Table 3. .
Assayed Genes, Primers, Probes, and Efficiencies
| Primer |
Efficiencyc |
||||||||||
| Gene | Accession Number | Source | Chromosome | Positiona (kb) |
Categoryb | Forward | Reverse | Probe | BLTd | Lymphoblasts | Fibroblasts |
| GBAS | NM_001483 | RefSeq | HSA7 | 55′807 | 2 | GGGCAGCTGTACATGGTGC | GCATTCCGTATGTCTTCCCTG | CCATCTTTGGGCTTACAGGGATCTTCAGA | ND | 1.04 | 1.00 |
| PSPH | NM_004577 | RefSeq | HSA7 | 55′853 | 2 | ATCATGATTGGAGATGGTGCC | TTCCTCCAAATCCAATGAAAGC | CAGATATGGAAGCCTGTCCTCCTGCTGA | ND | 1.00 | 1.02 |
| ZFD25 | NM_016220 | RefSeq | HSA7 | 63′596 | 2 | CTCACATCTGTAATGCCAGCACT | TGGTCTCAGACTCCTGCCCT | CCACCCACCTTGGCCTCCCA | ND | .95 | 1.00 |
| VKORC1L1 | NM_173517 | RefSeq | HSA7 | 64′782 | 2 | GGCCCTGGGTGAAGTGCT | AATGGAACCCAAAAGACCAAATC | CGCCGCCCTTGCCTCCAG | ND | .96 | .99 |
| GUSB | NM_000181 | RefSeq | HSA7 | 64′870 | 2 | GTGTCCCGGCGTGGG | TGGTGATGCAGAGAAACGTTG | CTGGCGCTGCCGCAGTTCTTC | ND | .99 | 1.04 |
| ASL | NM_000048 | RefSeq | HSA7 | 64′985 | 2 | AACCAGCTGTCACTGCAGGA | TCCCACACGCAGATCACGT | CTGCAGACCATCAGCCCCCTGTTC | ND | .98 | .99 |
| RCP9 | NM_014478 | RefSeq | HSA7 | 65′024 | 2 | GCCTGTGACTGCTGTGGAGA | TTCAATCTGCTCCTCCGTGAG | GCTCTTCACTCTCTTCCACCATCAGCTGG | ND | BE/NE | BE/NE |
| TPST1 | NM_003596 | RefSeq | HSA7 | 65′163 | 2 | TGCACCATGAAGAGATGATTGG | GCTCCTACATTGACTGGCTTGA | AGTGTCTCTGTCAAAAGTGGAGAGATCTACAGACCA | .99 | BE/NE | BE/NE |
| RABGEF1 | NM_014504 | RefSeq | HSA7 | 65′315 | 2 | CCAGGGTCGGATCAAAGAAG | CTGGTTTGCCGGTTTATGGA | AATTCAGGAAGCAAAAGCTCCCAGTC | BE/NE | BE/NE | BE/NE |
| KCTD7 | NM_153033 | RefSeq | HSA7 | 65′510 | 2 | TCCGAGGGCCGGTACTTC | GCGCAGGAAATTCAGCACAT | CGACCGAGATGGCACACACTTTGG | 1.00 | .95 | .95 |
| NM_017994 | NM_017994 | RefSeq | HSA7 | 65′827 | 2 | TGGAAAAGTCTATCATGCTTTAAATCC | GGTGTGCATGAGATGCAAATTTAT | CAGTGATTGTTCCAGATGATGACCGTTCA | .95 | .96 | .95 |
| RSAFD1/NM_018264 | NM_018264 | RefSeq | HSA7 | 65′906 | 2 | CCTGGGCCTCTTCCCCTT | GTGCAATTCAATGCTAAGTGGC | CCCGGCCCTTAGATTTCATGGAGC | .96 | 1.01 | 1.00 |
| AUTS2 | NM_015570 | RefSeq | HSA7 | 69′662 | 2 | TGGGCCACCTCCTCATCA | CGGCCGATTAAAAGGCTCTA | AGCAACTTCCTCAACCCTGCTGCCC | BE/NE | 1.03 | .98 |
| WBSCR17 | NM_022479 | RefSeq | HSA7 | 70′542 | 2 | GATGGACGATTACAAGTCTCATGTG | CGATGTCAATTCCCGGATTC | ACATAGCGTGGAACCTGCCGC | .97 | BE/NE | BE/NE |
