TABLE 2.
APOBEC3G allele frequencies among eight patients with marked G→A hypermutationa
| NCBI dbSNP IDb | Positionc | Frequency ofd:
|
No. of HM-3G patients that weree:
|
||||||
|---|---|---|---|---|---|---|---|---|---|
| Control sample
|
Allele 2 from the work of Do et al. (7) | HM-3G patient
|
A1.A1 | A1.A2 | A2.A2 | ||||
| Allele 1 | Allele 2 | Allele 1 | Allele 2 | ||||||
| 7291971 | −1,193 | 0.60 | 0.40 | 0.40 | 0.44 | 0.56 | 2 | 3 | 3 |
| 6519166 | −1,190 | 0.70 | 0.30 | 0.31 | 0.56 | 0.44 | 2 | 5 | 1 |
| 5750743 | −321 | 0.50 | 0.50 | 0.28 | 0.44 | 0.56 | 1 | 5 | 2 |
| 12160242 | 480 | >0.90 | <0.10 | 0.09 | 0.94 | 0.06 | 7 | 1 | 0 |
| 9607609 | 625 | 0.80 | 0.20 | ND | 0.38 | 0.62 | 2 | 2 | 4 |
| 5757465 | 3,756† | 0.60 | 0.40 | 0.51 | 0.75 | 0.25 | 4 | 4 | 0 |
| 12158985 | 5,985 | >0.90 | <0.10 | 0.07 | 0.88 | 0.12 | 6 | 2 | 0 |
| 2294366 | 5,986 | 0.70 | 0.30 | 0.34 | 0.56 | 0.44 | 2 | 5 | 1 |
| 2294367 | 6,207 | 0.60 | 0.40 | 0.42 | 0.44 | 0.56 | 2 | 3 | 3 |
| NL | 6,848 | >0.90 | <0.10 | ND | 0.88 | 0.12 | 6 | 2 | 0 |
| 3091374 | 6,878 | 0.50 | 0.50 | ND | 0.44 | 0.56 | 2 | 3 | 3 |
| 5757467 | 6,892 | 0.70 | 0.30 | ND | 0.31 | 0.69 | 0 | 5 | 3 |
| 5757468 | 6,893 | 0.70 | 0.30 | ND | 0.56 | 0.44 | 2 | 5 | 1 |
| NL | 6,894 | >0.90 | <0.10 | ND | 0.88 | 0.12 | 6 | 2 | 0 |
| NL | 8,984‡ | >0.90 | <0.10 | ND | 0.88 | 0.12 | 6 | 2 | 0 |
| 5757471 | 9,218 | >0.90 | <0.10 | ND | 0.94 | 0.06 | 7 | 1 | 0 |
| 28474760 | 9,250 | >0.90 | <0.10 | 0.07 | 0.88 | 0.12 | 6 | 2 | 0 |
| 28474761 | 9,432 | >0.90 | <0.10 | 0.12 | 0.88 | 0.12 | 6 | 2 | 0 |
| NL | 10,393 | 0.50 | 0.50 | ND | 0.92 | 0.08 | 5 | 1 | 0 |
| NL | 10,399 | 0.70 | 0.30 | ND | 1.00 | 0.0 | 8 | 0 | 0 |
| 5757472 | 10,600 | 0.50 | 0.50 | ND | 0.44 | 0.56 | 1 | 5 | 2 |
| 3891126 | 10,811 | >0.90 | <0.10 | ND | 0.88 | 0.12 | 6 | 2 | 0 |
Comparisons with a pooled DNA control sample and with results from a published study are shown. Results in boldface are those for which significant differences in allele frequencies between patients with hypermutated sequences and the pooled DNA control sample were evident.
NCBI dbSNP ID, National Center for Biotechnology Information SNP database reference number. NL, novel SNP.
Positions are relative to the transcription start site with reference to NCBI accession number NT_011520. †, synonymous SNP; ‡, nonsynonymous SNP.
Allele frequencies of the pooled DNA sample were estimated by chromatogram relative peak height. Significant differences in the allele frequencies of the 625 and 6,892 SNPs were evident between the hypermutated patients and the pooled DNA sample. A result of <0.10 indicates that allele frequency was below the limit of detection. ND, not determined.
A1.A1, homozygous for allele 1; A1.A2, heterozygous; A2.A2, homozygous for allele 2.