Table 2. .
AI of 9p in JAK2 Mutation-Positive MPDs[Note]
| 9p Status by AsCNAR |
Allele-Specific PCRc |
|||||||
| Case | Type | Break Pointd | %UPDe | Detection by SNP Call–Based Methoda | % JAK2 Mutationb | SNP | %UPDf | Pg |
| PV_02 | Gain | 42.9 | 99 | NA | 63 | rs2009991 | 84 | .004 |
| PV_03 | Gain | Whole | 60 | NA | 39 | rs10511431 | 63 | .008 |
| PV_04 | UPD | 37.0 | 93 | D | 95 | 5Homo | 5Homo | 5Homo |
| PV_08 | UPD | 34.2 | 91 | D | 93 | 5Homo | 5Homo | 5Homo |
| PV_07 | UPD | 23.8 | 88 | D | 90 | 5Homo | 5Homo | 5Homo |
| PV_06 | UPDh | 7.1/35.3 | 83 | D | 93 | 5Homo | 5Homo | 5Homo |
| PV_11 | UPD | 31.2 | 68 | D | 76 | 5Homo | 5Homo | 5Homo |
| PV_13 | UPD | 28.1 | 66 | ND | 48 | rs1416582 | 64 | .001 |
| PV_01 | UPD | 20.9 | 56 | ND | 62 | rs10511431 | 49 | .007 |
| PV_09 | UPD | 30.8 | 38 | ND | 30 | rs10491558 | 32 | .020 |
| PV_05 | UPD | 23.5 | 32 | ND | 33 | rs1374172 | 31 | .010 |
| IMF_04 | UPD | 33.8 | 79 | D | 90 | 5Homo | 5Homo | 5Homo |
| IMF_05 | UPD | 37.0 | 58 | ND | 57 | rs1416582 | 49 | .004 |
| IMF_07 | UPD | 20.3 | 52 | ND | 50 | rs1416582 | 57 | .005 |
| IMF_12 | UPDh | 26.8/42.9 | 52 | ND | 66 | 5Homo | 5Homo | 5Homo |
| IMF_14 | UPDh | 22.8/33.8 | 45 | ND | 56 | rs1374172 | 35 | .015 |
| IMF_19 | UPD | 34.4 | 26 | ND | 43 | rs10511431 | 33 | .017 |
| IMF_10 | UPD | 34.6 | 21 | ND | 36 | rs1374172 | 21 | .049 |
| IMF_15 | UPD | 33.8 | 21 | ND | 17 | rs10511431 | 20 | .084 |
| IMF_06 | UPD | 35.3 | 17 | ND | 28 | rs1374172 | 20 | .048 |
| IMF_16 | (−) | NA | NA | NA | 37 | NA | NA | NA |
| ET_12 | Gain | Whole | 42 | NA | 27 | rs2009991 | 36 | .046 |
| ET_14 | UPD | 42.9 | 63 | ND | 45 | rs1374172 | 54 | .006 |
| ET_01 | UPD | 35.4 | 19 | ND | 59 | rs10511431 | 33 | .017 |
| ET_05 | (−) | NA | NA | NA | 23 | NA | NA | NA |
| ET_08 | (−) | NA | NA | NA | 42 | NA | NA | NA |
| ET_09 | (−) | NA | NA | NA | 34 | NA | NA | NA |
| ET_10 | (−) | NA | NA | NA | 16 | NA | NA | NA |
| ET_15 | (−) | NA | NA | NA | 27 | NA | NA | NA |
| ET_18 | (−) | NA | NA | NA | 17 | NA | NA | NA |
| ET_19 | (−) | NA | NA | NA | 27 | NA | NA | NA |
| ET_21 | (−) | NA | NA | NA | 55 | NA | NA | NA |
Note.— NA = not applied; (−) = neither UPD nor gain of 9p was detected by AsCNAR analysis.
D = UPD was detected by SNP call–based method; ND = not detected.
Percentage of JAK2 mutant alleles, as measured by allele-specific PCR.
5Homo = all five tested SNPs were homozygous.
Position of the break point from the p-telomeric end (values are in Mb). The location of JAK2 corresponds to 5 Mb.
Percentage of tumor cell populations with either UPD or gain of 9p, as determined by AsCNAR analysis.
Percentage of tumor cell populations with either UPD or gain of 9p, as determined by the allele-specific PCR.
P values were derived from one-tailed t tests comparing triplicate analyses of the target sample and triplicate analyses of five normal samples.
Two UPD-positive populations exist.