| CALN1 | NM_031468 | RefSeq | HSA7 | 70′679 | 2 | CAGCATATTCTGGCAGTTTGACA | GTGGTCTCGGAAGGCATGAT | AGAATGTGCTTCAACTCTTCCAGAGTTATCCTTTG | 1.05 | BE/NE | BE/NE |
| WBSCR20C | AF416611 | GenBank | HSA7 | 71′830 | 6 | CCTGTTGGAAGTGGGATCCA | TGTTCACACGCACAAATCGA | CCTGGTCCAGCCTCCCAGCT | 1.05 | 1.00 | .97 |
| TRIM74 (TRIM50C) | AF498999 | GenBank | HSA7 | 71′843 | 6 | CTCATCGCCAAACTGGTGAA | GGATCACCCAGCTGAAGACATC | AACCGGACCCGAATCGTCAATGAGTC | 1.00 | .99 | BE/NE |
| Proximal breakpoint | Bayese | HSA7 | 72′013 | BE/NE | BE/NE | BE/NE | |||||
| WBSCR20A | AF412028 | GenBank | HSA7 | 72′129 | 6 | CCTGTTGGAAGTGGGATCCA | TGTTCACACGCACAAATCGA | CCTGGTCCAGCCTCCCAGCT | 1.05 | 1.00 | .97 |
| TRIM50 (TRIM50A) | AY081948 | GenBank | HSA7 | 72′146 | 6 | CTCATCGCCAAACTGGTGAA | GGATCACCCAGCTGAAGACATC | AACCGGACCCGAATCGTCAATGAGTC | 1.00 | .99 | BE/NE |
| FKBP6 | NM_003602 | RefSeq | HSA7 | 72′156 | 1 | AATGTGGCACCGCATGTTC | AGCTCTCTCCCCTCGTTGGT | GGTGAAGAACCTTCAACTTTCTCCTGCTGTAGA | BE/NE | BE/NE | BE/NE |
| FZD9 | NM_003508 | RefSeq | HSA7 | 72′262 | 1 | GTTGCGTTCCTCTGGAAGCT | TCCCAGCCAGAGAGGATCAG | ACTGGAATAAACCCCCGCGTGGC | BE/NE | BE/NE | BE/NE |
| BAZ1B | NM_032408 | RefSeq | HSA7 | 72′269 | 1 | AGTGTGAAGAGATCCTCCACAAGA | TGGTCACAGGCTCCCTGAA | TGAAGTACCGCTTCAGCTGGCC | BE/NE | .96 | 1.01 |
| BCL7B | NM_138707 | RefSeq | HSA7 | 72′369 | 1 | TGATGCCTCAGCCAATTCCT | CACGGAACTCTGGTTGCTGTT | TCTCCTTCTTGAATTCCAGGACG | .99 | .95 | 1.01 |
| TBL2 | NM_032988 | RefSeq | HSA7 | 72′397 | 1 | CAACACACACGCTGCTGTATCTC | GACTTCCCAAACCTTCACATCTG | ACGAGGCTACAAATCTGCCACAG | 1.04 | .98 | .97 |
| WBSCR14 | NM_032994 | RefSeq | HSA7 | 72′420 | 1 | GTACGCTGCACAACTGGAAGTT | CCCGTTGAAGGACTCAAACAG | CCCGTTGAAGGACTCAAACAG | BE/NE | BE/NE | BE/NE |
| WBSCR24 | NM_152560 | RefSeq | HSA7 | 72′495 | 1 | GCCCTGGCCATCAAATACC | CAGCGATGCATGCTTTCCT | CAGTTCTCGGCCACCTCACGAAGCT | 1.01 | BE/NE | 1.01 |
| WBSCR18 | NM_032317 | RefSeq | HSA7 | 72′509 | 1 | ACGCAGGCCCAAATCAAG | GCGGTCCGGGTGGTAGA | CGGCTTACTACCGTCAGTGCTTT | BE/NE | BE/NE | 1.00 |
| WBSCR22 | NM_017528 | RefSeq | HSA7 | 72′520 | 1 | TGAAGTTGAACCCAGGGAGTCT | CCCGCCTCGACATCCTTA | TGTTCACCAATGAGAGGTTCCCA | BE/NE | .98 | .97 |
