Table 2.
KIR haplotyping methodology – SNP ratios for gene copy number
| Gene copy determination using peak ratios | |||||
|---|---|---|---|---|---|
|
Amplicona |
Exon |
Genes amplifiedb |
Gene ratios |
SNP ratiosc |
Observed peak ratios |
|
2DL2-001 |
5 |
2DL2, 2DL3, 2DS2, 2DP1 (3DL2) |
(2DS2+2DL2+2DL3):2DP1 |
C:T at 137 |
1:1, 2:1, 3:1, 3:2, or 4:1 |
| (2DL2+2DL3):2DP1 |
A:C at 206 |
1:1 or 2:1 |
|||
| (2DL2+2DL3):2DS2 |
206(A):209(T) |
1:1 or 2:1 |
|||
|
2DL3-006 |
7/8 |
2DL3, 2DS3/5 |
2DL3:2DS35 |
G:T at 136 |
1:1, 2:1, 1:2 |
|
2DL5 |
3 |
2DL1/4/5 3DP1 |
2DL5:(2DL4+3DP1) |
G:C at 170 |
1 or multiple copies |
|
2DP1-002 |
3 |
2DP1 |
No ratio data |
|
|
|
2DS2-002 |
4 |
2DL1/2/3, 2DS2, 3DP1 |
No ratio data |
|
|
|
2DS35-005 |
4 |
2DS1, 2DS3/5, 3DP1, (2DL1) |
2DS1:2DS3 |
A:G at 446 |
1:1 or 1:2 |
| 2DS3:2DS5 |
446(G):447(A) |
1:1, 2:1, 1:2 |
|||
|
3DL1-002 |
4 |
3DL1, 3DS1 |
|
|
|
|
3DL1-005 |
4 |
3DL1, 3DS1 |
3DL1:3DS1 |
T:G at 167 |
1:1 |
|
KIR-2DL2-N1 |
4 |
2DL2/3, 2DS2 2DP1 |
2DS2:2DP1 |
213(A):217(C) |
1:1 or 1:2 |
|
KIR-2DS2-N1 |
5 |
2DL2/3 2DP1 2DS2 |
No ratio data |
|
|
|
2DS1-4-002 |
4 |
2DS1, 2DL1, 2DS4 (2DS35) |
2DS1:2DL1:2DS4 |
A:C:T at 257 |
1:1:1, 1:2:1, 0:1:1, 0:2:1, or 0:1:2 |
|
2DS1-004 |
4 |
2DS1, 2DL1, (2DS4) |
No ratio data |
|
|
|
3DL1-3DS1-01 |
4 |
3DL1, 3DS1, 3DL2 |
(3DL1+3DS1):3DL2 |
Multiple SNPs |
1:1, 0:2, 1:2 or 3:2 |
| 3DL1-3DS1-05 | 4 | 3DL1, 3DS1, 3DL2 | (3DL1+3DS1):3DL2 | Multiple SNPs | 1:1, 0:2, 1:2 or 3:2 |
a see supplementary Additional file 1: Table S3 for primer sequences.
b loci listed in parenthesis indicate secondary PCR products amplified only in the absence of the target locus.
c SNPs in parenthesis indicate ratios determined on nonoverlapping positions.