del | C9orf3 (part) | 114 | 55 |
| 11 | p15.5 | chr11:200300–332720 c | dup | RIC8A, SIRT3, PSMD13, NLRP6, ATHL1, IFITM5, IFITM2, IFITM1, IFITM3 | 133 | 17 |
| 11 | p13 | chr11:32989228–33445279 | dup | DEPDC7, TCP11L1, CSTF3, HIPK3 | 456 | 24 |
| 11 | q13.2 | chr11:68358122–68452839 | dup | CPT1A (part), MRPL21, IGHMBP2 (part) | 95 | 33 |
| 21 | q22.3 | chr21:42945519–43196797 | dup | PDE9A, WDR4, NDUFV3 (part) | 252 | 54 |
| X | q13.1 | chrX:71771657–71876745 | dup | PHKA1 (part) | 105 | 19 |
Abbreviations: CNV, copy number variation; DGV, Database of Genomic Variants; del, deletion; dup, duplication; LFS, Li-Fraumeni syndrome; part, partial rearrangement of the gene.
a
Defined according to the genomic positions of the first oligonucleotides of the first and last deviated probes, respectively.
b
Genes in bold are involved in chromatin remodelling.
c
On chromosome 11, the first telomeric probe starts on genomic position 2 00 300, consequently no information before this position is available.