Skip to main content

Table 2 List of genes interrogated in this study, mapping information, coordinates, and imprinting status

From: CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel

Gene Description Reference Map RefSEQ Position UCSC h19 coordinates Amplicon length Position with respect to the TSS Number of interrogated CpG Imprinting status
ZAP70 Zeta chain of T cell receptor-associated protein kinase 70 15; 19 2q11.2 NM_001079 Exon 3 Chr2 98340750–98340885 180 10,728 20 No
GP1BB Glycoprotein Ib platelet beta subunit 15; 19 22q11.21 NM_000407 Exon 1 Chr22: 19710829–19710960 192 363 18 No
KIF1A Kinesin family member 1A 15; 5 2q37.3 NM_001244008 Exon 1 Chr2: 241759586–241759727 189 −1 27 No
PARP15 Poly(ADP-ribose) polymerase family member 15 20 3q21.1 NM_001113523 Exon 1 Chr3:122296564–122296725 206 93 19 No
ITGA4 Integrin subunit alpha 4 20 2q31.3 NM_000885 Exon 2 Chr2: 182322887–182323053 214 912 14 No
NTM Neurotrimin 20 11q25 NM_016522 Exon 1 Chr11: 131781042–131781185 190 62 15 Yes, maternal,
No SNP
MIR193A MicroRNA 193a 18; 60 17q11.2 NR_029710 Promoter Chr17: 29886860–29887068 256 −178 26 No
MIR137HG MIR137 host gene7 15; 19; 41 1p21.3 NR_046105 Exon 1 Chr1: 98511645–98511814 216 136 16 No
EPHX3 Epoxide hydrolase 3 20 19p13.12 NM_024794 Exon 1 Chr19: 15342826–15343049 223 215 29 No
LINC00599 Long intergenic non-protein coding RNA 599 20 8p23.1 NR_029668 Exon 1 Chr8: 9760739–9760890 199 69 20 No
FLI1 Fli-1 proto-oncogene, ETS transcription factor 20 11q24.3 NM_001271010 Exon 1 Chr11: 128564020–128564160 186 187 12 No
MIR296 MicroRNA 296 20; 51 20q13.32 NR_029844 Exon 1 Chr20: 57392355–57392545 238 180 15 Yes, paternal,
No SNP
LRRTM1 Leucine-rich repeat transmembrane neuronal 1 20 2p12 NM_178839 Promoter Chr2: 80531676–80531807 179 −431 24 Yes, paternal,
No SNP
TERT Telomerase reverse transcriptase 53 5p15.33 NM_198253 Intron4–5 Chr5: 1279743–1279851 109 14,976 6 No, SNP at rs10069690
DNMT1 DNA methyltransferase 1 26 19p13.2 NG_028016.3 Exon 1 Chr19: 10305498–10305665 216 142 28 Yes, paternal, No SNP
TERC Telomerase RNA component 22 3q26.1 NG_016363.1 Exon 1 Chr3: 169764557–169764699 191 357 19 No
PAX1 Paired box 1 20 20p11.23 NM_001257096 Exon 1 Chr20: 21705602–21705713 159 −60 13 No
H19 H19 conserved region 1 24 11p15.4 NR_002196 Exon 1 Chr11: 1996891–1997062 219 159 13 Yes, maternal, SNP rs2067051
LINE1 Long interspersed element 1 36; 25 Wide M80343.1 Exon 1 Genome-wide distribution 267 458 21 No