| STX1A | NM_004603 | RefSeq | HSA7 | 72′526 | 1 | GCGCGCCGGAAGAAA | CCAACAGTGGAGGCGATGA | CATCATCTGCTGTGTGATCCTGGGCAT | 1.05 | 1.05 | 1.01 |
| WBSCR21 | NM_148916 | RefSeq | HSA7 | 72′563 | 1 | CCTTGGTGGAAACTCCCAGTT | AGGGAAGAGCCGCATAATCTC | TGCATCCCAGCCACCACCC | .97 | .95 | .98 |
| CLDN4 | NM_001305 | RefSeq | HSA7 | 72′568 | 1 | TCTGGCCCACTCGGACAA | GAGGGTGGACTCTGTTCTTGCT | TTCCCAAGGCCGCCTCCTGC | BE/NE | BE/NE | BE/NE |
| CLDN3 | NM_001306 | RefSeq | HSA7 | 72′596 | 1 | TTCATCGGCAGCAACATCA | CTCTGCACCACGCAGTTCA | CCCTCCCAGATGTTCTGCGACGTG | .97 | BE/NE | 1.05 |
| WBSCR27 | NM_152559 | RefSeq | HSA7 | 72′661 | 1 | TGCGATACCTGAGCTACATGTCA | TTGAAGGTTGGACGAGTTGGT | GACACACCAGCCCACCTGGCTTG | .96 | BE/NE | BE/NE |
| WBSCR28 | NM_182504 | GenBank | HSA7 | 72′687 | 1 | CCAGTCAGATCCAGCCTTTTG | TGATCTCGGTTCTGAACCAACA | CTGAGAGCCTCGTAACCTGCAACAGGAT | 1.04 | BE/NE | BE/NE |
| ELN | NM_000501 | RefSeq | HSA7 | 72′879 | 1 | GCTAAGGCAGCCAAGTATGGA | CAACTACTCCCGGGCCAAA | TGGCCCACCAGGCACTAAGCCTG | .97 | BE/NE | .99 |
| LIMK1 | NM_016735 | RefSeq | HSA7 | 72′947 | 1 | GTGCGCTGTTGCGATCTG | GAGGGTCTCCAGCCAGTGTTC | ACCCCGAGAAGAGGCCATCCTTTG | BE/NE | 1.04 | 1.02 |
| WBSCR1/EIF4H | NM_031992 | RefSeq | HSA7 | 73′021 | 1 | CCCTCCCCTCGGTGGAT | GAGTCGTGGTCTCTGTGCGCTTT | CAACATGGATTTCAGAGAACCCACAGAAGAG | 1.02 | 1.05 | 1.00 |
| WBSCR5 | NM_032464 | RefSeq | HSA7 | 73′046 | 1 | GGAAGGACAAGCTGTTGCAATT | GCTGAAGTTCTGGTACCTGGAAGA | TACCCCAGCCTGGAGGATCCAGC | BE/NE | 1.01 | 1.03 |
| RFC2 | NM_181471 | RefSeq | HSA7 | 73′062 | 1 | CCAACATTGACGAAGCCTACAA | TGCCAATGATATCTTCTGGTGAGT | ATTCTTGCTCACTTGTGGCATCTGGGC | BE/NE | 1.02 | 1.01 |
| CYLN2 | NM_032719 | RefSeq | HSA7 | 73′226 | 1 | AAGCTGATGGAGGCCATGAG | TTTGCAGAACCGGAATTGC | CTGCCCTGACAAGGCCCAGACC | BE/NE | .99 | .99 |
| GTF2IRD1 | NM_016328 | RefSeq | HSA7 | 73′428 | 1 | GCATCGGCCAACCAGATCT | CGTTCAGGCCGGCATAGT | ACTCGTGCAATGGCCAATGTACA | .95 | 1.05 | .98 |
| GTF2I | NM_033003 | RefSeq | HSA7 | 73′585 | 1 | CAGCTGAACCAAGCCAGTTG | TTGCTTGATCTGAGAGCTTCCA | AAGTTCCAGCCACAGAAGAAATAAAAGAGACT | BE/NE | .99 | 1.05 |
| Distal breakpoint | Bayese | HSA7 | 74′032 | BE/NE | BE/NE | BE/NE | |||||
| WBSCR16 | NM_030798 | RefSeq | HSA7 | 74′388 | 2 | CCGCATCCGATGTGGACT | TGCCCCATACAAACAGCTCTC | AGCCACTTTGCTGCACTGACCAACAA | .95 | BE/NE | BE/NE |
