Table 11.
Summary of imprinted genes identified by WGS
| Imprinted genes | Status | Expressed allele | LiPSC-ER2.2 | LiPSC-GR1.1 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Allelic depth | SNP-HET | INS-HET | DEL-HET | Allelic depth | SNP-HET | INS-HET | DEL-HET | |||
| ABCC9 | Predicted | Maternal | 27.4 | 50 | 2 | 3 | 26.0 | 54 | 5 | 5 |
| ABCG8 | Predicted | Maternal | 27.0 | 73 | 4 | 5 | 25.8 | 65 | 3 | 3 |
| ACD | Predicted | Maternal | 26.5 | 2 | 23.0 | 1 | ||||
| ADAMTS16 | Predicted | Maternal | 28.0 | 254 | 20 | 23 | 26.0 | 319 | 20 | 24 |
| AIM1 | Imprinted | Paternal | 29.3 | 82 | 4 | 10 | 23.4 | 54 | 4 | |
| ALDH1L1 | Predicted | Maternal | 25.5 | 148 | 3 | 9 | 25.9 | 47 | 6 | 6 |
| ANO1 | Imprinted | Maternal | 22.8 | 42 | 1 | 2 | 26.0 | 1 | ||
| APBA1 | Predicted | Paternal | 29.0 | 118 | 8 | 11 | 27.5 | 8 | 4 | |
| ATP10A | Imprinted | Maternal | 25.3 | 256 | 12 | 18 | 24.0 | 203 | 10 | 20 |
| B4GALNT4 | Predicted | Maternal | 24.3 | 17 | 2 | 1 | 23.4 | 21 | 3 | 1 |
| BLCAP | Imprinted | Isoform Dependent | 23.8 | 12 | 5 | 26.5 | 4 | 3 | 1 | |
| BMP8B | Predicted | Paternal | 23.4 | 3 | 22.4 | 10 | 2 | |||
| BTNL2 | Predicted | Maternal | 27.8 | 34 | 2 | 3 | 25.5 | 80 | 4 | 6 |
| C10orf91 | Predicted | Maternal | 25.5 | 1 | 35.0 | |||||
| C20orf20 | Predicted | Maternal | 25.4 | 14 | 1 | 2 | 27.8 | 14 | 1 | 2 |
| C9orf116 | Predicted | Paternal | 18.9 | |||||||
| C9orf85 | Predicted | Paternal | 27.9 | 3 | 26.8 | |||||
| CCDC85A | Predicted | Paternal | 27.1 | 245 | 19 | 14 | ||||
| CDH18 | Predicted | Paternal | 28.3 | 893 | 83 | 94 | 25.6 | 244 | 28 | 29 |
| CDK4 | Predicted | Maternal | 24.3 | 1 | 2 | 21.8 | 3 | 1 | ||
| CDKN1C | Imprinted | Maternal | 27.0 | 1 | 15.0 | |||||
| CHMP2A | Predicted | Maternal | 31.0 | 1 | 23.5 | 4 | ||||
| CHST8 | Predicted | Maternal | 24.3 | 96 | 4 | 6 | 25.1 | 121 | 8 | 8 |
| COL9A3 | Predicted | Maternal | 23.1 | 50 | 2 | 2 | 21.9 | 34 | 6 | |
| CPA4 | Imprinted | Maternal | 25.9 | 2 | 22.5 | 8 | 1 | 1 | ||
| CSF2 | Predicted | Maternal | 19.0 | 1 | 27.0 | |||||
| CYP1B1 | Predicted | Paternal | 26.1 | 1 | 28.4 | 9 | 2 | |||
| DDC | Imprinted | Isoform Dependent | 26.3 | 190 | 11 | 9 | 25.6 | 138 | 5 | 8 |
| DGCR6 | Imprinted | Random | 23.2 | 2 | 24.1 | 8 | 1 | |||
| DGCR6L | Imprinted | Random | 22.6 | 22.1 | 6 | 1 | ||||
| DIRAS3 | Imprinted | Paternal | 15.0 | 1 | ||||||
| DLGAP2 | Imprinted | Paternal | 25.7 | 4 | 2 | 24.8 | 21 | 2 | 1 | |
| DLK1 | Imprinted | Paternal | 20.4 | 9 | 1 | 21.7 | ||||
| DLX5 | Imprinted | Maternal | 25.3 | 1 | 1 | 1 | 23.7 | 1 | 1 | |
| DNMT1 | Imprinted | Paternal | 23.2 | 36 | 1 | 9 | 23.0 | 50 | 3 | 5 |
