Table 2. Allelic ratios of SNP loci within and closely surrounding the POLR3A gene.
NI: Noninformative; i.e., the SNP was not heterozygous in the normal cells of the patient (see supplementary materials and methods).
| Chr. 10 position | SNP ID | Patients with RPC-1 antibodies
|
Patients without RPC-1 antibodies
|
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SCL-1 | SCL-2 | SCL-4 | SCL-13 | SCL-35 | SCL-42 | SCL-81 | SCL-82 | SCL-5 | SCL-8 | SCL-11 | SCL-12 | SCL-19 | SCL-24 | SCL-32 | SCL-85 | ||
| 79,213,314 | rs1054608 | 55% | 88% | 102% | NI | NI | 68% | 83% | NI | NI | NI | 99% | NI | 99% | 103% | NI | NI |
| 79,222,098 | rs2165046 | 52% | 88% | 99% | NI | NI | 69% | 76% | NI | NI | NI | 99% | NI | 94% | 102% | NI | NI |
| 79,222,113 | rs1058203 | NI | NI | NI | NI | 100% | NI | 78% | NI | NI | 102% | NI | NI | NI | 99% | NI | 99% |
| 79,222,157 | rs1058202 | 50% | NI | 102% | NI | NI | NI | NI | NI | NI | 102% | NI | NI | NI | NI | NI | 97% |
| 79,230,809 | rs10762763 | 53% | 86% | 103% | NI | NI | 69% | 85% | NI | NI | NI | 102% | NI | 102% | 104% | NI | NI |
| 79,235,661 | rs2289311 | 55% | 91% | 103% | NI | NI | 66% | 88% | NI | 97% | NI | 104% | NI | 100% | 103% | NI | NI |
| 79,260,691 | rs10824579 | NI | 93% | 97% | NI | NI | 70% | 73% | NI | NI | NI | 96% | NI | 97% | 103% | NI | NI |
| 79,323,400 | rs1248888 | 80% | NI | NI | NI | 102% | NI | 87% | NI | 101% | 102% | NI | NI | NI | 101% | NI | 96% |
| 79,406,970 | rs2241547 | 78% | NI | NI | NI | 104% | NI | NI | NI | NI | NI | NI | NI | NI | NI | NI | 102% |
| 79,415,741 | rs12241228 | NI | NI | NI | NI | NI | NI | NI | NI | 100% | NI | NI | NI | NI | NI | NI | NI |
| 79,415,795 | rs3815891 | 70% | NI | NI | NI | NI | NI | NI | NI | 103% | NI | NI | NI | NI | NI | NI | 102% |
| 79,419,810 | rs7094028 | 79% | NI | NI | NI | NI | NI | NI | NI | 98% | NI | NI | NI | NI | NI | NI | 104% |
| 79,424,105 | rs2818827 | 75% | NI | 104% | NI | 100% | NI | NI | NI | NI | 102% | NI | NI | NI | NI | NI | 102% |
| 79,424,140 | rs12267816 | NI | NI | NI | NI | NI | NI | NI | NI | 104% | NI | NI | NI | NI | NI | NI | NI |
| 79,442,860 | rs2493568 | 76% | NI | 96% | 44% | 101% | NI | 91% | NI | NI | 103% | NI | NI | NI | NI | NI | 101% |
| 79,514,037 | rs67287610 | NI | NI | NI | 45% | 100% | NI | 95% | NI | 99% | NI | NI | NI | NI | NI | NI | NI |
| 79,514,072 | rs4979801 | 85% | NI | NI | 46% | 101% | NI | 95% | NI | NI | 96% | NI | NI | NI | NI | NI | 104% |
| 79,546,360 | rs2253909 | NI | NI | 94% | 40% | 102% | NI | 76% | NI | 102% | 99% | NI | NI | NI | NI | NI | NI |
| 79,549,686 | rs2253513 | 78% | NI | 102% | 41% | 102% | NI | 88% | NI | NI | 100% | NI | NI | NI | NI | NI | 90% |
| 79,573,735 | rs2114907 | 82% | NI | 103% | 43% | 104% | NI | 78% | 96% | NI | 104% | 100% | NI | NI | NI | NI | NI |
| 79,615,946 | rs1249134 | 86% | 90% | 98% | 44% | 102% | NI | 85% | NI | NI | NI | 99% | NI | 104% | NI | NI | NI |
| 79,618,728 | rs1249126 | 75% | 91% | 103% | 46% | 101% | NI | 74% | NI | NI | NI | NI | NI | 98% | NI | NI | NI |
| 79,654,802 | rs2434123 | NI | NI | NI | 46% | NI | 67% | NI | 102% | NI | 104% | NI | NI | NI | NI | NI | NI |
| Allelic ratio average* (%) | 71% | 88% | 99% | 44% | 101% | 69% | 83% | 99% | 99% | 101% | 100% | NI | 99% | 102% | NI | 100% | |
| Allelic ratio SD (%) | 13% | 4% | 6% | 2% | 4% | 3% | 7% | 4% | 5% | 3% | 2% | NI | 3% | 2% | NI | 4% | |
*
Entries represent the allelic ratios of the indicated SNPs. The values in normal individuals were 100% ± 3.10%. Allelic ratios less than 2 SDs from the mean (i.e., <94%) are highlighted in bold. A tumor was considered to exhibit LOH if more than 3/4 of the informative SNPs exhibited alleic ratios <94%.