| TRIM73 (TRIM50B) | AF498998 | GenBank | HSA7 | 74′645 | 6 | CTCATCGCCAAACTGGTGAA | GGATCACCCAGCTGAAGACATC | AACCGGACCCGAATCGTCAATGAGTC | 1.00 | .99 | BE/NE |
| WBSCR20B | AF416610 | GenBank | HSA7 | 74′657 | 6 | CCTGTTGGAAGTGGGATCCA | TGTTCACACGCACAAATCGA | CCTGGTCCAGCCTCCCAGCT | 1.05 | 1.00 | .97 |
| HIP1 | NM_005338 | RefSeq | HSA7 | 74′780 | 2 | CACTACGAGCTTGCTGGTGTTG | TTCTTGCAGTGTAGGTGGAGATG | TCTGTTCCTTCTTCCCAGCCCTCA | BE/NE | 1.05 | .98 |
| RHBDL7/NPD007 | NM_020684 | RefSeq | HSA7 | 75′120 | 2 | CGGGCCTCACGCTGAA | ACAAAGATGTAGGTTACCAGCCTGTA | TCCGAGGCCCTTCGCAACTGG | BE/NE | 1.01 | 1.00 |
| POR | NM_000941 | RefSeq | HSA7 | 75′227 | 2 | CGAGAGCACCTGTGGAAGTTG | CCGTGCATCCCCACAGA | CGAAGGCGGTGCCCACATCTAC | BE/NE | 1.04 | 1.04 |
| MK-STYX | NM_016086 | RefSeq | HSA7 | 75′270 | 2 | CCGCCATCATAGCCTACCTC | CACTTCTTGACATAGGCCCAGG | CCTCTGCAAGGTCTGCTCGTTACTATGCA | ND | BE/NE | BE/NE |
| MDH2 | NM_005918 | RefSeq | HSA7 | 75′322 | 2 | CTCCACACCGCTGCTGC | AGGAGACTTTGCCGATGCC | AGGTTCTTCTCGATGCCCTTTTTCCCA | ND | .99 | 1.00 |
| DTX2 | NM_020892 | RefSeq | HSA7 | 75′736 | 2 | CAGTGCTACCTTCCAGACAACG | TTCCAGGCCACCTTCAGG | CCAGGGCCGCAAGGTCCTAGAGC | ND | .98 | 1.05 |
| FGL2 | NM_006682 | RefSeq | HSA7 | 76′470 | 2 | AATTAAAGATGAAAGAGCAAAGGATGT | CCCCTGCCTCTTCGCAT | TCCCTCTGCTTTCTAGTCTCACTGGGCA | ND | BE/NE | BE/NE |
| AIP1 | NM_012301 | RefSeq | HSA7 | 77′291 | 2 | GGCGATCAGGTCCATCTCA | GCAATTACAAGGAGAGGGAATGA | AGGTCACACGTAATAGCCTCCCTGGGC | ND | BE/NE | BE/NE |
| CACNA2D1 | NM_000722 | RefSeq | HSA7 | 81′224 | 2 | CTTGAGTTTGACCTTTCCACGAC | ACAGGGAGGCCGTGAAGTC | TCATCCTCCATCTCAACTGCCTCAAGG | ND | BE/NE | 1.00 |
| GRM3 | NM_000840 | RefSeq | HSA7 | 85′918 | 2 | CGCTCAGAGGCCAAAATTCA | TGCACCAGGATCAGACCCA | CAGCCCCAGTTCTCAGGTTTTCATCTGC | ND | BE/NE | BE/NE |
| PSMA5 | NM_002790 | RefSeq | HSA1 | N | AGGAGAAGCTGAATGCAACAAAC | TTCCTTTGTGAACATGTGGAAATT | CCAGGCTGCACTGTGGCTAGCTCAA | 1.01 | .98 | .99 | |
| AGPAT1 | NM_032741 | RefSeq | HSA6 | N | CTCCTACCAAGACTTCTACTGCAAGA | AGCACCCGCACCTGACA | AGCGTCGCTTCACCTCGGGACA | 1.00 | 1.00 | 1.00 | |
| EEF1A1 | NM_001402 | RefSeq | HSA6 | N | AGCAAAAATGACCCACCAATG | GGCCTGGATGGTTCAGGATA | CACCTGAGCAGTGAAGCCAGCTGCTT | .98 | .98 | .98 | |
| B2M | NM_004048 | RefSeq | HSA15 | C | ACTTTGTCACAGCCCAAGATAGTTAA | CGGCATCTTCAAACCCTCC | TGGGATCGAGACATGTAAGCAGCATCA | .98 | .98 | .98 | |