| DVL1 | Predicted | Maternal | 26.3 | 1 | 1 | 23.6 | 3 | 1 | ||
| E2F7 | Predicted | Maternal | 30.2 | 28 | 29.6 | 23 | 1 | |||
| EGFL7 | Predicted | Paternal | 21.2 | 1 | 22.1 | 23 | ||||
| EVX1 | Predicted | Paternal | 24.0 | |||||||
| FAM50B | Imprinted | Paternal | 31.0 | 1 | 25.0 | 1 | ||||
| FBRSL1 | Predicted | Maternal | 23.7 | 128 | 7 | 8 | 20.5 | 10 | 3 | |
| FERMT2 | Predicted | Paternal | 29.0 | 6 | 28.2 | 86 | 11 | 3 | ||
| FGFRL1 | Predicted | Maternal | 21.6 | 19 | 1 | 2 | 22.9 | 17 | 4 | 2 |
| FOXF1 | Predicted | Maternal | 18.6 | 2 | 1 | 1 | 22.5 | 1 | ||
| FOXG1 | Predicted | Paternal | 27.8 | 54 | 4 | 25.0 | ||||
| FUCA1 | Predicted | Paternal | 27.7 | 1 | ||||||
| GAREM | Predicted | Paternal | 27.9 | 36 | 4 | 3 | ||||
| GATA3 | Predicted | Paternal | 24.3 | 28 | 4 | 1 | 21.0 | 9 | 1 | |
| GDAP1L1 | Imprinted | Paternal | 27.0 | 3 | 1 | 24.3 | 2 | 1 | ||
| GFI1 | Predicted | Paternal | 26.0 | 9 | 2 | 23.4 | 10 | 3 | ||
| GLI3 | Predicted | Maternal | 27.8 | 234 | 19 | 16 | 25.5 | 299 | 21 | 18 |
| GLIS3 | Imprinted | Paternal | 26.3 | 517 | 22 | 36 | 25.5 | 611 | 25 | 37 |
| GNAS | Imprinted | Isoform Dependent | 28.0 | 68 | 8 | 4 | 26.8 | 32 | 2 | 4 |
| GPT | Predicted | Maternal | 15.0 | 1 | 20.5 | |||||
| GRB10 | Imprinted | Isoform Dependent | 27.1 | 246 | 13 | 20 | 24.9 | 180 | 10 | 9 |
| H19 | Imprinted | Maternal | 21.5 | 6 | 22.2 | 6 | ||||
| HOXA11 | Predicted | Maternal | 23.1 | 4 | 1 | 24.8 | 1 | |||
| HOXA2 | Predicted | Maternal | 31.0 | 19.5 | 1 | |||||
| HOXA3 | Predicted | Maternal | 26.5 | 5 | 3 | 1 | 22.7 | 11 | 2 | 1 |
| HOXA4 | Predicted | Maternal | 21.0 | 25.0 | ||||||
| HOXA5 | Predicted | Maternal | 19.0 | 37.0 | 2 | |||||
| HOXB2 | Predicted | Maternal | 25.2 | 3 | 1 | 1 | 27.5 | |||
| HOXB3 | Predicted | Maternal | 25.2 | 15 | 1 | 2 | 22.9 | 7 | ||
| HOXC4 | Predicted | Maternal | 26.3 | 13 | 6 | 5 | 24.1 | 24 | 1 | 8 |
| HOXC9 | Predicted | Maternal | 23.3 | 4 | 21.0 | 1 | ||||
| HSPA6 | Predicted | Maternal | 23.5 | 1 | 23.8 | 4 | ||||
| HYMAI | Imprinted | Paternal | 27.0 | 21.5 | 2 | 1 | ||||
| IFITM1 | Predicted | Maternal | 24.5 | 1 | 13.0 | |||||
| IGF2 | Imprinted | Paternal | 21.8 | 1 | 2 | 22.1 | 20 | 4 | ||
| ISM1 | Predicted | Paternal | 26.8 | 121 | 5 | 13 | 25.5 | 48 | 4 | 5 |
| KBTBD3 | Predicted | Paternal | 31.8 | 5 | 1 | 29.5 | 2 | 1 | ||
| KCNK9 | Imprinted | Maternal | 24.1 | 135 | 5 | 4 | 23.0 | 38 | 1 | 3 |
| KCNQ1 | Imprinted | Maternal | 25.7 | 343 | 13 | 25 | 23.6 | 212 | 11 | 11 |
| KCNQ1DN | Imprinted | Maternal | 14.0 | 1 | 21.0 | |||||
| KLF14 | Imprinted | Maternal | 21.7 | 2 | 18.4 | 3 | ||||
| L3MBTL | Imprinted | Paternal | 25.2 | 2 | 21.5 | 14 | ||||
| LDB1 | Predicted | Maternal | 22.0 | 4 | 21.8 | 1 | 1 | |||
