Article Figures & Data
Figures
- Fig. 1.
A, H&E-stained section of a typical adenomatous polyp used in this study. The adenoma was 2 mm in greatest dimension. B, higher magnification demonstrates dysplastic epithelium overlying the lamina propria, with abundant lymphocytes and stromal cells that are typically observed in these lesions.
- Fig. 2.
A, examples of digital SNP genotyping data. DNA from microdissected normal (upper panel) and adenoma (bottom panel) samples was distributed to a 384-well PCR plate. After PCR, a pair of allele-specific Molecular Beacons, labeled with fluorescein or Hex, was added to each well to determine allelic status. The fluorescein: Hex fluorescence ratio was then determined. Wells that were green or red corresponded to those containing PCR products derived from only one of the two alleles. Wells with only background fluorescence were uncolored and represent wells that contained no DNA template molecules. Wells that were yellow contained an intermediate green: red fluorescence ratio, resulting from the presence of both alleles. Such results are expected based on a Poisson distribution.4 B, SPRT analysis of normal and adenoma samples from A. X axis, total number of alleles counted; Y axis, observed proportion of the two alleles. The allelic proportion of DNA from the normal colonic mucosae is below curve 2 and is therefore interpreted as being in allelic balance. In contrast, the allelic proportion in the DNA from the adenoma is above curve 1, and this tumor is interpreted to have AI.
- Fig. 3.
SPRT analysis on different chromosomal arms. X axis, total number of alleles counted; Y axis, observed proportion of the two alleles for each of the chromosome arms indicated. The boundary SPRT values corresponding to a likelihood ratio of 8 are shown as curved lines, as in Fig. 2 <$REFLINK> . All points above the upper boundary were interpreted to have AI, whereas those below the lower boundary were interpreted to have no AI.
- Fig. 4.
Summary of digital SNP results. ▪, chromosome arms in which AI was identified through digital SNP;
, chromosome arms in
which both alleles were in balance; □, chromosome arms that could not
be evaluated because all SNP markers tested were uninformative in the
normal mucosae or because the allelic ratio in SPRT analysis did not
fall above curve 1 or below curve 2.
Tables
- Table 1
Primers and probes used for digital SNP analysis
Ch SNPs Forward primer Reverse primer Internal primer Molecular Beacon-green (fluorescein) Molecular Beacon-red (Hex) 1p CGAP-C-51904 CCCTGGACCCCCTGATGG GCCGAGTCAGTGGCAAAAG GCCGAGTCAGTGGCAAAAG CACGCCGAGCTCGCTCCGGAACGTG CACGCCGAGCTCACTCCGGAACGTG 1p CGAP-C-53916 ACAGCTTGGGAACGCAGAGG TGTCTGATTTGCCACCTGGAT TGTCTGATTTGCCACCTGGAT CACGCCGTAACTGAACGTGCTCGTG CACGCCGTAACTCAACGTGCTCGTG 1p CGAP-C-50319 CAGGGCAAGACGCTGTGGT AACAGAATGTGCTTCCCTCCC AACAGAATGTGCTTCCCTCCC CACGCTGCCCAGCGCACGGCCGTG