Chromosome 16q22-linked familial AML: Exclusion of candidate genes, and possible disease risk modification by NQO1 polymorphisms

Table 1. Genes, gene structures, primers and special PCR conditions to amplify exons and surrounding intronic sequences
gene exon (*) 5' primer 3' primer product size bp T°  annealing    special PCR conditions
CTCF exon 1 CGTCCCTTCCCTTATCAGCA GGGAGATAGGTAAGCTAGCCGAGA 333 52°C -
exon 2 TCTGTCTTCAGTTTTCCCTCATTTT ATTAGCCAACAAATCCTCCAACTC 289 60°C -
exon 3a TGATGCCTAATTCATTCACCAAAG TGTTCTAGTGTCTCCACCTCTCCA 652 60°C -
exon 3b TGACTGTACCTGTTGCTACCACTTC ACCCACATAACGACCTTTTACAAATAC 533 60°C -
exon 4 TTTTAATCCCAAAGAAGAAGGAAATG GCTGGAGTCAGCTTGAATGAATAC 419 60°C -
exon 5 TTTTCGGAGCTGACTTTTGTATCT CGGTGTTGTGTGGGAGTGTT 428 60°C -
exon 6 ACCCGTATTCATTTACCCACTTCT ATTTTCATGCCAGTCTTCATTCAT 446 60°C -
exon 7 CCACCTGAGTTACCCTCCAGTTA TGAAGTTATTTTTGATCCCCATATTTC 309 60°C -
exon 8 GCTTGGGTGAGAAATACCTGTTG TAGAAACATCAAGATGGGGATGAC 412 60°C 2% DMSO
exon 9 GCTTGGGTGAGAAATACCTGTTG TAGAAACATCAAGATGGGGATGAC 437 60°C -
exon 10 TAGAGAACCCAGCCTTATCCATTT TCCCAGCATATCCATACATAAACAC 389 60°C -
exon 11 TTGTTTTCTTTCATCTTCCACCAC AAGCCATTTCCTGAGAGTTTGTTC 378 60°C -
exon 12 GACTGTCTCTGGACCGCTATCTAA TTGAAGTTTTCGTTCTCGGTATGT 456 60°C -
E2F4 exon 1 ACAGCAATAGCGCCACGTT CCGCACCAGCTTGAGGTC 294 56°C buffer for GC-rich sequences (Roche Diagnostics, Mannheim, Germany)
exon 2 ATCCAGATTACTCCCTTCCCAGAC GCTGAGAGGGACTGCTGAGAAC 320 60°C -
exon 3 GTAGAGTCTCCCACCCAGAAGTGT AAGACAAACTCCCAAGAGGAACAG 368 60°C -
exon 4 GGGCCTGTGTGTCAGACCTT TACCCTGCCTGGTTCCTCTCT 278 TD 60°C (1) -
exon 5 AAAGGCAGGCACCTCTGTTC CCAGGACTTATCAGGCTCCAC 204 60°C -
exon 6 CCTGGGTGGGAGAGGACACT TCTGAGCATGGTGTTCCACAAC 469 TD 62°C (1 ) -
exon 7 GGTTCCAGCACAGCCAGTTT CATCCCCAATTCTGTTTTCTGAC 377 TD 62°C (1 ) -
exon 8 AGCCTCAGGGTGGGTGGTATAG GTCCTCAAAAGGGCAAGAAAACA 233 TD 62°C (1 ) -
exon 9 GTTCCCTTTCCTGGGCTTTG AGAGAGCACTAGTCTCAGGCCC 212 TD 62°C (1 ) -
exon 10 GATGTCCTCAGAAGGTGGGTG TCTGTGGCTCTCAAGCTCTGTA 329 TD 62°C (1 ) -
NFATC3 exon 1 GCGGGGAACATTGGCTAAG ACAGGGAGGGAGCGAGAGA 437 63.5°C 5% DMSO and 2.5mM MgCl2
exon 2a TGCCACTTCTTTAGTGGAGCTAAT GCTGGCAGGACTAGGACTAAGAGA 558 TD 60°C (1 ) -
exon 2b AGAACGGGAATTTTTGGAAAGG CAGGTGAAGGAACAGGTGAGTG 485 TD 60°C (1 ) -
exon 2c ACATCCCCCTGTGGGAAAC GGATACTGAGATCCAAGGCCATC 344 TD 65°C (1 ) -
exon 2d TGACATCCCTCTCAAAACAAGG ATGCCACCAATGACCCATAA 295 TD 65°C (1 ) -
exon 3 AGGAAGAAATGTTGGTGCTGG TGAGTTTATGCTCTTTGCACTCTCT 359 TD 60°C (1 ) -
exon 4 TGCTCACTGGTTACTTTTGGTTGT CCTTCTGGAAATATGCTACCACTCT 518 TD 63°C (1 ) -
