Novel genetic and epigenetic alterations in ... - Ous-research.no

Gene name Multiplex Annealing Number of [primer] Fluorescent size in(HGNC) Group temperature PCR cycles in pmol dye bp Forward ReverseFragment analysis primersBAX1 58°C 27 0.8 VIC 94 ATCCAGGATCGAGCAGGGCG ACTCGCTCAGCTTCTTGGTGIGF2R 1 58°C 27 1.0 NED 111 GCAGGTCTCCTGACTCAGAA GAAGAAGATGGCTGTGGAGCPRKDC 1 58°C 27 1.6 6-FAM 113 GACTCATGGATGAATTTAAAATTGG TTTGAAAATAACATGTAAATGCATCTCSLC23A2 1 58°C 27 1.0 6-FAM 61 GACTACTACGCCTGTGCACG TGTTTATTGCGTGGATGGGTGFBR2 1 58°C 27 1.0 NED 73 CTTTATTCTGGAAGATGCTGC GAAGAAAGTCTCACCAGGAXIN2 2 60°C 27 1.6 6-FAM 123 CCTACCCCTTGGAGTCTGC CAGGGTCCTGGGTGAACAGRK4 2 60°C 27 1.6 NED 68 GGAAAAATGTATGCCTGCAA GCCATAGCTTCACCTTTCCTCMSH2 2 60°C 27 1.6 VIC 179 AGCAGTCAGAGCCCTTAACC GCCATTTAAAGCTAGTTATCTAATCCAPTHLH 2 60°C 27 1.6 PET 113 TTTCACTTTCAGTACAGCACTTCTG GAAGTAACAGGGGACTCTTAAATAATGSEC63 2 60°C 27 1.6 NED 145 GGAGGATGGCAACAGAAGAG CATTCCCAACGACTCCATTTSPINK5 2 60°C 27 1.2 VIC 99 TGAGGCGTTTGTTCACTTTG TGCTCCTGTCTTCATCCTCTTASTE1 3 60°C 27 1.0 VIC 117 ATATGCCCCCGCTGAAATA TTGGTGTGTGCAGTGGTTCTATR 3 60°C 27 2.0 PET 70 GCTTCTGTCTGCAAGCCATT TGAAAGCAAGTTTTACTGGACTAGGEP300, ex27 3 60°C 27 1.0 PET 156 ACACAACAGGGCATATTTGG CATGGACAATACGCTCTGATACARAD50 3 60°C 27 1.0 NED 86 GCGACTTGCTCCAGATAAAC GCACAAGTCCCAGCATTTCAACVR2A 4 58°C 27 1.6 VIC 113 GTTGCCATTTGAGGAGGAAA CAGCATGTTTCTGCCAATAATCMBD4 4 58°C 27 2.0 NED 98 TGACCAGTGAAGAAAACAGCC GTTTATGATGCCAGAAGTTTTTTGOGT 4 58°C 27 1.2 PET 116 TCACTTTTGGCTGGTCAGAG GGGAGGGAAAGGAGGTAAAGSYCP1 4 58°C 27 1.6 6-FAM 153 CCCCTTCATCTCTAACAACCC CACTGATTCTCTGAAATTAAACAAATAACTCF7L2 4 58°C 27 1.6 6-FAM 75 GCCTCTATTCACAGATAACTC GTTCACCTTGTATGTAGCGAACASP5 5 60°C 27 1.2 PET 141 CAGAGTTATGTCTTAGGTGAAGG ACCATGAAGAACATCTTTGCCCAGEP300, ex3 5 60°C 27 1.2 VIC 100 GCCTTGGTCTCCAGATTCAG ATGTTGGGCATTCCTCCAEPHB2 5 60°C 27 1.2 VIC 85 CACGAGACGTCACCAAGAAA CCCCTCCCAGGATCTGTTPA2G4 5 60°C 27 1.2 6-FAM 93 GCAAGTCGAAAAACCCAGAA GGGAGAAAGAGGGATCAGGTSEMG1 5 60°C 27 1.2 NED 152 ACAACGACCGAAACCCATTA CCCACAAAAGTCCTGGAGAGPCNXL2 6 57°C 27 1.0 NED 121 GGAAAATTATGAACAGCCACAA GCAGCCAAATGCTTGTTATGRCC2 6 57°C 27 1.6 VIC 143 GCATTTGTTCTGGAAGCTCGT GTGATGAGAAACCGGAGAGAATAF1B 6 57°C 27 1.2 VIC 115 CCAAATAAAAGCCCTCAACC TGTCCTGACATCATGAAGGTGZMYND8 6 57°C 27 1.2 6-FAM 83 CAAAGAAGGTTGTCAGATGGAC CCTCTTTAATCTCCACTGGGGRB14 7 53°C 27 1.6 6-FAM 80 GGCAATAGTGATATTTATGT GGCTTAAAGCAGAATCCATMRE11A 7 53°C 27 1.6 NED 122 AATATTTTGGAGGAGAATCT AATTGAAATGTTGAGGTTGCCPRDM2 7 53°C 27 1.2 VIC 145 TCTCACATCTGCCCTTACTG GTGATGAGTGTCCACCTTTCPTEN, ex7 7 53°C 27 1.6 6-FAM 236 CCTGTGAAATAATACTGGTATG GTTTCTTCTCCCAATGAAAGTAAAGTACAPTEN, ex8 7 