CACGCTGCCCAGTGCACGGCCGTG 1p AA290678 AGCAGCATGACTGAACATC GACACTTACCTGACAGCGGAT GACACTTACCTGACAGCGGAT CACGAGGCCAACGACGAGAGCCCACGTG CACGAGGCCAACGCCGAGAGCCCACGTG 15q CGAP-C-2077 CAAGACTGTAAGAACGTAGG AGTCTCTATTTATTTGTCCTCTT AGTGAAGGAAGGATGCTCG CACGTTAGACTTTGACCCAGAGCCGTG CACGTTAGACTTTGACCCAGCGCGTG 15q CGAP-C-1861 ACAGCCATTTATTATGTTTACTTGG AGAATAATTGTGATAAGAATTCCCC CCCACCAAAATCACCTCC CACGAGCCAACACGGAGGTGACGTG CACGAGCCAACATGGAGGTGACGTG 15q CGAP-C-362 TCACACCTGAGGGGGAAG AGCCATAGGAAGGTGAGGAA TGTCATCTGTAGTCCAAGGTC CACGCTGACGAGACACAGAGACCTCGTG CACGGACGAGACGCAGAGACCTCGTG 15q CGAP-C-425 GTCTCACTTTCTTGTCTAGGCTG AGGAATAACTGGATTTCATCGG TGATTAAGTATTCCCCACCC CACGAAGACTCACCAGAACAGGGCGTG CACGAAGACTCACCAGAAGAGGGCGTG 8p CGAP-C-3833 GCCCAACACTGAGCTCTTTC GGTCTGATGTCAGTAACGG GGTCTGATGTCAGTAACGG CACGTTGCTCTTCAATTCCGTTCCGTG CACGTTGCTCTTCAGTTCCGTTCCGTG 8p CGAP-C-1596 CCACTTGGGTCTCTTTCAA GCAGAAAAACAGACTAAGGC GGCTTTAGAACAGGAACG CACGTCAAGTGAATGTTCCTTTCGTCGTG CACGTCAAGTGAATTTTCCTTTCGTCGTG 8p CGAP-C-28254 GAAATCAGGTTAGTTTAGTCTACAGC GTGTGTTGAGATAAATTCAGATAC GTGTGTTGAGATAAATTCAGATAC CACGCGATGACTACTCTCTCTTGCCGTG CACGCGATGATTACTCTCTCTTGCCGTG 8p CGAP-C-1745 CATGAAAGGAAAGGGTGCC AGCGACTTCACCTAAACCG CTGAATGCTCTGCCATGAG CACGGCTGCTTGCGGCTCATCGTG CACGTGCTGCTTGTGGCTCATCGTG 8p CGAP-C-32628 AAATGGGAGCAGTGAGTGGC CCCTCCTAAGCCAGCTCAC CCCTCCTAAGCCAGCTCAC CACGGAACAACTGTTGAATGATGCGTG CACGGAACAACTGCTGAATGATGGCGTG 8p CGAP-C-1085 CACTGAATGCTCTGCCATGA AACCTGTCCTTGTGGGTGAT GGTGATGATCACTGTGCTGC CACGATGAGCCACAAGCAGCACGTG CACGATGAGCCGCAAGCAGCCGTG 18q CGAP-C-1239 AAGGATGGCGCACGCTGG TCACTATCTCCCGGTTGTCG TCACTATCTCCCGGTTGTCG CACGTGGGAGGACAGGGTACGCGTG CCAGGGGAGAACGGGGTACGCGTG 18q CGAP-C-700 CTGAAACTAATGAGGTGCTAAATCA GCCCATTGCATTATCATCG CATTCTTTGACCTTTCACCAAT CACGTATCCTTCCATGAAATTGGCGTG CACGTATCCTTCCGTGAAATTGGCGTG 18q CGAP-C-331 GACAAAGAGGCAGTTTCTGTAGTT TGTTCATTAATTTCACTTACAGGAA ACTTACAGGAATGGCATGGC CACGTTGAGACTACGTGGCCATCGTG CACGTTGAGACTATGTGGCCATGCGTG 18q CGAP-C-801 AGATGTCAGTTTGAATGTATTCCTG TGAGTCTCACTCATATTTTCGGG TGAGTCTCACTCATATTTTCGGG CACGTATTCCTGATGTTTTCCTTTCGTG CACGTATTCCTGATCTTTTCCTTTCGTG 18q CGAP-C-1432 GGAGAAATTTCTTTGATTTATGC TGTTTATCTTAGTGTTTCTGGC CCTTGGTCTTTATTATTAGATTG CACGTGTGAATTGCAGGTTTCCCGTG CACGATGTGAATTGTAGGTTTCCACGTG 18q CGAP-C-1468 AGCGAGCATCAGAATCACCT CGGGACAAGCAGCATCT GCAACACTTAGGAAGGTCT CACGTGGGGCTTACAAATTAGTATCGTG CACGTGGGGCTTACGAATTAGTATCGTG 5q 486 GGACTACAGGCCATTGCAGAA TCCAGCATATCGTCTTAGTGT TCCAGCATATCGTCTTAGTGT CACGGTGAAATGTACGGGCTTACTCGTG CACGGTGAAATGTATGGGCTTACTACGTG 5q 310 AGAGGATGAGCATGCTGGTGG AGGTTACTCTGGATGCACT AGGTTACTCTGGATGCACT CACGGTAGGAAGACAGCGCGAGCGTG CACGAATCCAATGCCACAGCGCTGCGTG 5q 1756 GTCACAAGCCTTTCCGTGTGAAA GGTATAGGTTTTACTGGTGAAGTTGG GGTATAGGTTTTACTGGTGAAGTTGG CACGTCTGCGTCGTCTTCTGCCGTG CACGATCTGCGTCTTCTTCTGCCGTG 5q 1960 AGGGGCAGCAACTGATGAAAAG CTTGGTCAATGTCACTGAGAGA CTTGGTCAATGTCACTGAGAGA CACGGAAAATACTCCAGTTTGCTTCGTG CACGGAAAATACTCCGGTTTGCCGTG
Volume 61, Issue 3