exon 5 TCTATGTAGTTGAGTTGATAACCATGA TTGCACTTCAGACGCATACATTAC 336 56°C -
exon 6 TGAATCCCAAAATTTGCTTCTC TGCAAAATGACACCCATAGCTT 383 TD 65°C (1 ) 5% DMSO and 2.5mM MgCl2
exon 7 ACTATCCATGCATTAGATTTTGTCTGT GTCATCCATACCATAAAGCAGCA 216 TD 63°C (1 ) -
exon 8 ATCTATGCTGGAGCCTTGTAGTTAAGA CATCTGTTGGTGTTTTCATTGTTT 358 TD 60°C (1 ) -
exon 9a AGTTGTGTAACCTAGCATGAAGGC CAGCCAAGATTCACTAAACCAGAA 522 TD 63°C (1 ) -
exon 9b TCATTCTGTGCATACCCTGC AACTGAGACGAAGGCTGACC 120 TD 65°C (1 ) -
exon 9c GCCTTCGTCTCAGTTACAACCTATTAC TGGGAGAATAAAGTCCCTGAATCTT 451 TD 63°C (1 ) -
exon 10 AAACAGGCTGGGCACTGT TGCATACCCCCTCCTCTGTA 250 TD 65°C (1 ) 2% DMSO
exon 11 TGCTTATCAAGATTGCTAATGACTT CAATAACTTGAGCCGAGTGTTAAT 230 55.8°C 5% DMSO and 2.5mM MgCl2
exon 12 CTCAGCGTTGGGCATCATA AGCAGCACCTCGGAAACAA 493 57°C 5% DMSO and 2.5mM MgCl2
NFAT5 exon 1a CTCGGCCCAGTGGAAGTC CCTGTCTCCCTGTCTCCCTGT 294 TD 60°C (1 ) -
exon 1b CTGGTCACCGAGAATCAGTCC GGGCTGAGAGCGGCTAGA 582 TD 60°C (1 ) buffer for GC-rich sequences (Roche Diagnostics, Mannheim, Germany)
exon 2 GAGATGTATGCTATCCTTGGCATTT TTCCCATTTAAACTCCATTTCAGA 203 TD 63°C (1 ) -
exon 3 GAGAAAAGACATACTCATTTTGTGCAT ATTTTGCCAGCACTGTTCATGTT 293 TD 60°C (1 ) -
exon 4 GTGACAATACCAGTTCCATTTTGC AATATATGCTGGTGGTCCACATTC 300 TD 63°C (1 ) -
exon 5a ATCACATTTTCAATGGGACTGCT ATCATTGTAGGAACTGGTGCTCAT 459 TD 60°C (1 ) -
exon 5b GATGAGGGGTGTGGATTGG TTTGTTTGTTTTGCATAATGATGATAG 330 TD 63°C (1 ) -
exon 6 AAAAACTCTTTTTGATACTTTCTCCA GGACATATTCTCATTCCCCTTTAC 302 TD 63°C (1 ) -
exon 7 AGGATTTGGTCTTAAATATTTGATTTT TGAACAATTCTGCCTAACACAAG 338 TD 63°C (1 ) -
exon 8 TTGTACTTTTTGAACTTGGAACTTTGT GCCGGAGCATATGAAATATCTAAA 424 TD 63°C (1 ) -
exon 9 GGATGATTGCAAGTTGATTTTAGGT TTCATCTGATTGAAATAAAAAGTGATT 341 TD 63°C (1 ) -
exon 10 TTGTATGTTTTCACTTTGTTATATGGA CAAAACAAAACTGAATTGCTCAGA 211 TD 63°C (1 ) -
exon 11 ACTTTTTAAACTTTACAGCTAACAGGA ATCTTAGTGAGCAACTTTCTTTTTG 340 TD 63°C (1 ) -
exon 12 AGAATTTAAGATACGAGGTTTTTAGGA GGTGTGCTAGAGAAAACATACAGG 216 TD 63°C (1 ) -
exon 13 CATGGCTAATAACAAATTTTAGAATGA TTAAGTGCATCCAAAGTAAAAATAATG 332 TD 63°C (1 ) -
exon 14a GAGCAATAGTGATTTTTGATGTATGTT AATATTTGATGAAATCTGCTGCTGTA 496 TD 63°C (1 ) -
exon 14b AGCAGGCTACACAGTTTCAGACAA ACGTGTTTTCAGACTGTGGATGA 510 TD 65°C (1 ) -
exon 14c AACAAGTCAGTCAAATTCAGAGTGGT TTTTGCTTGTGTTCCAGTTTCTTC 500 TD 63°C (1 ) -
exon 14d TTTTCTTCTCCTCCTGCAGTTTCT CAGCAATGGTACTTTGAGAGTGAA 511 TD 63°C (1 ) -
exon 14e TGCCGATGCTCAGAACCTT CTGTTCCTGGGATGGAGAGTTAC 517 TD 63°C (1 ) -
exon 14f CGCAGCAGGGTTTATTTCAG AACAAGGGGGTCTGTGATGATT 445 TD 63°C (1 ) -
exon 14g AGTAACATGGCCCCAATGAATC CACTGCACTCTGCTTCCTTCTAAT 492 TD 63°C (1 ) -