53°C 27 1.6 PET 166 GTGCAGATAATGACAAGGAATA GTTTCTTACACATCACATACATACAAGTCAIM2 8 60°C 27 1.6 PET 76 TTCTCCATCCAGGTTATTAAGGC TTAGACCAGTTGGCTTGAATTGE2F4 8 60°C 27 2.4 PET 97 TGCAGTCTTCTGCCCTGCT GGGTTGGGTCCGGACGAAMSH6 8 60°C 27 1.2 6-FAM 94 GGGTGATGGTCCTATGTGTC CGTAATGCAAGGATGGCGTRBBP8 8 60°C 27 2.0 VIC 88 GAATACAAGTTTGTCCCCTTC GCTAGATATACAAGTGTTGCTAADCY1 9 58°C 27 1.2 NED 98 CCAGAAGCAAATTCACAAGAC TTTTGCGTGTTCCTTCCTTCBLM 9 58°C 27 1.2 6-FAM 88 GAGTAGCAACTGGGCTGAAA GACAGCAGTGCTTGTGAGAAMSH3 9 58°C 27 1.2 VIC 153 AGATGTGAATCCCCTAATCAAGC ACTCCCACAATGCCAATAAAAATMARCKS 10 58°C 30 3.5 PET 109 GACTTCTTCGCCCAAGGC GCCGCTCAGCTTGAAAGAUVRAG 10 58°C 30 4.5 PET 116 TTTATTTTTAAACATTGTGAGTATG TTTTTAACTGCAGGCATTCACWIPS3 10 58°C 30 7.0 PET 126 TCTCCCTTTGTTTTAGC ATTGGTCACCCTGTTAGConsensus MSI-primersBAT25 NA 55°C 27 1.2 NED 124 TCGCCTCCAAGAATGTAAGT TCTGCATTTTAACTATGGCTCBAT26 NA 55°C 27 1.6 6-FAM 122 TGACTACTTTTGACTTCAGCC AACCATTCAACATTTTTAACCCD 2S123 NA 55°C 27 1.6 NED 211 AAACAGGATGCCTGCCTTTA GGACTTTCCACCTATGGGACD5S346 NA 55°C 27 1.2 VIC 125 ACTCACTCTAGTGATAAATCGGG AGCAGATAAGACAGTATTACTAGTTD17S250 NA 55°C 27 3.0 6-FAM 152 GGAAGAATCAAATAGACAAT GCTGGCCATATATATATTTAAACCSequencing primersACVR2A NA 58°C 40 10.0 NA 311 CCAGTTTGAAAGTCAGGAGGA TGTGAAGATCACCTTCCAGAAAAIM2 NA 58°C 40 10.0 NA 348 GATCCAAGGCAGACCAATGT TTCTGAATTTGTTTATCCAGCAAASTE1 NA 58°C 40 10.0 NA 395 TCCTGTTGCACTGAATTACTTCTT AACTGAGTTTTATTCAATGTTGGAGAXIN2 NA 58°C 40 10.0 NA 398 CCCAGTTTCTTTCCTTCTGTTTT TTCTCATGGGAGGGTTTGAGBLM NA 58°C 40 10.0 NA 392 CCCTATGGAGGGTGATTCCT CCCAGTCATCATCATCATCAAEPHB2 NA 58°C 40 10.0 NA 322 CTCGGCTCACCTCTTCCTC TGGACACATCGCATGAATCTGRK4 NA 58°C 40 10.0 NA 298 CCTAAGAAATGCCAGGTGGA AATGACTTCCACGGCTTCAGMBD4 NA 58°C 40 10.0 NA 302 CTGCATTTCTGATGCTGGAG TTGGTGAGCAGTTGTTGTCCPTHLH NA 58°C 40 10.0 NA 370 CCACGGCTAAAAGACCTGAG GATGGGTTTGCCAGCTTAAARAD50 NA 58°C 40 10.0 NA 276 CCCCGTTTGTCAGAGAGTTT GGCATACCAGCTCAGAGTCCRBBP8 NA 58°C 40 10.0 NA 398 TTCCTCTGCTTTTCCCCTTC TGATGTGTGAAAAGGGCACTARCC2 NA 58°C 40 10.0 NA 328 CCGCACATGTGTTTCTGTTT ATCCGCCTTCCTTCCTCTTSEMG1 NA 58°C 40 10.0 NA 246 AGTGATCGTCATTTGGCACA GGGGAGGCTCATCTTCCTACSLC23A2 NA 58°C 40 10.0 NA 341 ACTGGTCCTGGTCACTTTCG GTCGCTAGAGTCCTGCTGCTSYCP1NA 58°C 40 10.0 NA 228 TGTACTCAGGCCCCTTCATC TTTGGCTCTGGCAAATAAGAATAF1B NA 58°C 40 10.0 NA 266 GGTCCTGGCACTCACAATTT TGTCCTGACATCATGAAGGTGWISP3 NA 58°C 40 10.0 NA 350 ATTTTGGGGTTGGGAAAGAG CTGTCGCAAGGCTGAATGTAZMYND8 NA 58°C 40 10.0 NA 376 CCACATGCTGGGTTTTCTTT TTTATGGGGTGAGGTGAAGGSupplementary Table. Primer and PCR details.Abbreviations: HGNC - Human Genome Nomenclature Comittee; NA - not applicable;pmol - picomol; bp - base pair28