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Table 2 KIR haplotyping methodology – SNP ratios for gene copy number

From: Recombinant structures expand and contract inter and intragenic diversification at the KIR locus

   

Gene copy determination using peak ratios

Amplicon a

Exon

Genes amplified b

Gene ratios

SNP ratios c

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

  1. a see supplementary Additional file1: Table S3 for primer sequences.
  2. b loci listed in parenthesis indicate secondary PCR products amplified only in the absence of the target locus.
  3. c SNPs in parenthesis indicate ratios determined on nonoverlapping positions.