| LILRB4 | Predicted | Maternal | 21.4 | 7 | 21.4 | 7 | 1 | |||
| LIN28B | Imprinted | Paternal | 26.9 | 17 | 1 | 5 | 27.6 | 48 | 3 | 4 |
| LMX1B | Predicted | Maternal | 24.0 | 68 | 8 | 5 | 24.1 | 53 | 1 | 3 |
| LRRTM1 | Imprinted | Paternal | 15.5 | 1 | ||||||
| LY6D | Predicted | Paternal | 27.3 | 3 | 1 | 25.0 | ||||
| MAGEL2 | Imprinted | Paternal | 33.5 | 2 | ||||||
| MAGI2 | Imprinted | Maternal | 29.4 | 1035 | 78 | 79 | 27.4 | 1485 | 120 | 112 |
| MEG3 | Imprinted | Maternal | 22.1 | 21 | 2 | 3 | 21.7 | 24 | 1 | |
| MEG8 | Imprinted | Maternal | 21.1 | 2 | 19.7 | 6 | ||||
| MEST | Imprinted | Paternal | 26.3 | 9 | 26.4 | 16 | 1 | |||
| MESTIT1 | Imprinted | Paternal | 29.5 | 2 | 23.0 | 1 | ||||
| MIMT1 | Imprinted | Paternal | 27.0 | 28.2 | ||||||
| MYEOV2 | Predicted | Paternal | 23.7 | 16 | 1 | 21.5 | ||||
| MZF1 | Predicted | Maternal | 23.8 | 4 | 24.7 | 12 | 1 | |||
| NAA60 | Imprinted | Maternal | 24.0 | 10 | 1 | 23.5 | ||||
| NAP1L5 | Imprinted | Paternal | 25.5 | 1 | 1 | |||||
| NDN | Imprinted | Paternal | 26.0 | 1 | 22.0 | 1 | ||||
| NKAIN3 | Predicted | Paternal | 27.2 | 539 | 28 | 35 | 25.9 | 924 | 69 | 53 |
| NKX6-2 | Predicted | Maternal | 19.0 | |||||||
| NLRP2 | Imprinted | Maternal | 22.5 | 62 | 5 | 4 | 20.5 | 39 | 5 | |
| NPAP1 | Imprinted | Unknown | 25.0 | 1 | 1 | 24.0 | ||||
| NTM | Imprinted | Maternal | 28.2 | 793 | 53 | 68 | 25.9 | 585 | 49 | 49 |
| OBSCN | Predicted | Paternal | 25.2 | 160 | 7 | 7 | 23.7 | 169 | 10 | 6 |
| OR11L1 | Predicted | Paternal | 24.7 | 23.4 | ||||||
| OSBPL5 | Imprinted | Maternal | 23.8 | 115 | 9 | 9 | 22.4 | 89 | 4 | 4 |
| OTX1 | Predicted | Maternal | 21.8 | 4 | 20.7 | 3 | ||||
| PAOX | Predicted | Maternal | 25.8 | 6 | 1 | 21.2 | 2 | 1 | ||
| PEG10 | Imprinted | Paternal | 34.6 | 2 | 1 | 27.0 | 4 | |||
| PEG3 | Imprinted | Paternal | 25.4 | 1 | 23.7 | 2 | ||||
| PEX10 | Predicted | Maternal | 19.8 | 8 | 1 | 19.5 | 12 | |||
| PHLDA2 | Imprinted | Maternal | 16.0 | 1 | ||||||
| PHPT1 | Predicted | Maternal | 21.5 | |||||||
| PLAGL1 | Imprinted | Paternal | 28.2 | 29 | 3 | 4 | 26.6 | 13 | 2 | 1 |
| PPAP2C | Predicted | Maternal | 18.3 | 16 | 1 | 26.3 | 276 | 16 | 26 | |
| PPP1R9A | Imprinted | Maternal | 26.5 | 71 | 4 | 9 | 22.1 | 12 | 2 | |
| PRDM16 | Predicted | Paternal | 21.8 | 231 | 10 | 17 | 21.7 | 382 | 10 | 19 |
| PTPN14 | Predicted | Maternal | 27.0 | 10 | 2 | 3 | 27.3 | 55 | 4 | 6 |
| PURG | Predicted | Paternal | 28.2 | 26.8 | 20 | 3 | 2 | |||
| PYY2 | Predicted | Paternal | 31.0 | 1 | ||||||
| RAB1B | Predicted | Maternal | 25.1 | 7 | 2 | 2 | 23.7 | 3 | 1 | |
| RB1 | Imprinted | Maternal | 26.9 | 52 | 7 | 9 | 26.2 | 11 | 1 | 1 |