exon 15 CAGTAATGAATTTTCCCCAACAAC CATCTTGTGAGAAAGCCACATTTTA 489 TD 63°C (1 ) -
exon 16a TAGGATCATTCAGGGTGTCAGAAA TGAACTTTACTTTTTCAAAAGCCATT 508 TD 63°C (1 ) -
exon 16b CAAGGCTGGACCACTCAGTTATTA CAGCCTAAGACTGGGTTAAGAAGAAA 521 TD 63°C (1 ) -
exon 16c TAAGGGGTTTAGCCATAACTGTGC CTATTAGAGGGAAAAATTTGAAGACT 407 TD 63°C (1 ) -
NQO1 exon 1 TAGGCTGTCCACCTCAAACG CAAGCCCCTACAACCTCCTC 267 TD 60°C (1 ) -
exon 2 CGCCCCCTCCTTTACAGACT CAAAGCTGGGCCAGAGGA 337 TD 60°C (1 ) -
exon 3 GGAGTTCCTCCTCCCCTCTT CCCTTATTTGCAGAGAATGCAG 364 TD 60°C (1 ) -
exon 4 TGCTAACTCCCCAGGAGGAA GCAACAAGAGGGAAGCTCCA 366 64°C elongation 2 minutes
exon 5 TAGCTCAGGGGAGCCAAAGT GGGCGGAGCTTGTAGTGAA 356 TD 60°C (1 ) 2% DMSO
exon 6a TGTGCCTGAGGCCTCCTTAT GAGGCTGCTTGGAGCAAAAT 284 TD 60°C (1 ) -
exon 6b CCCGAATTCAAATCCTGGAA AAATGATCCAAAAATGCACGAA 384 TD 60°C (1 ) 2% DMSO
exon 6c CAGGCTTCCCTGACTTGCTT TCTGAGCAATTCCCTTCTGC 343 TD 60°C (1 ) -
CDH1 exon 1 CAGGTGAACCCTCAGCCAAT GAACTTTCTTGGAAGAAGGGAAGC 365 TD 65°C (1 )
exon 2 CTGTTGGTTTCGGTGAGCAG CCTTTCCAACCCCTCCCTACT 237 TD 65°C (1 )
exon 3 CAAGTTCGCTCTTTGGAGAAGG CACAGGACAACCCCTACAACAC 427 56°C
exon 4 CGTCTTGAATTGTCTTATCTTGTTCCTCATC TCCCTCCCAGAGAAACAGAGAAC 224 55°C
exon 5 CAGAGAAGTACCAAGGAGAGAAAGG GGGTTGACCAAAAAATCCTGG 306 55°C
exon 6 CCCATGTTTTCTTCCTCATCAGAG GAAGGATCAGCTTTAGTTACACAACC 303 55°C
exon 7 GCTTGTCTAAACCTTCATCTCCTTG CACATTTGTCCTCCACACCCTC 255 57°C
exon 8 TGTTCCTGGTCCTGACTTGGTTG GAGAGTTTTCAAAGACTTCGCCC 269 56°C
exon 9 ATCCTTTAGCCCCCTGAGACTC GCCAGTTTCTGCATCTTGCC 294 56°C
exon 10 CCAAAAGCAACAGTTAAGG CAGACAAATGACAAAATGCC 437 53°C
exon 11 TTTGCTGGTCCTATTCTAAAAGCC AATGAACTCTTCCCTCCAAAAGAAG 280 57°C
exon 12 GGAAGGCAATGGGGATTCATTAC GTTGAGAAGGGAAATTGAAAGGTG 378 56°C
exon 13 GGAATGAGCTTTTTATTTTCCTCCC CCTCCATTTTTTTAAGTCAAAGGCTGAGTC 337 56°C
exon 14 TTCAGGGATGTGAGTGTCACG AAATGTTAGCTGTGTTGGTGATGA 492 TD 65°C (1 )
exon 15 ACTGAACATAGCCCTGTGTGTATGAC CACAACTCCTCCTGAGCTTAGAGATG 277 56°C
exon 16 TCTGGGTGCATTGTCGTACC TCAAGGGAAGGGAGCTGAAA 400 TD 65°C (1 )
(*) when more than one primer pair was necessary to amplify one exon due to exon size, letters were added to the exon number
(1) TD, touch-down: initial 10 cycles of amplification (denaturation, annealing and elongation) with annealing temperature of the first cycle mentioned in table and then decreasing by 1 degree Celsius in each successive cycle, followed by 30 cycles with annealing at the lowest temperature of the initial 10 cycles.
Last modified on the 20th February 2004.
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