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Table 2 Comparison between cloning and RSCA in 24 individuals

From: Genotyping of black grouse MHC class II B using reference Strand-Mediated Conformational Analysis (RSCA)

 

Cloning

  

RSCA

 

Individual

N clones

Alleles by seq

N alleles

RSCA peaks

N alleles

D320

17

1,6,7,

3

1,6,7

3

H070

16

1,5,6

3

1,5,9,11,23

5

H070.3

23

1,3,6,9

4

1,3,6,9

4

H070.4

17

6,9

2

1,2,6,7,9

5

D375

16

1,5

2

1,5

2

H071

20

1,2,4,5

4

1,2,3,4,5,18,

6

H071.2

19

1,5

2

1,5

2

H071.3

20

1,2,4,5

4

1,4,5

3

H071.7

17

1,2,4,5

4

1,4,5

3

D476

17

1,3,5,9

4

1,2,3,5

4

D870

26

1,2,3,4

4

1,2,3,4,11

5

H904

16

1,5

2

1,5

2

D115804

16

1,4

2

1,4

2

H369

21

1,2,5

3

1,2,4,5

4

D249

20

6,11

2

1,2,6,11,23

5

H393

20

1,4,5,6,

4

4,5,6

3

Ref4

32

9,13,18

3

9

1

Ref24

28

22

1

1,9,22

3

Ref25

33

5,22

2

1,5,22

3

Ref26

27

1,5,22

3

1,5,22

3

Ref30

35

5,7,9,16

4

1,5,7,16

4

Ne36

17

1,22,

2

1

1

D248

33

4,6,7,9

4

1,9

2

10222

31

5,14,22

3

5

1

Sum alleles

  

71

 

76

Mean alleles

  

2.96

 

3.17

  1. The two methods of cloning/sequencing and RSCA for scoring MHC class II B in black were compared. The table shows the different alleles "Alleles by seq" and number of alleles per individual "N alleles". The numbers below the columns named "Alleles by seq" refers to confirmed Tete BLB alleles. "N clones" refers to the number of clones sequenced per individual. Black grouse named "Ref" where sampled in England, "Ne36" from Netherlands, and had their DNA extracted from moulted feathers. Individual 10222 was sampled in Norway and the DNA was extracted from muscle. For the remaining (Finnish) samples, DNA was extracted from blood. 71 alleles were found by cloning and 76 by RSCA. 2.96 alleles (SD 0.95) were obtained in cloning, and 3.17 alleles (SD 1.40) in RSCA.