| RBP5 | Imprinted | Maternal | 32.0 | 1 | 1 | 18.8 | 1 | 1 | ||
| RPL22 | Predicted | Paternal | 31.9 | 7 | 26.0 | 1 | ||||
| RTL1 | Imprinted | Paternal | 20.3 | 3 | 22.0 | 1 | ||||
| SALL1 | Predicted | Maternal | 26.9 | 2 | 2 | 23.3 | 5 | 3 | 1 | |
| SGCE | Imprinted | Paternal | 30.3 | 18 | 3 | 2 | 28.8 | 17 | 3 | 1 |
| SGK2 | Imprinted | Paternal | 23.3 | 6 | 1 | 1 | 25.1 | 18 | 2 | 1 |
| SIM2 | Predicted | Paternal | 26.9 | 28 | 3 | 2 | 24.2 | 16 | 1 | |
| SLC22A18 | Imprinted | Maternal | 22.8 | 29 | 3 | |||||
| SLC22A18AS | Provisional Data | Maternal | 22.3 | 56 | 4 | 1 | ||||
| SLC22A2 | Imprinted | Maternal | 28.9 | 5 | 1 | 25.8 | 4 | |||
| SLC22A3 | Imprinted | Maternal | 27.0 | 82 | 2 | 8 | 26.8 | 119 | 2 | 7 |
| SLC26A10 | Predicted | Maternal | 27.0 | 1 | 25.7 | 2 | ||||
| SLC4A2 | Predicted | Maternal | 21.6 | 1 | 23.2 | 9 | ||||
| SNRPN | Imprinted | Paternal | 24.9 | 117 | 15 | 13 | 24.3 | 156 | 9 | 18 |
| SNURF | Imprinted | Paternal | 25.7 | 13 | 2 | 2 | ||||
| SOX8 | Predicted | Paternal | 19.1 | 10 | 20.9 | 1 | ||||
| SPON2 | Predicted | Paternal | 21.7 | 30 | 2 | 22.3 | 1 | 1 | ||
| TCEB3C | Imprinted | Maternal | 73.0 | 1 | ||||||
| TFPI2 | Imprinted | Maternal | 24.0 | |||||||
| TIGD1 | Predicted | Paternal | 28.4 | 7 | 25.6 | 7 | ||||
| TMEM52 | Predicted | Paternal | 24.7 | 2 | 1 | 16.0 | ||||
| TMEM60 | Predicted | Paternal | 29.0 | 3 | 28.3 | 1 | ||||
| TP73 | Imprinted | Maternal | 23.6 | 73 | 4 | 5 | 23.0 | 93 | 3 | 7 |
| TSHZ3 | Predicted | Paternal | 26.6 | 34 | 4 | 8 | 24.7 | 77 | 7 | 10 |
| UBE3A | Imprinted | Maternal | 28.3 | 11 | 1 | 2 | 26.6 | 105 | 7 | 10 |
| VAX2 | Predicted | Maternal | 28.0 | 27 | 2 | 4 | 24.7 | 14 | 3 | 2 |
| VENTX | Predicted | Maternal | 25.0 | 1 | 24.0 | 12 | ||||
| WT1 | Imprinted | Paternal | 28.3 | 53 | 4 | 2 | 24.9 | 9 | 1 | 3 |
| ZC3H12C | Imprinted | Paternal | 28.0 | 106 | 7 | 11 | 26.9 | 102 | 9 | 18 |
| ZDBF2 | Imprinted | Paternal | 28.4 | 10 | 2 | 29.8 | 7 | |||
| ZFAT | Imprinted | Paternal | 24.1 | 2 | 1 | 23.1 | 268 | 9 | 16 | |
| ZFAT-AS1 | Imprinted | Paternal | 28.6 | 7 | ||||||
| ZFP36L2 | Predicted | Maternal | 21.0 | 1 | 1 | 15.0 | 1 | |||
| ZIC1 | Predicted | Maternal | 37.7 | 2 | 1 | 30.7 | 2 | 1 | ||
| ZIM2 | Imprinted | Paternal | 26.0 | 1 | 23.8 | 14 | ||||
| ZNF225 | Predicted | Paternal | 22.1 | 25.4 | 1 | |||||
| ZNF229 | Predicted | Maternal | 27.5 | 4 | 2 | 25.8 | 22 | 5 | ||
| ZNF264 | Unknown | Unknown | 27.1 | 34 | 5 | 2 | 25.2 | 30 | 1 | 4 |
| ZNF597 | Imprinted | Maternal | 33.0 | 1 | 1 | 24.8 | 1 | |||
For each cell line the mean depth of the alternate allele, the number of heterozygous and homozygous variants identified from WGS is provided