| BTG3 | NM_006806 | RefSeq | HSA21 | C | GCTCACTCTCTGGGTGGACC | GCTGGCAACAATGAATGCAT | ATGTGAGGTGTGCTGTCGGTATGGAGAGA | .98 | .98 | .98 | |
| SON | NM_138927 | RefSeq | HSA21 | C | CAGCAATTTGCCCTCAGAGG | CGGGTTGTTTCATCTGTCGTC | CCGGGTTAAACGGCAGGGCC | .98 | .98 | .98 | |
| ATP50 | NM_001697 | RefSeq | HSA21 | C | TCCATCGCGGAGAGGTACC | TGAGGACAGTTTTTAATTCAGAGAGTG | CACAGTGACCTCTGCATCTCCTTTAGAAGAAGC | .97 | .97 | BE/NE | |
| SIM2 | NM_009586 | RefSeq | HSA21 | C | AAGCTGAGAACAAACCCTTACCC | GCTGGCCGCATTCCAGT | CCACAGCAATACAGCTCGTTCCAAATGG | BE/NE | .96 | BE/NE | |
| DSCR2 | NM_203433 | RefSeq | HSA21 | C | TCCATTGCTAGAACAACCGAATATAG | GCTGGGATTTTCCATACTTGACA | ACACGACCTTCCTGCAGCAGTTCTAAGC | .97 | .97 | .97 | |
| GABPA | NM_002040 | RefSeq | HSA21 | C | CAAAGAGCGCCGAGGATTT | TGGATTTGGCCATTGTTTCC | AGGAGAAGATAGAAGCTCACCTGGGAACAGAA | .98 | BE/NE | .98 | |
| IL10RB | NM_000628 | RefSeq | HSA21 | C | GACAAAGTACGCCTTCTCCCC | GTTATGATGAGGATGGCCCAA | AGGAATTCTCTTCCACAGCACCTGAAAGAGTT | .99 | .99 | .99 | |
| IFNAR1 | NM_000629 | RefSeq | HSA21 | C | TGAAAAGCTGAATAAAAGCAGTGTTT | TCCAACTATAAGCCAAATTTTAGAGGT | TAGTGACGCTGTATGTGAGAAAACAAAACCAGG | 1.03 | 1.03 | 1.03 | |
| IFNGR2 | NM_005534 | RefSeq | HSA21 | C | GGCCTGATTAAATACTGGTTTCACA | TGGGCTGAGTTGGGTCTTTT | TCCACCAAGCATCCCATTACAGATAGAAGAGTATT | .97 | BE/NE | .97 | |
| USP18 | NM_017414 | RefSeq | HSA22 | C | CGAGAGTCTTGTGATGCTGAGG | TTCCCACGTGCGCAATC | CAGTCTGGAGGGCAGTATGAGCTTTTTGC | ND | 1.02 | .98 | |
| DGCR8 | NM_022720 | RefSeq | HSA22 | C | GAGATGAAGAGGCTAGCTGAGGA | GCGGACGCCACAATGG | AGGGAGGAGACTCGAAAGAAGCCCAAGAT | ND | BE/NE | .96 | |
| UFD1L | NM_005659 | RefSeq | HSA22 | C | TCATCAGAAATTCACGTCCCC | GAGAAAGCGACGAATCTGCC | TGTCAAAAAGGTTGAAGAGGATGAAGCTGG | ND | .98 | BE/NE | |
a
On NCBI 34/Ensembl.
b
1 = HSA7 hemizygous in WBS; 2 = HSA7 nonhemizygous in WBS; 6 = genes mapping in the LCR flanking the WBS commonly deleted region (i.e., present in six copies/genome ([LCRs]); C = control genes; N = normalization genes.
c
ND = Not done; BE/NE = bad efficiency (efficiency⩽0.95 or ⩾1.05) or not expressed.
d
BLT = mix of cDNA samples from brain, liver, and testis.
e
Most common breakpoint, as described in Bayes et al.18