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Table 5 Variant candidate validation by Sanger sequencing

From: Whole exome sequencing in the rat

Chromosome #: Position Gene Exon Codon Change C6 FAT7 DSL 6A/C1 NBTII
Coverage AF Coverage AF Coverage AF Coverage AF
Total Allele   Total Allele   Total Allele   Total Allele  
Chr10:56196111 Tp53 a R271H cGt/cAt WT WT 71 d 71 1.000 WT WT WT WT
Chr10:56195619 Tp53 R211W Cgg/Tgg WT WT WT WT WT WT 197 e 113 0.574
Chr10:56195677 Tp53 I230T aTc/aCc WT WT WT WT WT WT 174 90 0.529
Chr10:48699815 Ncor1 E544D gaG/gaC 194 85 0.438 157 157 1.000 166 166 1.000 191 191 1.000
Chr2:118851700 Pik3ca b M811 T aTg/aCg WT WT WT WT WT WT 227 111 0.489
Chr2:118831618 Pik3ca C90Y tGt/tAt 129 62 0.481 WT WT WT WT WT WT
Chr5 Cdkn2a Deletion   WT WT WT WT WT WT WT WT
Chr5 Cdkn2b Deletion   WT WT WT WT WT WT WT WT
Chr10:66790063 Nf1 Q962* Cag/Tag 151 79 0.523 WT WT WT WT WT WT
Chr1:208011800 Mki67 G207R Ggg/Agg 314/− f 68/− 0.217/− WT WT 442/− 202/− 0.457/− WT WT
Chr1:53731379 Mllt4 Q1440* Caa/Taa WT WT 111/− 30/− 0.270/− WT WT WT WT
Chr1:200672370 Fgfr2 V70 M Gtg/Atg 126 126 1.000 159 159 1.000 WT WT WT WT
Chr8:129618253 Ctnnb1 D32V gAt/gTt WT WT WT WT 55 20 0.364 WT WT
Chr16:50398579 Fat1 L2464P cTc/cCc WT WT WT WT WT WT 154 62 0.403
Chr16:50485429 Fat1 M536 T aTg/aCg 131 67 0.511 149 149 1.000 WT WT 196 98 0.500
Chr16:50485954 Fat1 F361S tTc/tCc WT WT 175 175 1.000 WT WT WT WT
Chr3:72125722 Clp1 c M417 atg/ WT WT WT WT 165/− 25/− 0.152/− WT WT
Chr2:125846677 Fat4 I3077V Att/Gtt WT WT WT WT 200 200 1.000 WT WT
Chr2:125754029 Fat4 S627 T aGt/aCt WT WT WT WT WT WT 94 37 0.394
Chr2:125754184 Fat4 L679F Ctc/Tcc WT WT WT WT WT WT 143 84 0.587
Chr5:151918885 Arid1a Y658* taT/taA WT WT WT WT WT WT 78 29 0.372
Chr16:23972323 Nat1 S15 L tCa/tTa WT WT WT WT WT WT 300 154 0.513
Chr16:23961976 Nat2 L52* tTa/tAa WT WT WT WT WT WT 197 90 0.457
Chr8:118824049 Setd2 R792TEPSVR agg/aCTGAACCTTCAGTTAgg WT WT 95 95 1.000 103 103 1.000 WT WT
Chr8:118824049 Setd2 R79TESSVR agg/aCTGAATCTTCAGTTAgg WT WT WT WT WT WT 120 38 0.317
Chr8:87845140 Impg1 T133I aCc/aTc 151 74 0.490 WT WT WT WT WT WT
Chr6:38567303 Nbas T837 N aCc/aAc 56 56 1.000 WT/+ WT/+ 60 60 1.000 WT/+ WT/+
Chr6:38567315 Nbas A841V gCg/gTg 53 53 1.000 WT/+ WT/+ 58 58 1.000 WT/+ WT/+
Chr8:58154526 Npat K1186R aAg/aGg 68 68 1.000 50 50 1.000 WT WT WT WT
  1. aIn the gene column, bold and italics indicates the variant found in the rat exome platform matches the amino acid substitution and location in COSMIC
  2. bIn the gene column, italics indicates the variant found in the rat exome platform matches only the amino acid substitution in COSMIC
  3. cIn the gene column, bold, italics and underline indicates the variant found in the rat exome platform matches only the location in COSMIC
  4. dIn a cell line column, bold cell line indicates a homozygous mutation
  5. eIn a cell line column, italicized indicates a heterozygous mutation
  6. fIn a cell line column, Rat WES platform variant call/Sanger-based sequencing variant call. (WT: -, Variant: +). Bold and italics implies a sequencing discrepancy between the WES and Sanger